PMC:1860061 JSON TXT 8 Projects

Annnotations TAB TSV DIC JSON TextAE

Id	Subject	Object	Predicate	Lexical cue
T456	0-9	VBG	denotes	Combining
T457	0-154	sentence	denotes	Combining global genome and transcriptome approaches to identify the candidate genes of small-effect quantitative trait loci in collagen-induced arthritis
T458	10-16	JJ	denotes	global
T460	17-23	NN	denotes	genome
T461	24-27	CC	denotes	and
T462	28-41	NN	denotes	transcriptome
T459	42-52	NNS	denotes	approaches
T463	53-55	TO	denotes	to
T464	56-64	VB	denotes	identify
T465	65-68	DT	denotes	the
T467	69-78	NN	denotes	candidate
T466	79-84	NNS	denotes	genes
T468	85-87	IN	denotes	of
T469	88-93	JJ	denotes	small
T471	93-94	HYPH	denotes	-
T470	94-100	NN	denotes	effect
T473	101-113	JJ	denotes	quantitative
T474	114-119	NN	denotes	trait
T472	120-124	NNS	denotes	loci
T475	125-127	IN	denotes	in
T476	128-136	NN	denotes	collagen
T478	136-137	HYPH	denotes	-
T477	137-144	VBN	denotes	induced
T479	145-154	NN	denotes	arthritis
T480	154-155	sentence	denotes
T482	165-177	JJ	denotes	Quantitative
T481	165-283	sentence	denotes	Quantitative traits such as complex diseases are controlled by many small-effect genes that are difficult to identify.
T483	178-184	NNS	denotes	traits
T485	185-189	JJ	denotes	such
T486	190-192	IN	denotes	as
T487	193-200	JJ	denotes	complex
T488	201-209	NNS	denotes	diseases
T489	210-213	VBP	denotes	are
T484	214-224	VBN	denotes	controlled
T490	225-227	IN	denotes	by
T491	228-232	JJ	denotes	many
T493	233-238	JJ	denotes	small
T495	238-239	HYPH	denotes	-
T494	239-245	NN	denotes	effect
T492	246-251	NNS	denotes	genes
T496	252-256	WDT	denotes	that
T497	257-260	VBP	denotes	are
T498	261-270	JJ	denotes	difficult
T499	271-273	TO	denotes	to
T500	274-282	VB	denotes	identify
T501	282-283	.	denotes	.
T502	283-481	sentence	denotes	Here we present a novel strategy to identify the candidate genes for small-effect quantitative trait loci (QTL) in collagen induced arthritis (CIA) using global genome and transcriptome approaches.
T503	284-288	RB	denotes	Here
T505	289-291	PRP	denotes	we
T504	292-299	VBP	denotes	present
T506	300-301	DT	denotes	a
T508	302-307	JJ	denotes	novel
T507	308-316	NN	denotes	strategy
T509	317-319	TO	denotes	to
T510	320-328	VB	denotes	identify
T511	329-332	DT	denotes	the
T513	333-342	NN	denotes	candidate
T512	343-348	NNS	denotes	genes
T514	349-352	IN	denotes	for
T515	353-358	JJ	denotes	small
T517	358-359	HYPH	denotes	-
T516	359-365	NN	denotes	effect
T518	366-378	JJ	denotes	quantitative
T519	379-384	NN	denotes	trait
T520	385-389	NNS	denotes	loci
T521	390-391	-LRB-	denotes	(
T522	391-394	NN	denotes	QTL
T523	394-395	-RRB-	denotes	)
T524	396-398	IN	denotes	in
T525	399-407	NN	denotes	collagen
T526	408-415	VBN	denotes	induced
T527	416-425	NN	denotes	arthritis
T528	426-427	-LRB-	denotes	(
T529	427-430	NN	denotes	CIA
T530	430-431	-RRB-	denotes	)
T531	432-437	VBG	denotes	using
T532	438-444	JJ	denotes	global
T534	445-451	NN	denotes	genome
T535	452-455	CC	denotes	and
T536	456-469	NN	denotes	transcriptome
T533	470-480	NNS	denotes	approaches
T537	480-481	.	denotes	.
T538	481-616	sentence	denotes	First, we performed genome linkage analysis in F2 progeny of the CIA susceptible and resistant strains to search for small-effect QTL.
T539	482-487	RB	denotes	First
T541	487-489	,	denotes	,
T542	489-491	PRP	denotes	we
T540	492-501	VBD	denotes	performed
T543	502-508	NN	denotes	genome
T544	509-516	NN	denotes	linkage
T545	517-525	NN	denotes	analysis
T546	526-528	IN	denotes	in
T547	529-531	NN	denotes	F2
T548	532-539	NN	denotes	progeny
T549	540-542	IN	denotes	of
T550	543-546	DT	denotes	the
T552	547-550	NN	denotes	CIA
T553	551-562	JJ	denotes	susceptible
T554	563-566	CC	denotes	and
T555	567-576	JJ	denotes	resistant
T551	577-584	NNS	denotes	strains
T556	585-587	TO	denotes	to
T557	588-594	VB	denotes	search
T558	595-598	IN	denotes	for
T559	599-604	JJ	denotes	small
T561	604-605	HYPH	denotes	-
T560	605-611	NN	denotes	effect
T562	612-615	NN	denotes	QTL
T563	615-616	.	denotes	.
T564	616-689	sentence	denotes	Second, we detected gene expression patterns of both strains during CIA.
T565	617-623	RB	denotes	Second
T567	623-625	,	denotes	,
T568	625-627	PRP	denotes	we
T566	628-636	VBD	denotes	detected
T569	637-641	NN	denotes	gene
T570	642-652	NN	denotes	expression
T571	653-661	NNS	denotes	patterns
T572	662-664	IN	denotes	of
T573	665-669	DT	denotes	both
T574	670-677	NNS	denotes	strains
T575	678-684	IN	denotes	during
T576	685-688	NN	denotes	CIA
T577	688-689	.	denotes	.
T578	689-952	sentence	denotes	The candidate genes were identified using three criteria: they are located in a genomic region linked to CIA; they are disease-specific differentially expressed during CIA; and they are strain-specific differentially expressed regarding the two parental strains.
T579	690-693	DT	denotes	The
T581	694-703	NN	denotes	candidate
T580	704-709	NNS	denotes	genes
T583	710-714	VBD	denotes	were
T582	715-725	VBN	denotes	identified
T585	726-731	VBG	denotes	using
T586	732-737	CD	denotes	three
T587	738-746	NNS	denotes	criteria
T588	746-748	:	denotes	:
T589	748-752	PRP	denotes	they
T590	753-756	VBP	denotes	are
T584	757-764	VBN	denotes	located
T591	765-767	IN	denotes	in
T592	768-769	DT	denotes	a
T594	770-777	JJ	denotes	genomic
T593	778-784	NN	denotes	region
T595	785-791	VBN	denotes	linked
T596	792-794	IN	denotes	to
T597	795-798	NN	denotes	CIA
T598	798-799	:	denotes	;
T599	800-804	PRP	denotes	they
T601	805-808	VBP	denotes	are
T602	809-816	NN	denotes	disease
T604	816-817	HYPH	denotes	-
T603	817-825	RB	denotes	specific
T605	826-840	RB	denotes	differentially
T600	841-850	VBN	denotes	expressed
T606	851-857	IN	denotes	during
T607	858-861	NN	denotes	CIA
T608	861-862	:	denotes	;
T609	863-866	CC	denotes	and
T610	867-871	PRP	denotes	they
T612	872-875	VBP	denotes	are
T613	876-882	NN	denotes	strain
T615	882-883	HYPH	denotes	-
T614	883-891	RB	denotes	specific
T616	892-906	RB	denotes	differentially
T611	907-916	VBN	denotes	expressed
T617	917-926	VBG	denotes	regarding
T618	927-930	DT	denotes	the
T620	931-934	CD	denotes	two
T621	935-943	JJ	denotes	parental
T619	944-951	NNS	denotes	strains
T622	951-952	.	denotes	.
T623	952-1017	sentence	denotes	Eight small-effect QTL controlling CIA severity were identified.
T624	953-958	CD	denotes	Eight
T626	959-964	JJ	denotes	small
T628	964-965	HYPH	denotes	-
T627	965-971	NN	denotes	effect
T625	972-975	NN	denotes	QTL
T630	976-987	VBG	denotes	controlling
T631	988-991	NN	denotes	CIA
T632	992-1000	NN	denotes	severity
T633	1001-1005	VBD	denotes	were
T629	1006-1016	VBN	denotes	identified
T634	1016-1017	.	denotes	.
T635	1017-1131	sentence	denotes	Of 22,000 screened genes, 117 were both strain-specific and disease-specific differentially expressed during CIA.
T636	1018-1020	IN	denotes	Of
T638	1021-1027	CD	denotes	22,000
T640	1028-1036	VBN	denotes	screened
T639	1037-1042	NNS	denotes	genes
T641	1042-1044	,	denotes	,
T642	1044-1047	CD	denotes	117
T643	1048-1052	VBD	denotes	were
T644	1053-1057	CC	denotes	both
T646	1058-1064	NN	denotes	strain
T647	1064-1065	HYPH	denotes	-
T645	1065-1073	RB	denotes	specific
T648	1074-1077	CC	denotes	and
T649	1078-1085	NN	denotes	disease
T651	1085-1086	HYPH	denotes	-
T650	1086-1094	RB	denotes	specific
T652	1095-1109	RB	denotes	differentially
T637	1110-1119	VBN	denotes	expressed
T653	1120-1126	IN	denotes	during
T654	1127-1130	NN	denotes	CIA
T655	1130-1131	.	denotes	.
T656	1131-1267	sentence	denotes	Of these 117 genes, 21 were located inside the support intervals of the 8 small-effect QTL and thus were considered as candidate genes.
T657	1132-1134	IN	denotes	Of
T659	1135-1140	DT	denotes	these
T661	1141-1144	CD	denotes	117
T660	1145-1150	NNS	denotes	genes
T662	1150-1152	,	denotes	,
T663	1152-1154	CD	denotes	21
T664	1155-1159	VBD	denotes	were
T658	1160-1167	VBN	denotes	located
T665	1168-1174	IN	denotes	inside
T666	1175-1178	DT	denotes	the
T668	1179-1186	NN	denotes	support
T667	1187-1196	NNS	denotes	intervals
T669	1197-1199	IN	denotes	of
T670	1200-1203	DT	denotes	the
T672	1204-1205	CD	denotes	8
T673	1206-1211	JJ	denotes	small
T675	1211-1212	HYPH	denotes	-
T674	1212-1218	NN	denotes	effect
T671	1219-1222	NN	denotes	QTL
T676	1223-1226	CC	denotes	and
T677	1227-1231	RB	denotes	thus
T679	1232-1236	VBD	denotes	were
T678	1237-1247	VBN	denotes	considered
T680	1248-1250	IN	denotes	as
T681	1251-1260	NN	denotes	candidate
T682	1261-1266	NNS	denotes	genes
T683	1266-1267	.	denotes	.
T2422	1282-1296	NN	denotes	Susceptibility
T2424	1297-1299	IN	denotes	to
T2425	1300-1304	RBS	denotes	most
T2427	1305-1312	JJ	denotes	complex
T2426	1313-1321	NNS	denotes	diseases
T2428	1322-1324	VBZ	denotes	is
T2423	1325-1335	VBN	denotes	controlled
T2429	1336-1338	IN	denotes	by
T2430	1339-1343	JJ	denotes	many
T2431	1344-1349	NNS	denotes	genes
T2432	1349-1351	,	denotes	,
T2433	1351-1355	RB	denotes	each
T2434	1356-1362	VBG	denotes	having
T2435	1363-1364	DT	denotes	a
T2437	1365-1370	JJ	denotes	small
T2436	1371-1377	NN	denotes	effect
T2438	1378-1380	IN	denotes	on
T2439	1381-1384	DT	denotes	the
T2440	1385-1392	NN	denotes	disease
T2441	1392-1393	.	denotes	.
T2442	1393-1487	sentence	denotes	One example is rheumatoid arthritis (RA), a common complex multifactorial autoimmune disease.
T2443	1394-1397	CD	denotes	One
T2444	1398-1405	NN	denotes	example
T2445	1406-1408	VBZ	denotes	is
T2446	1409-1419	JJ	denotes	rheumatoid
T2447	1420-1429	NN	denotes	arthritis
T2448	1430-1431	-LRB-	denotes	(
T2449	1431-1433	NN	denotes	RA
T2450	1433-1434	-RRB-	denotes	)
T2451	1434-1436	,	denotes	,
T2452	1436-1437	DT	denotes	a
T2454	1438-1444	JJ	denotes	common
T2455	1445-1452	NN	denotes	complex
T2456	1453-1467	JJ	denotes	multifactorial
T2457	1468-1478	JJ	denotes	autoimmune
T2453	1479-1486	NN	denotes	disease
T2458	1486-1487	.	denotes	.
T2459	1487-1640	sentence	denotes	Several studies have been carried out to detect the genetic basis of RA, and more than 30 genomic regions have shown evidence of linkage to the disease.
T2460	1488-1495	JJ	denotes	Several
T2461	1496-1503	NNS	denotes	studies
T2463	1504-1508	VBP	denotes	have
T2464	1509-1513	VBN	denotes	been
T2462	1514-1521	VBN	denotes	carried
T2465	1522-1525	RP	denotes	out
T2466	1526-1528	TO	denotes	to
T2467	1529-1535	VB	denotes	detect
T2468	1536-1539	DT	denotes	the
T2470	1540-1547	JJ	denotes	genetic
T2469	1548-1553	NN	denotes	basis
T2471	1554-1556	IN	denotes	of
T2472	1557-1559	NN	denotes	RA
T2473	1559-1561	,	denotes	,
T2474	1561-1564	CC	denotes	and
T2475	1565-1569	JJR	denotes	more
T2477	1570-1574	IN	denotes	than
T2476	1575-1577	CD	denotes	30
T2479	1578-1585	JJ	denotes	genomic
T2478	1586-1593	NNS	denotes	regions
T2481	1594-1598	VBP	denotes	have
T2480	1599-1604	VBN	denotes	shown
T2482	1605-1613	NN	denotes	evidence
T2483	1614-1616	IN	denotes	of
T2484	1617-1624	NN	denotes	linkage
T2485	1625-1627	IN	denotes	to
T2486	1628-1631	DT	denotes	the
T2487	1632-1639	NN	denotes	disease
T2488	1639-1640	.	denotes	.
T2489	1640-1782	sentence	denotes	Most of these genomic regions did not reach a genome-wide significant threshold value of linkage, with P values between 0.05 and 0.001 [1-5].
T2490	1641-1645	JJS	denotes	Most
T2492	1646-1648	IN	denotes	of
T2493	1649-1654	DT	denotes	these
T2495	1655-1662	JJ	denotes	genomic
T2494	1663-1670	NNS	denotes	regions
T2496	1671-1674	VBD	denotes	did
T2497	1675-1678	RB	denotes	not
T2491	1679-1684	VB	denotes	reach
T2498	1685-1686	DT	denotes	a
T2500	1687-1693	NN	denotes	genome
T2502	1693-1694	HYPH	denotes	-
T2501	1694-1698	JJ	denotes	wide
T2503	1699-1710	JJ	denotes	significant
T2504	1711-1720	NN	denotes	threshold
T2499	1721-1726	NN	denotes	value
T2505	1727-1729	IN	denotes	of
T2506	1730-1737	NN	denotes	linkage
T2507	1737-1739	,	denotes	,
T2508	1739-1743	IN	denotes	with
T2509	1744-1745	NN	denotes	P
T2510	1746-1752	NNS	denotes	values
T2511	1753-1760	IN	denotes	between
T2512	1761-1765	CD	denotes	0.05
T2513	1766-1769	CC	denotes	and
T2514	1770-1775	CD	denotes	0.001
T2515	1776-1777	-LRB-	denotes	[
T2516	1777-1778	CD	denotes	1
T2517	1778-1779	SYM	denotes	-
T2518	1779-1780	CD	denotes	5
T2519	1780-1781	-RRB-	denotes	]
T2520	1781-1782	.	denotes	.
T2521	1782-1831	sentence	denotes	Thus, these loci only have a small effect on RA.
T2522	1783-1787	RB	denotes	Thus
T2524	1787-1789	,	denotes	,
T2525	1789-1794	DT	denotes	these
T2526	1795-1799	NNS	denotes	loci
T2527	1800-1804	RB	denotes	only
T2523	1805-1809	VBP	denotes	have
T2528	1810-1811	DT	denotes	a
T2530	1812-1817	JJ	denotes	small
T2529	1818-1824	NN	denotes	effect
T2531	1825-1827	IN	denotes	on
T2532	1828-1830	NN	denotes	RA
T2533	1830-1831	.	denotes	.
T2534	1831-1983	sentence	denotes	Small genetic contributions could also be seen from the susceptibility genes of RA identified so far, including HLA-DR4, PADI4, PTPN22 and FCRL3 [6-9].
T2535	1832-1837	JJ	denotes	Small
T2537	1838-1845	JJ	denotes	genetic
T2536	1846-1859	NNS	denotes	contributions
T2539	1860-1865	MD	denotes	could
T2540	1866-1870	RB	denotes	also
T2541	1871-1873	VB	denotes	be
T2538	1874-1878	VBN	denotes	seen
T2542	1879-1883	IN	denotes	from
T2543	1884-1887	DT	denotes	the
T2545	1888-1902	NN	denotes	susceptibility
T2544	1903-1908	NNS	denotes	genes
T2546	1909-1911	IN	denotes	of
T2547	1912-1914	NN	denotes	RA
T2548	1915-1925	VBN	denotes	identified
T2549	1926-1928	RB	denotes	so
T2550	1929-1932	RB	denotes	far
T2551	1932-1934	,	denotes	,
T2552	1934-1943	VBG	denotes	including
T2553	1944-1947	NN	denotes	HLA
T2555	1947-1948	HYPH	denotes	-
T2554	1948-1951	NN	denotes	DR4
T2556	1951-1953	,	denotes	,
T2557	1953-1958	NN	denotes	PADI4
T2558	1958-1960	,	denotes	,
T2559	1960-1966	NN	denotes	PTPN22
T2560	1967-1970	CC	denotes	and
T2561	1971-1976	NN	denotes	FCRL3
T2562	1977-1978	-LRB-	denotes	[
T2563	1978-1979	CD	denotes	6
T2564	1979-1980	SYM	denotes	-
T2565	1980-1981	CD	denotes	9
T2566	1981-1982	-RRB-	denotes	]
T2567	1982-1983	.	denotes	.
T2568	1983-2117	sentence	denotes	Except for HLA-DR4, which is strongly associated with RA, all the other susceptibility genes have only a small effect on the disease.
T2569	1984-1990	IN	denotes	Except
T2571	1991-1994	IN	denotes	for
T2572	1995-1998	NN	denotes	HLA
T2574	1998-1999	HYPH	denotes	-
T2573	1999-2002	NN	denotes	DR4
T2575	2002-2004	,	denotes	,
T2576	2004-2009	WDT	denotes	which
T2578	2010-2012	VBZ	denotes	is
T2579	2013-2021	RB	denotes	strongly
T2577	2022-2032	VBN	denotes	associated
T2580	2033-2037	IN	denotes	with
T2581	2038-2040	NN	denotes	RA
T2582	2040-2042	,	denotes	,
T2583	2042-2045	PDT	denotes	all
T2585	2046-2049	DT	denotes	the
T2586	2050-2055	JJ	denotes	other
T2587	2056-2070	NN	denotes	susceptibility
T2584	2071-2076	NNS	denotes	genes
T2570	2077-2081	VBP	denotes	have
T2588	2082-2086	RB	denotes	only
T2590	2087-2088	DT	denotes	a
T2591	2089-2094	JJ	denotes	small
T2589	2095-2101	NN	denotes	effect
T2592	2102-2104	IN	denotes	on
T2593	2105-2108	DT	denotes	the
T2594	2109-2116	NN	denotes	disease
T2595	2116-2117	.	denotes	.
T2596	2117-2196	sentence	denotes	In the mouse model of RA, small genetic contributions are also often observed.
T2597	2118-2120	IN	denotes	In
T2599	2121-2124	DT	denotes	the
T2601	2125-2130	NN	denotes	mouse
T2600	2131-2136	NN	denotes	model
T2602	2137-2139	IN	denotes	of
T2603	2140-2142	NN	denotes	RA
T2604	2142-2144	,	denotes	,
T2605	2144-2149	JJ	denotes	small
T2607	2150-2157	JJ	denotes	genetic
T2606	2158-2171	NNS	denotes	contributions
T2608	2172-2175	VBP	denotes	are
T2609	2176-2180	RB	denotes	also
T2610	2181-2186	RB	denotes	often
T2598	2187-2195	VBN	denotes	observed
T2611	2195-2196	.	denotes	.
T2612	2196-2387	sentence	denotes	For example, in a previous study, we carried out a genome screen to identify the quantitative trait loci (QTL) in collagen-induced arthritis (CIA), which is a widely used animal model of RA.
T2613	2197-2200	IN	denotes	For
T2615	2201-2208	NN	denotes	example
T2616	2208-2210	,	denotes	,
T2617	2210-2212	IN	denotes	in
T2618	2213-2214	DT	denotes	a
T2620	2215-2223	JJ	denotes	previous
T2619	2224-2229	NN	denotes	study
T2621	2229-2231	,	denotes	,
T2622	2231-2233	PRP	denotes	we
T2614	2234-2241	VBD	denotes	carried
T2623	2242-2245	RP	denotes	out
T2624	2246-2247	DT	denotes	a
T2626	2248-2254	NN	denotes	genome
T2625	2255-2261	NN	denotes	screen
T2627	2262-2264	TO	denotes	to
T2628	2265-2273	VB	denotes	identify
T2629	2274-2277	DT	denotes	the
T2631	2278-2290	JJ	denotes	quantitative
T2632	2291-2296	NN	denotes	trait
T2630	2297-2301	NNS	denotes	loci
T2633	2302-2303	-LRB-	denotes	(
T2634	2303-2306	NN	denotes	QTL
T2635	2306-2307	-RRB-	denotes	)
T2636	2308-2310	IN	denotes	in
T2637	2311-2319	NN	denotes	collagen
T2639	2319-2320	HYPH	denotes	-
T2638	2320-2327	VBN	denotes	induced
T2640	2328-2337	NN	denotes	arthritis
T2641	2338-2339	-LRB-	denotes	(
T2642	2339-2342	NN	denotes	CIA
T2643	2342-2343	-RRB-	denotes	)
T2644	2343-2345	,	denotes	,
T2645	2345-2350	WDT	denotes	which
T2646	2351-2353	VBZ	denotes	is
T2647	2354-2355	DT	denotes	a
T2649	2356-2362	RB	denotes	widely
T2650	2363-2367	VBN	denotes	used
T2651	2368-2374	NN	denotes	animal
T2648	2375-2380	NN	denotes	model
T2652	2381-2383	IN	denotes	of
T2653	2384-2386	NN	denotes	RA
T2654	2386-2387	.	denotes	.
T2655	2387-2565	sentence	denotes	Only one QTL, Cia2, was identified for the phenotype of CIA severity, but this QTL contributes to only 16% of the phenotype variations for CIA susceptibility in F2 progeny [10].
T2656	2388-2392	RB	denotes	Only
T2658	2393-2396	CD	denotes	one
T2657	2397-2400	NN	denotes	QTL
T2660	2400-2402	,	denotes	,
T2661	2402-2406	NN	denotes	Cia2
T2662	2406-2408	,	denotes	,
T2663	2408-2411	VBD	denotes	was
T2659	2412-2422	VBN	denotes	identified
T2664	2423-2426	IN	denotes	for
T2665	2427-2430	DT	denotes	the
T2666	2431-2440	NN	denotes	phenotype
T2667	2441-2443	IN	denotes	of
T2668	2444-2447	NN	denotes	CIA
T2669	2448-2456	NN	denotes	severity
T2670	2456-2458	,	denotes	,
T2671	2458-2461	CC	denotes	but
T2672	2462-2466	DT	denotes	this
T2673	2467-2470	NN	denotes	QTL
T2674	2471-2482	VBZ	denotes	contributes
T2675	2483-2485	IN	denotes	to
T2676	2486-2490	RB	denotes	only
T2677	2491-2493	CD	denotes	16
T2678	2493-2494	NN	denotes	%
T2679	2495-2497	IN	denotes	of
T2680	2498-2501	DT	denotes	the
T2682	2502-2511	NN	denotes	phenotype
T2681	2512-2522	NNS	denotes	variations
T2683	2523-2526	IN	denotes	for
T2684	2527-2530	NN	denotes	CIA
T2685	2531-2545	NN	denotes	susceptibility
T2686	2546-2548	IN	denotes	in
T2687	2549-2551	NN	denotes	F2
T2688	2552-2559	NN	denotes	progeny
T2689	2560-2561	-LRB-	denotes	[
T2690	2561-2563	CD	denotes	10
T2691	2563-2564	-RRB-	denotes	]
T2692	2564-2565	.	denotes	.
T2693	2565-2738	sentence	denotes	This suggests that there must be other susceptibility genes whose contributions were not big enough to reach the stringent significance threshold value of linkage analysis.
T2694	2566-2570	DT	denotes	This
T2695	2571-2579	VBZ	denotes	suggests
T2696	2580-2584	IN	denotes	that
T2698	2585-2590	EX	denotes	there
T2699	2591-2595	MD	denotes	must
T2697	2596-2598	VB	denotes	be
T2700	2599-2604	JJ	denotes	other
T2702	2605-2619	NN	denotes	susceptibility
T2701	2620-2625	NNS	denotes	genes
T2703	2626-2631	WP$	denotes	whose
T2704	2632-2645	NNS	denotes	contributions
T2705	2646-2650	VBD	denotes	were
T2706	2651-2654	RB	denotes	not
T2707	2655-2658	JJ	denotes	big
T2708	2659-2665	RB	denotes	enough
T2709	2666-2668	TO	denotes	to
T2710	2669-2674	VB	denotes	reach
T2711	2675-2678	DT	denotes	the
T2713	2679-2688	JJ	denotes	stringent
T2714	2689-2701	NN	denotes	significance
T2715	2702-2711	NN	denotes	threshold
T2712	2712-2717	NN	denotes	value
T2716	2718-2720	IN	denotes	of
T2717	2721-2728	NN	denotes	linkage
T2718	2729-2737	NN	denotes	analysis
T2719	2737-2738	.	denotes	.
T2720	2738-2840	sentence	denotes	One aim of using animal models for complex diseases is to detect the genetic basis of these diseases.
T2721	2739-2742	CD	denotes	One
T2722	2743-2746	NN	denotes	aim
T2724	2747-2749	IN	denotes	of
T2725	2750-2755	VBG	denotes	using
T2726	2756-2762	NN	denotes	animal
T2727	2763-2769	NNS	denotes	models
T2728	2770-2773	IN	denotes	for
T2729	2774-2781	JJ	denotes	complex
T2730	2782-2790	NNS	denotes	diseases
T2723	2791-2793	VBZ	denotes	is
T2731	2794-2796	TO	denotes	to
T2732	2797-2803	VB	denotes	detect
T2733	2804-2807	DT	denotes	the
T2735	2808-2815	JJ	denotes	genetic
T2734	2816-2821	NN	denotes	basis
T2736	2822-2824	IN	denotes	of
T2737	2825-2830	DT	denotes	these
T2738	2831-2839	NNS	denotes	diseases
T2739	2839-2840	.	denotes	.
T2740	2840-3064	sentence	denotes	With controllable environmental factors as well as the known genetic background, animal models are powerful tools to search for susceptibility genes for complex diseases, and have been intensively employed for that purpose.
T2741	2841-2845	IN	denotes	With
T2743	2846-2858	JJ	denotes	controllable
T2745	2859-2872	JJ	denotes	environmental
T2744	2873-2880	NNS	denotes	factors
T2746	2881-2883	RB	denotes	as
T2748	2884-2888	RB	denotes	well
T2747	2889-2891	IN	denotes	as
T2749	2892-2895	DT	denotes	the
T2751	2896-2901	JJ	denotes	known
T2752	2902-2909	JJ	denotes	genetic
T2750	2910-2920	NN	denotes	background
T2753	2920-2922	,	denotes	,
T2754	2922-2928	NN	denotes	animal
T2755	2929-2935	NNS	denotes	models
T2742	2936-2939	VBP	denotes	are
T2756	2940-2948	JJ	denotes	powerful
T2757	2949-2954	NNS	denotes	tools
T2758	2955-2957	TO	denotes	to
T2759	2958-2964	VB	denotes	search
T2760	2965-2968	IN	denotes	for
T2761	2969-2983	NN	denotes	susceptibility
T2762	2984-2989	NNS	denotes	genes
T2763	2990-2993	IN	denotes	for
T2764	2994-3001	JJ	denotes	complex
T2765	3002-3010	NNS	denotes	diseases
T2766	3010-3012	,	denotes	,
T2767	3012-3015	CC	denotes	and
T2768	3016-3020	VBP	denotes	have
T2770	3021-3025	VBN	denotes	been
T2771	3026-3037	RB	denotes	intensively
T2769	3038-3046	VBN	denotes	employed
T2772	3047-3050	IN	denotes	for
T2773	3051-3055	DT	denotes	that
T2774	3056-3063	NN	denotes	purpose
T2775	3063-3064	.	denotes	.
T2776	3064-3197	sentence	denotes	More than 27,000 QTL have been identified in the mouse genome since the first QTL was identified at the beginning of the 1990s [11].
T2777	3065-3069	JJR	denotes	More
T2779	3070-3074	IN	denotes	than
T2778	3075-3081	CD	denotes	27,000
T2780	3082-3085	NN	denotes	QTL
T2782	3086-3090	VBP	denotes	have
T2783	3091-3095	VBN	denotes	been
T2781	3096-3106	VBN	denotes	identified
T2784	3107-3109	IN	denotes	in
T2785	3110-3113	DT	denotes	the
T2787	3114-3119	NN	denotes	mouse
T2786	3120-3126	NN	denotes	genome
T2788	3127-3132	IN	denotes	since
T2790	3133-3136	DT	denotes	the
T2792	3137-3142	JJ	denotes	first
T2791	3143-3146	NN	denotes	QTL
T2793	3147-3150	VBD	denotes	was
T2789	3151-3161	VBN	denotes	identified
T2794	3162-3164	IN	denotes	at
T2795	3165-3168	DT	denotes	the
T2796	3169-3178	NN	denotes	beginning
T2797	3179-3181	IN	denotes	of
T2798	3182-3185	DT	denotes	the
T2799	3186-3191	NNS	denotes	1990s
T2800	3192-3193	-LRB-	denotes	[
T2801	3193-3195	CD	denotes	11
T2802	3195-3196	-RRB-	denotes	]
T2803	3196-3197	.	denotes	.
T2804	3197-3304	sentence	denotes	By 2005, approximately 20 quantitative trait genes (QTGs) in the mouse genome had been identified [12,13].
T2805	3198-3200	IN	denotes	By
T2807	3201-3205	CD	denotes	2005
T2808	3205-3207	,	denotes	,
T2809	3207-3220	RB	denotes	approximately
T2810	3221-3223	CD	denotes	20
T2812	3224-3236	JJ	denotes	quantitative
T2813	3237-3242	NN	denotes	trait
T2811	3243-3248	NNS	denotes	genes
T2814	3249-3250	-LRB-	denotes	(
T2815	3250-3254	NNS	denotes	QTGs
T2816	3254-3255	-RRB-	denotes	)
T2817	3256-3258	IN	denotes	in
T2818	3259-3262	DT	denotes	the
T2820	3263-3268	NN	denotes	mouse
T2819	3269-3275	NN	denotes	genome
T2821	3276-3279	VBD	denotes	had
T2822	3280-3284	VBN	denotes	been
T2806	3285-3295	VBN	denotes	identified
T2823	3296-3297	-LRB-	denotes	[
T2825	3297-3299	CD	denotes	12
T2826	3299-3300	,	denotes	,
T2824	3300-3302	CD	denotes	13
T2827	3302-3303	-RRB-	denotes	]
T2828	3303-3304	.	denotes	.
T2829	3304-3485	sentence	denotes	Interestingly, most QTGs identified in animal models have the causal polymorphisms in the protein-coding region [14], which provoke protein structure changes or protein deficiency.
T2830	3305-3318	RB	denotes	Interestingly
T2832	3318-3320	,	denotes	,
T2833	3320-3324	JJS	denotes	most
T2834	3325-3329	NNS	denotes	QTGs
T2835	3330-3340	VBN	denotes	identified
T2836	3341-3343	IN	denotes	in
T2837	3344-3350	NN	denotes	animal
T2838	3351-3357	NNS	denotes	models
T2831	3358-3362	VBP	denotes	have
T2839	3363-3366	DT	denotes	the
T2841	3367-3373	JJ	denotes	causal
T2840	3374-3387	NNS	denotes	polymorphisms
T2842	3388-3390	IN	denotes	in
T2843	3391-3394	DT	denotes	the
T2845	3395-3402	NN	denotes	protein
T2847	3402-3403	HYPH	denotes	-
T2846	3403-3409	VBG	denotes	coding
T2844	3410-3416	NN	denotes	region
T2848	3417-3418	-LRB-	denotes	[
T2849	3418-3420	CD	denotes	14
T2850	3420-3421	-RRB-	denotes	]
T2851	3421-3423	,	denotes	,
T2852	3423-3428	WDT	denotes	which
T2853	3429-3436	VBP	denotes	provoke
T2854	3437-3444	NN	denotes	protein
T2856	3445-3454	NN	denotes	structure
T2855	3455-3462	NNS	denotes	changes
T2857	3463-3465	CC	denotes	or
T2858	3466-3473	NN	denotes	protein
T2859	3474-3484	NN	denotes	deficiency
T2860	3484-3485	.	denotes	.
T2861	3485-3760	sentence	denotes	This suggests, on the one hand, that small-effect QTL are difficult to identify with traditional strategies and, on the other hand, that the polymorphisms regulating gene expression might only slightly affect the quantitative traits, and thus are more difficult to identify.
T2862	3486-3490	DT	denotes	This
T2863	3491-3499	VBZ	denotes	suggests
T2864	3499-3501	,	denotes	,
T2865	3501-3503	IN	denotes	on
T2867	3504-3507	DT	denotes	the
T2869	3508-3511	CD	denotes	one
T2868	3512-3516	NN	denotes	hand
T2870	3516-3518	,	denotes	,
T2871	3518-3522	IN	denotes	that
T2872	3523-3528	JJ	denotes	small
T2874	3528-3529	HYPH	denotes	-
T2873	3529-3535	NN	denotes	effect
T2875	3536-3539	NN	denotes	QTL
T2866	3540-3543	VBP	denotes	are
T2876	3544-3553	JJ	denotes	difficult
T2877	3554-3556	TO	denotes	to
T2878	3557-3565	VB	denotes	identify
T2879	3566-3570	IN	denotes	with
T2880	3571-3582	JJ	denotes	traditional
T2881	3583-3593	NNS	denotes	strategies
T2882	3594-3597	CC	denotes	and
T2883	3597-3599	,	denotes	,
T2884	3599-3601	IN	denotes	on
T2886	3602-3605	DT	denotes	the
T2888	3606-3611	JJ	denotes	other
T2887	3612-3616	NN	denotes	hand
T2889	3616-3618	,	denotes	,
T2890	3618-3622	IN	denotes	that
T2891	3623-3626	DT	denotes	the
T2892	3627-3640	NNS	denotes	polymorphisms
T2893	3641-3651	VBG	denotes	regulating
T2894	3652-3656	NN	denotes	gene
T2895	3657-3667	NN	denotes	expression
T2896	3668-3673	MD	denotes	might
T2897	3674-3678	RB	denotes	only
T2898	3679-3687	RB	denotes	slightly
T2885	3688-3694	VB	denotes	affect
T2899	3695-3698	DT	denotes	the
T2901	3699-3711	JJ	denotes	quantitative
T2900	3712-3718	NNS	denotes	traits
T2902	3718-3720	,	denotes	,
T2903	3720-3723	CC	denotes	and
T2904	3724-3728	RB	denotes	thus
T2905	3729-3732	VBP	denotes	are
T2906	3733-3737	RBR	denotes	more
T2907	3738-3747	JJ	denotes	difficult
T2908	3748-3750	TO	denotes	to
T2909	3751-3759	VB	denotes	identify
T2910	3759-3760	.	denotes	.
T2911	3760-3860	sentence	denotes	Microarray-based global gene expression is a powerful technique for investigating complex diseases.
T2912	3761-3771	NN	denotes	Microarray
T2914	3771-3772	HYPH	denotes	-
T2913	3772-3777	VBN	denotes	based
T2916	3778-3784	JJ	denotes	global
T2917	3785-3789	NN	denotes	gene
T2915	3790-3800	NN	denotes	expression
T2918	3801-3803	VBZ	denotes	is
T2919	3804-3805	DT	denotes	a
T2921	3806-3814	JJ	denotes	powerful
T2920	3815-3824	NN	denotes	technique
T2922	3825-3828	IN	denotes	for
T2923	3829-3842	VBG	denotes	investigating
T2924	3843-3850	JJ	denotes	complex
T2925	3851-3859	NNS	denotes	diseases
T2926	3859-3860	.	denotes	.
T2927	3860-3961	sentence	denotes	During disease development, genes involved in the disease are likely to be differentially regulated.
T2928	3861-3867	IN	denotes	During
T2930	3868-3875	NN	denotes	disease
T2931	3876-3887	NN	denotes	development
T2932	3887-3889	,	denotes	,
T2933	3889-3894	NNS	denotes	genes
T2934	3895-3903	VBN	denotes	involved
T2935	3904-3906	IN	denotes	in
T2936	3907-3910	DT	denotes	the
T2937	3911-3918	NN	denotes	disease
T2929	3919-3922	VBP	denotes	are
T2938	3923-3929	JJ	denotes	likely
T2939	3930-3932	TO	denotes	to
T2941	3933-3935	VB	denotes	be
T2942	3936-3950	RB	denotes	differentially
T2940	3951-3960	VBN	denotes	regulated
T2943	3960-3961	.	denotes	.
T2944	3961-4124	sentence	denotes	Therefore, signature genes of the diseases could be identified by detecting the expression patterns of the disease-related cells/tissues and their ideal controls.
T2945	3962-3971	RB	denotes	Therefore
T2947	3971-3973	,	denotes	,
T2948	3973-3982	NN	denotes	signature
T2949	3983-3988	NNS	denotes	genes
T2950	3989-3991	IN	denotes	of
T2951	3992-3995	DT	denotes	the
T2952	3996-4004	NNS	denotes	diseases
T2953	4005-4010	MD	denotes	could
T2954	4011-4013	VB	denotes	be
T2946	4014-4024	VBN	denotes	identified
T2955	4025-4027	IN	denotes	by
T2956	4028-4037	VBG	denotes	detecting
T2957	4038-4041	DT	denotes	the
T2959	4042-4052	NN	denotes	expression
T2958	4053-4061	NNS	denotes	patterns
T2960	4062-4064	IN	denotes	of
T2961	4065-4068	DT	denotes	the
T2963	4069-4076	NN	denotes	disease
T2965	4076-4077	HYPH	denotes	-
T2964	4077-4084	VBN	denotes	related
T2966	4085-4090	NNS	denotes	cells
T2967	4090-4091	HYPH	denotes	/
T2962	4091-4098	NNS	denotes	tissues
T2968	4099-4102	CC	denotes	and
T2969	4103-4108	PRP$	denotes	their
T2971	4109-4114	JJ	denotes	ideal
T2970	4115-4123	NNS	denotes	controls
T2972	4123-4124	.	denotes	.
T2973	4124-4228	sentence	denotes	In the past decade, many studies applied this technique to study both RA and its animal models [15-22].
T2974	4125-4127	IN	denotes	In
T2976	4128-4131	DT	denotes	the
T2978	4132-4136	JJ	denotes	past
T2977	4137-4143	NN	denotes	decade
T2979	4143-4145	,	denotes	,
T2980	4145-4149	JJ	denotes	many
T2981	4150-4157	NNS	denotes	studies
T2975	4158-4165	VBD	denotes	applied
T2982	4166-4170	DT	denotes	this
T2983	4171-4180	NN	denotes	technique
T2984	4181-4183	TO	denotes	to
T2985	4184-4189	VB	denotes	study
T2986	4190-4194	CC	denotes	both
T2987	4195-4197	NN	denotes	RA
T2988	4198-4201	CC	denotes	and
T2989	4202-4205	PRP$	denotes	its
T2991	4206-4212	NN	denotes	animal
T2990	4213-4219	NNS	denotes	models
T2992	4220-4221	-LRB-	denotes	[
T2993	4221-4223	CD	denotes	15
T2994	4223-4224	SYM	denotes	-
T2995	4224-4226	CD	denotes	22
T2996	4226-4227	-RRB-	denotes	]
T2997	4227-4228	.	denotes	.
T2998	4228-4357	sentence	denotes	Indeed, genes involved in arthritis show distinct expression patterns in certain tissues and pathological stages of the disease.
T2999	4229-4235	RB	denotes	Indeed
T3001	4235-4237	,	denotes	,
T3002	4237-4242	NNS	denotes	genes
T3003	4243-4251	VBN	denotes	involved
T3004	4252-4254	IN	denotes	in
T3005	4255-4264	NN	denotes	arthritis
T3000	4265-4269	VBP	denotes	show
T3006	4270-4278	JJ	denotes	distinct
T3008	4279-4289	NN	denotes	expression
T3007	4290-4298	NNS	denotes	patterns
T3009	4299-4301	IN	denotes	in
T3010	4302-4309	JJ	denotes	certain
T3011	4310-4317	NNS	denotes	tissues
T3012	4318-4321	CC	denotes	and
T3013	4322-4334	JJ	denotes	pathological
T3014	4335-4341	NNS	denotes	stages
T3015	4342-4344	IN	denotes	of
T3016	4345-4348	DT	denotes	the
T3017	4349-4356	NN	denotes	disease
T3018	4356-4357	.	denotes	.
T3019	4357-4474	sentence	denotes	Genes involved in immunoinflammatory responses were differentially expressed in the blood cells in RA patients [18].
T3020	4358-4363	NNS	denotes	Genes
T3022	4364-4372	VBN	denotes	involved
T3023	4373-4375	IN	denotes	in
T3024	4376-4394	JJ	denotes	immunoinflammatory
T3025	4395-4404	NNS	denotes	responses
T3026	4405-4409	VBD	denotes	were
T3027	4410-4424	RB	denotes	differentially
T3021	4425-4434	VBN	denotes	expressed
T3028	4435-4437	IN	denotes	in
T3029	4438-4441	DT	denotes	the
T3031	4442-4447	NN	denotes	blood
T3030	4448-4453	NNS	denotes	cells
T3032	4454-4456	IN	denotes	in
T3033	4457-4459	NN	denotes	RA
T3034	4460-4468	NNS	denotes	patients
T3035	4469-4470	-LRB-	denotes	[
T3036	4470-4472	CD	denotes	18
T3037	4472-4473	-RRB-	denotes	]
T3038	4473-4474	.	denotes	.
T3039	4474-4757	sentence	denotes	Chemokines and adhesion molecules were upregulated in the joint at the initiation phase of arthritis in animal models [21,22], while genes involved in cartilage destruction and bone erosion were differentially expressed at the late phase of arthritis in animal models of RA [15,16].
T3040	4475-4485	NNS	denotes	Chemokines
T3042	4486-4489	CC	denotes	and
T3043	4490-4498	NN	denotes	adhesion
T3044	4499-4508	NNS	denotes	molecules
T3045	4509-4513	VBD	denotes	were
T3041	4514-4525	VBN	denotes	upregulated
T3046	4526-4528	IN	denotes	in
T3047	4529-4532	DT	denotes	the
T3048	4533-4538	NN	denotes	joint
T3049	4539-4541	IN	denotes	at
T3050	4542-4545	DT	denotes	the
T3052	4546-4556	NN	denotes	initiation
T3051	4557-4562	NN	denotes	phase
T3053	4563-4565	IN	denotes	of
T3054	4566-4575	NN	denotes	arthritis
T3055	4576-4578	IN	denotes	in
T3056	4579-4585	NN	denotes	animal
T3057	4586-4592	NNS	denotes	models
T3058	4593-4594	-LRB-	denotes	[
T3060	4594-4596	CD	denotes	21
T3061	4596-4597	,	denotes	,
T3059	4597-4599	CD	denotes	22
T3062	4599-4600	-RRB-	denotes	]
T3063	4600-4602	,	denotes	,
T3064	4602-4607	IN	denotes	while
T3066	4608-4613	NNS	denotes	genes
T3067	4614-4622	VBN	denotes	involved
T3068	4623-4625	IN	denotes	in
T3069	4626-4635	NN	denotes	cartilage
T3070	4636-4647	NN	denotes	destruction
T3071	4648-4651	CC	denotes	and
T3072	4652-4656	NN	denotes	bone
T3073	4657-4664	NN	denotes	erosion
T3074	4665-4669	VBD	denotes	were
T3075	4670-4684	RB	denotes	differentially
T3065	4685-4694	VBN	denotes	expressed
T3076	4695-4697	IN	denotes	at
T3077	4698-4701	DT	denotes	the
T3079	4702-4706	JJ	denotes	late
T3078	4707-4712	NN	denotes	phase
T3080	4713-4715	IN	denotes	of
T3081	4716-4725	NN	denotes	arthritis
T3082	4726-4728	IN	denotes	in
T3083	4729-4735	NN	denotes	animal
T3084	4736-4742	NNS	denotes	models
T3085	4743-4745	IN	denotes	of
T3086	4746-4748	NN	denotes	RA
T3087	4749-4750	-LRB-	denotes	[
T3089	4750-4752	CD	denotes	15
T3090	4752-4753	,	denotes	,
T3088	4753-4755	CD	denotes	16
T3091	4755-4756	-RRB-	denotes	]
T3092	4756-4757	.	denotes	.
T3093	4757-5028	sentence	denotes	Besides detecting genes involved in complex diseases, microarrays could also be used to detect the genetic polymorphisms regulating gene expression because differential expressions between two strains might be the result of a polymorphism located in regulatory elements.
T3094	4758-4765	IN	denotes	Besides
T3095	4766-4775	VBG	denotes	detecting
T3097	4776-4781	NNS	denotes	genes
T3098	4782-4790	VBN	denotes	involved
T3099	4791-4793	IN	denotes	in
T3100	4794-4801	JJ	denotes	complex
T3101	4802-4810	NNS	denotes	diseases
T3102	4810-4812	,	denotes	,
T3103	4812-4823	NNS	denotes	microarrays
T3104	4824-4829	MD	denotes	could
T3105	4830-4834	RB	denotes	also
T3106	4835-4837	VB	denotes	be
T3096	4838-4842	VBN	denotes	used
T3107	4843-4845	TO	denotes	to
T3108	4846-4852	VB	denotes	detect
T3109	4853-4856	DT	denotes	the
T3111	4857-4864	JJ	denotes	genetic
T3110	4865-4878	NNS	denotes	polymorphisms
T3112	4879-4889	VBG	denotes	regulating
T3113	4890-4894	NN	denotes	gene
T3114	4895-4905	NN	denotes	expression
T3115	4906-4913	IN	denotes	because
T3117	4914-4926	JJ	denotes	differential
T3118	4927-4938	NNS	denotes	expressions
T3119	4939-4946	IN	denotes	between
T3120	4947-4950	CD	denotes	two
T3121	4951-4958	NNS	denotes	strains
T3122	4959-4964	MD	denotes	might
T3116	4965-4967	VB	denotes	be
T3123	4968-4971	DT	denotes	the
T3124	4972-4978	NN	denotes	result
T3125	4979-4981	IN	denotes	of
T3126	4982-4983	DT	denotes	a
T3127	4984-4996	NN	denotes	polymorphism
T3128	4997-5004	VBN	denotes	located
T3129	5005-5007	IN	denotes	in
T3130	5008-5018	JJ	denotes	regulatory
T3131	5019-5027	NNS	denotes	elements
T3132	5027-5028	.	denotes	.
T3133	5028-5233	sentence	denotes	To identify the small-effect QTL of CIA as well as the potential candidate genes inside them, we investigated CIA genetically susceptible and resistant strains at both the genome and transcriptome levels.
T3134	5029-5031	TO	denotes	To
T3135	5032-5040	VB	denotes	identify
T3137	5041-5044	DT	denotes	the
T3139	5045-5050	JJ	denotes	small
T3141	5050-5051	HYPH	denotes	-
T3140	5051-5057	NN	denotes	effect
T3138	5058-5061	NN	denotes	QTL
T3142	5062-5064	IN	denotes	of
T3143	5065-5068	NN	denotes	CIA
T3144	5069-5071	RB	denotes	as
T3146	5072-5076	RB	denotes	well
T3145	5077-5079	IN	denotes	as
T3147	5080-5083	DT	denotes	the
T3149	5084-5093	JJ	denotes	potential
T3150	5094-5103	NN	denotes	candidate
T3148	5104-5109	NNS	denotes	genes
T3151	5110-5116	IN	denotes	inside
T3152	5117-5121	PRP	denotes	them
T3153	5121-5123	,	denotes	,
T3154	5123-5125	PRP	denotes	we
T3136	5126-5138	VBD	denotes	investigated
T3155	5139-5142	NN	denotes	CIA
T3157	5143-5154	RB	denotes	genetically
T3156	5155-5166	JJ	denotes	susceptible
T3159	5167-5170	CC	denotes	and
T3160	5171-5180	JJ	denotes	resistant
T3158	5181-5188	NNS	denotes	strains
T3161	5189-5191	IN	denotes	at
T3162	5192-5196	CC	denotes	both
T3164	5197-5200	DT	denotes	the
T3163	5201-5207	NN	denotes	genome
T3166	5208-5211	CC	denotes	and
T3167	5212-5225	NN	denotes	transcriptome
T3165	5226-5232	NNS	denotes	levels
T3168	5232-5233	.	denotes	.
T3169	5233-5420	sentence	denotes	At the genome level, F2 progeny of the CIA susceptible (DBA/1) and resistant (FVB/N) strains were generated and a genome-wide linkage analysis was performed to identify small-effect QTL.
T3170	5234-5236	IN	denotes	At
T3172	5237-5240	DT	denotes	the
T3174	5241-5247	NN	denotes	genome
T3173	5248-5253	NN	denotes	level
T3175	5253-5255	,	denotes	,
T3176	5255-5257	NN	denotes	F2
T3177	5258-5265	NN	denotes	progeny
T3178	5266-5268	IN	denotes	of
T3179	5269-5272	DT	denotes	the
T3181	5273-5276	NN	denotes	CIA
T3182	5277-5288	JJ	denotes	susceptible
T3183	5289-5290	-LRB-	denotes	(
T3184	5290-5293	NN	denotes	DBA
T3185	5293-5294	HYPH	denotes	/
T3186	5294-5295	CD	denotes	1
T3187	5295-5296	-RRB-	denotes	)
T3188	5297-5300	CC	denotes	and
T3189	5301-5310	JJ	denotes	resistant
T3190	5311-5312	-LRB-	denotes	(
T3192	5312-5315	NN	denotes	FVB
T3193	5315-5316	HYPH	denotes	/
T3191	5316-5317	NN	denotes	N
T3194	5317-5318	-RRB-	denotes	)
T3180	5319-5326	NNS	denotes	strains
T3195	5327-5331	VBD	denotes	were
T3171	5332-5341	VBN	denotes	generated
T3196	5342-5345	CC	denotes	and
T3197	5346-5347	DT	denotes	a
T3199	5348-5354	NN	denotes	genome
T3201	5354-5355	HYPH	denotes	-
T3200	5355-5359	JJ	denotes	wide
T3202	5360-5367	NN	denotes	linkage
T3198	5368-5376	NN	denotes	analysis
T3204	5377-5380	VBD	denotes	was
T3203	5381-5390	VBN	denotes	performed
T3205	5391-5393	TO	denotes	to
T3206	5394-5402	VB	denotes	identify
T3207	5403-5408	JJ	denotes	small
T3209	5408-5409	HYPH	denotes	-
T3208	5409-5415	NN	denotes	effect
T3210	5416-5419	NN	denotes	QTL
T3211	5419-5420	.	denotes	.
T3212	5420-5558	sentence	denotes	At the transcriptome level, we detected the gene expression patterns of both the DBA/1 and FVB/N strains at four different phases of CIA.
T3213	5421-5423	IN	denotes	At
T3215	5424-5427	DT	denotes	the
T3217	5428-5441	NN	denotes	transcriptome
T3216	5442-5447	NN	denotes	level
T3218	5447-5449	,	denotes	,
T3219	5449-5451	PRP	denotes	we
T3214	5452-5460	VBD	denotes	detected
T3220	5461-5464	DT	denotes	the
T3222	5465-5469	NN	denotes	gene
T3223	5470-5480	NN	denotes	expression
T3221	5481-5489	NNS	denotes	patterns
T3224	5490-5492	IN	denotes	of
T3225	5493-5497	CC	denotes	both
T3227	5498-5501	DT	denotes	the
T3228	5502-5505	NN	denotes	DBA
T3229	5505-5506	HYPH	denotes	/
T3230	5506-5507	CD	denotes	1
T3231	5508-5511	CC	denotes	and
T3232	5512-5515	NN	denotes	FVB
T3234	5515-5516	HYPH	denotes	/
T3233	5516-5517	NN	denotes	N
T3226	5518-5525	NNS	denotes	strains
T3235	5526-5528	IN	denotes	at
T3236	5529-5533	CD	denotes	four
T3238	5534-5543	JJ	denotes	different
T3237	5544-5550	NNS	denotes	phases
T3239	5551-5553	IN	denotes	of
T3240	5554-5557	NN	denotes	CIA
T3241	5557-5558	.	denotes	.
T3242	5558-5849	sentence	denotes	The potential candidate genes were identified based on three criteria: they are located within the genomic region linked to CIA; they are disease-specific differentially expressed during CIA; and they are strain-specific differentially expressed between the two parental strains during CIA.
T3243	5559-5562	DT	denotes	The
T3245	5563-5572	JJ	denotes	potential
T3246	5573-5582	NN	denotes	candidate
T3244	5583-5588	NNS	denotes	genes
T3248	5589-5593	VBD	denotes	were
T3247	5594-5604	VBN	denotes	identified
T3250	5605-5610	VBN	denotes	based
T3251	5611-5613	IN	denotes	on
T3252	5614-5619	CD	denotes	three
T3253	5620-5628	NNS	denotes	criteria
T3254	5628-5630	:	denotes	:
T3255	5630-5634	PRP	denotes	they
T3256	5635-5638	VBP	denotes	are
T3249	5639-5646	VBN	denotes	located
T3257	5647-5653	IN	denotes	within
T3258	5654-5657	DT	denotes	the
T3260	5658-5665	JJ	denotes	genomic
T3259	5666-5672	NN	denotes	region
T3261	5673-5679	VBN	denotes	linked
T3262	5680-5682	IN	denotes	to
T3263	5683-5686	NN	denotes	CIA
T3264	5686-5687	:	denotes	;
T3265	5688-5692	PRP	denotes	they
T3267	5693-5696	VBP	denotes	are
T3268	5697-5704	NN	denotes	disease
T3270	5704-5705	HYPH	denotes	-
T3269	5705-5713	RB	denotes	specific
T3271	5714-5728	RB	denotes	differentially
T3266	5729-5738	VBN	denotes	expressed
T3272	5739-5745	IN	denotes	during
T3273	5746-5749	NN	denotes	CIA
T3274	5749-5750	:	denotes	;
T3275	5751-5754	CC	denotes	and
T3276	5755-5759	PRP	denotes	they
T3278	5760-5763	VBP	denotes	are
T3279	5764-5770	NN	denotes	strain
T3281	5770-5771	HYPH	denotes	-
T3280	5771-5779	RB	denotes	specific
T3282	5780-5794	RB	denotes	differentially
T3277	5795-5804	VBN	denotes	expressed
T3283	5805-5812	IN	denotes	between
T3284	5813-5816	DT	denotes	the
T3286	5817-5820	CD	denotes	two
T3287	5821-5829	JJ	denotes	parental
T3285	5830-5837	NNS	denotes	strains
T3288	5838-5844	IN	denotes	during
T3289	5845-5848	NN	denotes	CIA
T3290	5848-5849	.	denotes	.
T4044	5874-5881	NNS	denotes	Animals
T4045	5881-5883	,	denotes	,
T4046	5883-5895	NN	denotes	immunisation
T4047	5896-5899	CC	denotes	and
T4048	5900-5910	NN	denotes	assessment
T4049	5911-5913	IN	denotes	of
T4050	5914-5923	NN	denotes	arthritis
T4051	5923-6139	sentence	denotes	Both DBA/1 and FVB/N mice used in this study were obtained from the Jackson Laboratory and kept in a climate-controlled environment with 12 hour light/dark cycles in the animal facility at the University of Rostock.
T4052	5924-5928	CC	denotes	Both
T4053	5929-5932	NN	denotes	DBA
T4055	5932-5933	HYPH	denotes	/
T4056	5933-5934	CD	denotes	1
T4057	5935-5938	CC	denotes	and
T4058	5939-5942	NN	denotes	FVB
T4060	5942-5943	HYPH	denotes	/
T4059	5943-5944	NN	denotes	N
T4054	5945-5949	NNS	denotes	mice
T4062	5950-5954	VBN	denotes	used
T4063	5955-5957	IN	denotes	in
T4064	5958-5962	DT	denotes	this
T4065	5963-5968	NN	denotes	study
T4066	5969-5973	VBD	denotes	were
T4061	5974-5982	VBN	denotes	obtained
T4067	5983-5987	IN	denotes	from
T4068	5988-5991	DT	denotes	the
T4070	5992-5999	NNP	denotes	Jackson
T4069	6000-6010	NNP	denotes	Laboratory
T4071	6011-6014	CC	denotes	and
T4072	6015-6019	VBN	denotes	kept
T4073	6020-6022	IN	denotes	in
T4074	6023-6024	DT	denotes	a
T4076	6025-6032	NN	denotes	climate
T4078	6032-6033	HYPH	denotes	-
T4077	6033-6043	VBN	denotes	controlled
T4075	6044-6055	NN	denotes	environment
T4079	6056-6060	IN	denotes	with
T4080	6061-6063	CD	denotes	12
T4081	6064-6068	NN	denotes	hour
T4083	6069-6074	NN	denotes	light
T4085	6074-6075	HYPH	denotes	/
T4084	6075-6079	NN	denotes	dark
T4082	6080-6086	NNS	denotes	cycles
T4086	6087-6089	IN	denotes	in
T4087	6090-6093	DT	denotes	the
T4089	6094-6100	NN	denotes	animal
T4088	6101-6109	NN	denotes	facility
T4090	6110-6112	IN	denotes	at
T4091	6113-6116	DT	denotes	the
T4092	6117-6127	NNP	denotes	University
T4093	6128-6130	IN	denotes	of
T4094	6131-6138	NNP	denotes	Rostock
T4095	6138-6139	.	denotes	.
T4096	6139-6216	sentence	denotes	All animal experiments were pre-approved by the State Animal Care Committee.
T4097	6140-6143	DT	denotes	All
T4099	6144-6150	NN	denotes	animal
T4098	6151-6162	NNS	denotes	experiments
T4101	6163-6167	VBD	denotes	were
T4100	6168-6180	VBN	denotes	pre-approved
T4102	6181-6183	IN	denotes	by
T4103	6184-6187	DT	denotes	the
T4105	6188-6193	NNP	denotes	State
T4106	6194-6200	NNP	denotes	Animal
T4107	6201-6205	NNP	denotes	Care
T4104	6206-6215	NNP	denotes	Committee
T4108	6215-6216	.	denotes	.
T4109	6216-6330	sentence	denotes	CIA was induced in control and experimental animals according to established protocols described previously [10].
T4110	6217-6220	NN	denotes	CIA
T4112	6221-6224	VBD	denotes	was
T4111	6225-6232	VBN	denotes	induced
T4113	6233-6235	IN	denotes	in
T4114	6236-6243	NN	denotes	control
T4116	6244-6247	CC	denotes	and
T4117	6248-6260	JJ	denotes	experimental
T4115	6261-6268	NNS	denotes	animals
T4118	6269-6278	VBG	denotes	according
T4119	6279-6281	IN	denotes	to
T4120	6282-6293	VBN	denotes	established
T4121	6294-6303	NNS	denotes	protocols
T4122	6304-6313	VBN	denotes	described
T4123	6314-6324	RB	denotes	previously
T4124	6325-6326	-LRB-	denotes	[
T4125	6326-6328	CD	denotes	10
T4126	6328-6329	-RRB-	denotes	]
T4127	6329-6330	.	denotes	.
T4128	6330-6549	sentence	denotes	In brief, DBA/1J, FVB/N and (DBA/1J × FVB/N)F2 progeny were immunised at 8 to 12 weeks at the base of the tail with 125 μg of bovine Collagen II (Chondrex, Redmond, WA, USA) emulsified in CFA (DIFCO, Detroit, MI, USA).
T4129	6331-6333	IN	denotes	In
T4131	6334-6339	NN	denotes	brief
T4132	6339-6341	,	denotes	,
T4133	6341-6344	NN	denotes	DBA
T4135	6344-6345	HYPH	denotes	/
T4134	6345-6347	NN	denotes	1J
T4137	6347-6349	,	denotes	,
T4138	6349-6352	NN	denotes	FVB
T4140	6352-6353	HYPH	denotes	/
T4139	6353-6354	NN	denotes	N
T4141	6355-6358	CC	denotes	and
T4142	6359-6360	-LRB-	denotes	(
T4144	6360-6363	NN	denotes	DBA
T4145	6363-6364	HYPH	denotes	/
T4143	6364-6366	NN	denotes	1J
T4146	6367-6368	SYM	denotes	×
T4147	6369-6372	NN	denotes	FVB
T4149	6372-6373	HYPH	denotes	/
T4148	6373-6374	NN	denotes	N
T4150	6374-6375	-RRB-	denotes	)
T4151	6375-6377	NN	denotes	F2
T4136	6378-6385	NN	denotes	progeny
T4152	6386-6390	VBD	denotes	were
T4130	6391-6400	VBN	denotes	immunised
T4153	6401-6403	IN	denotes	at
T4154	6404-6405	CD	denotes	8
T4156	6406-6408	IN	denotes	to
T4155	6409-6411	CD	denotes	12
T4157	6412-6417	NNS	denotes	weeks
T4158	6418-6420	IN	denotes	at
T4159	6421-6424	DT	denotes	the
T4160	6425-6429	NN	denotes	base
T4161	6430-6432	IN	denotes	of
T4162	6433-6436	DT	denotes	the
T4163	6437-6441	NN	denotes	tail
T4164	6442-6446	IN	denotes	with
T4165	6447-6450	CD	denotes	125
T4166	6451-6453	NN	denotes	μg
T4167	6454-6456	IN	denotes	of
T4168	6457-6463	JJ	denotes	bovine
T4169	6464-6472	NN	denotes	Collagen
T4170	6473-6475	CD	denotes	II
T4171	6476-6477	-LRB-	denotes	(
T4172	6477-6485	NNP	denotes	Chondrex
T4173	6485-6487	,	denotes	,
T4174	6487-6494	NNP	denotes	Redmond
T4175	6494-6496	,	denotes	,
T4176	6496-6498	NNP	denotes	WA
T4177	6498-6500	,	denotes	,
T4178	6500-6503	NNP	denotes	USA
T4179	6503-6504	-RRB-	denotes	)
T4180	6505-6515	VBN	denotes	emulsified
T4181	6516-6518	IN	denotes	in
T4182	6519-6522	NN	denotes	CFA
T4183	6523-6524	-LRB-	denotes	(
T4184	6524-6529	NNP	denotes	DIFCO
T4185	6529-6531	,	denotes	,
T4186	6531-6538	NNP	denotes	Detroit
T4187	6538-6540	,	denotes	,
T4188	6540-6542	NNP	denotes	MI
T4189	6542-6544	,	denotes	,
T4190	6544-6547	NNP	denotes	USA
T4191	6547-6548	-RRB-	denotes	)
T4192	6548-6549	.	denotes	.
T4193	6549-6685	sentence	denotes	The clinical scoring of arthritis commenced 18 days after immunisation, and animals were monitored three times weekly for signs of CIA.
T4194	6550-6553	DT	denotes	The
T4196	6554-6562	JJ	denotes	clinical
T4195	6563-6570	NN	denotes	scoring
T4198	6571-6573	IN	denotes	of
T4199	6574-6583	NN	denotes	arthritis
T4197	6584-6593	VBD	denotes	commenced
T4200	6594-6596	CD	denotes	18
T4201	6597-6601	NNS	denotes	days
T4202	6602-6607	IN	denotes	after
T4203	6608-6620	NN	denotes	immunisation
T4204	6620-6622	,	denotes	,
T4205	6622-6625	CC	denotes	and
T4206	6626-6633	NNS	denotes	animals
T4208	6634-6638	VBD	denotes	were
T4207	6639-6648	VBN	denotes	monitored
T4209	6649-6654	CD	denotes	three
T4210	6655-6660	NNS	denotes	times
T4211	6661-6667	RB	denotes	weekly
T4212	6668-6671	IN	denotes	for
T4213	6672-6677	NNS	denotes	signs
T4214	6678-6680	IN	denotes	of
T4215	6681-6684	NN	denotes	CIA
T4216	6684-6685	.	denotes	.
T4217	6685-6805	sentence	denotes	Arthritis development was monitored in all four limbs using a three-score system per limb as described previously [10].
T4218	6686-6695	NN	denotes	Arthritis
T4219	6696-6707	NN	denotes	development
T4221	6708-6711	VBD	denotes	was
T4220	6712-6721	VBN	denotes	monitored
T4222	6722-6724	IN	denotes	in
T4223	6725-6728	DT	denotes	all
T4225	6729-6733	CD	denotes	four
T4224	6734-6739	NNS	denotes	limbs
T4226	6740-6745	VBG	denotes	using
T4227	6746-6747	DT	denotes	a
T4229	6748-6753	CD	denotes	three
T4231	6753-6754	HYPH	denotes	-
T4230	6754-6759	NN	denotes	score
T4228	6760-6766	NN	denotes	system
T4232	6767-6770	IN	denotes	per
T4233	6771-6775	NN	denotes	limb
T4234	6776-6778	IN	denotes	as
T4235	6779-6788	VBN	denotes	described
T4236	6789-6799	RB	denotes	previously
T4237	6800-6801	-LRB-	denotes	[
T4238	6801-6803	CD	denotes	10
T4239	6803-6804	-RRB-	denotes	]
T4240	6804-6805	.	denotes	.
T4241	6805-6890	sentence	denotes	Eight-week old FVB/N and DBA/1J mice were used for the detection of gene expression.
T4242	6806-6811	CD	denotes	Eight
T4244	6811-6812	HYPH	denotes	-
T4243	6812-6816	NN	denotes	week
T4245	6817-6820	JJ	denotes	old
T4247	6821-6824	NN	denotes	FVB
T4249	6824-6825	HYPH	denotes	/
T4248	6825-6826	NN	denotes	N
T4250	6827-6830	CC	denotes	and
T4251	6831-6834	NN	denotes	DBA
T4253	6834-6835	HYPH	denotes	/
T4252	6835-6837	NN	denotes	1J
T4246	6838-6842	NNS	denotes	mice
T4255	6843-6847	VBD	denotes	were
T4254	6848-6852	VBN	denotes	used
T4256	6853-6856	IN	denotes	for
T4257	6857-6860	DT	denotes	the
T4258	6861-6870	NN	denotes	detection
T4259	6871-6873	IN	denotes	of
T4260	6874-6878	NN	denotes	gene
T4261	6879-6889	NN	denotes	expression
T4262	6889-6890	.	denotes	.
T4263	6890-7093	sentence	denotes	They were divided into four experimental groups according to the different phases of CIA, namely naive control (NC), post-immunisation (PI), onset of arthritis (OA) and chronic arthritis (CA) (Table 1).
T4264	6891-6895	PRP	denotes	They
T4266	6896-6900	VBD	denotes	were
T4265	6901-6908	VBN	denotes	divided
T4267	6909-6913	IN	denotes	into
T4268	6914-6918	CD	denotes	four
T4270	6919-6931	JJ	denotes	experimental
T4269	6932-6938	NNS	denotes	groups
T4271	6939-6948	VBG	denotes	according
T4272	6949-6951	IN	denotes	to
T4273	6952-6955	DT	denotes	the
T4275	6956-6965	JJ	denotes	different
T4274	6966-6972	NNS	denotes	phases
T4276	6973-6975	IN	denotes	of
T4277	6976-6979	NN	denotes	CIA
T4278	6979-6981	,	denotes	,
T4279	6981-6987	RB	denotes	namely
T4281	6988-6993	JJ	denotes	naive
T4280	6994-7001	NN	denotes	control
T4282	7002-7003	-LRB-	denotes	(
T4283	7003-7005	NN	denotes	NC
T4284	7005-7006	-RRB-	denotes	)
T4285	7006-7008	,	denotes	,
T4286	7008-7025	NN	denotes	post-immunisation
T4287	7026-7027	-LRB-	denotes	(
T4288	7027-7029	NN	denotes	PI
T4289	7029-7030	-RRB-	denotes	)
T4290	7030-7032	,	denotes	,
T4291	7032-7037	NN	denotes	onset
T4292	7038-7040	IN	denotes	of
T4293	7041-7050	NN	denotes	arthritis
T4294	7051-7052	-LRB-	denotes	(
T4295	7052-7054	NN	denotes	OA
T4296	7054-7055	-RRB-	denotes	)
T4297	7056-7059	CC	denotes	and
T4298	7060-7067	JJ	denotes	chronic
T4299	7068-7077	NN	denotes	arthritis
T4300	7078-7079	-LRB-	denotes	(
T4301	7079-7081	NN	denotes	CA
T4302	7081-7082	-RRB-	denotes	)
T4303	7083-7084	-LRB-	denotes	(
T4304	7084-7089	NN	denotes	Table
T4305	7090-7091	CD	denotes	1
T4306	7091-7092	-RRB-	denotes	)
T4307	7092-7093	.	denotes	.
T4308	7093-7179	sentence	denotes	The NC group contained non-immunised mice that were sacrificed at the age of 8 weeks.
T4309	7094-7097	DT	denotes	The
T4311	7098-7100	NN	denotes	NC
T4310	7101-7106	NN	denotes	group
T4312	7107-7116	VBD	denotes	contained
T4313	7117-7130	JJ	denotes	non-immunised
T4314	7131-7135	NNS	denotes	mice
T4315	7136-7140	WDT	denotes	that
T4317	7141-7145	VBD	denotes	were
T4316	7146-7156	VBN	denotes	sacrificed
T4318	7157-7159	IN	denotes	at
T4319	7160-7163	DT	denotes	the
T4320	7164-7167	NN	denotes	age
T4321	7168-7170	IN	denotes	of
T4322	7171-7172	CD	denotes	8
T4323	7173-7178	NNS	denotes	weeks
T4324	7178-7179	.	denotes	.
T4325	7179-7250	sentence	denotes	The mice in the PI group were sacrificed on day 10 after immunisation.
T4326	7180-7183	DT	denotes	The
T4327	7184-7188	NNS	denotes	mice
T4329	7189-7191	IN	denotes	in
T4330	7192-7195	DT	denotes	the
T4332	7196-7198	NN	denotes	PI
T4331	7199-7204	NN	denotes	group
T4333	7205-7209	VBD	denotes	were
T4328	7210-7220	VBN	denotes	sacrificed
T4334	7221-7223	IN	denotes	on
T4335	7224-7227	NN	denotes	day
T4336	7228-7230	CD	denotes	10
T4337	7231-7236	IN	denotes	after
T4338	7237-7249	NN	denotes	immunisation
T4339	7249-7250	.	denotes	.
T4340	7250-7321	sentence	denotes	The mice in the OA group were sacrificed on day 35 after immunisation.
T4341	7251-7254	DT	denotes	The
T4342	7255-7259	NNS	denotes	mice
T4344	7260-7262	IN	denotes	in
T4345	7263-7266	DT	denotes	the
T4347	7267-7269	NN	denotes	OA
T4346	7270-7275	NN	denotes	group
T4348	7276-7280	VBD	denotes	were
T4343	7281-7291	VBN	denotes	sacrificed
T4349	7292-7294	IN	denotes	on
T4350	7295-7298	NN	denotes	day
T4351	7299-7301	CD	denotes	35
T4352	7302-7307	IN	denotes	after
T4353	7308-7320	NN	denotes	immunisation
T4354	7320-7321	.	denotes	.
T4355	7321-7485	sentence	denotes	Three FVB/N non-arthritic mice and three DBA/1 mice that showed signs of arthritis on day 33 or 34 after immunisation were sacrificed on day 35 after immunisation.
T4356	7322-7327	CD	denotes	Three
T4358	7328-7331	NN	denotes	FVB
T4360	7331-7332	HYPH	denotes	/
T4359	7332-7333	NN	denotes	N
T4361	7334-7347	JJ	denotes	non-arthritic
T4357	7348-7352	NNS	denotes	mice
T4363	7353-7356	CC	denotes	and
T4364	7357-7362	CD	denotes	three
T4366	7363-7366	NN	denotes	DBA
T4367	7366-7367	HYPH	denotes	/
T4368	7367-7368	CD	denotes	1
T4365	7369-7373	NNS	denotes	mice
T4369	7374-7378	WDT	denotes	that
T4370	7379-7385	VBD	denotes	showed
T4371	7386-7391	NNS	denotes	signs
T4372	7392-7394	IN	denotes	of
T4373	7395-7404	NN	denotes	arthritis
T4374	7405-7407	IN	denotes	on
T4375	7408-7411	NN	denotes	day
T4376	7412-7414	CD	denotes	33
T4377	7415-7417	CC	denotes	or
T4378	7418-7420	CD	denotes	34
T4379	7421-7426	IN	denotes	after
T4380	7427-7439	NN	denotes	immunisation
T4381	7440-7444	VBD	denotes	were
T4362	7445-7455	VBN	denotes	sacrificed
T4382	7456-7458	IN	denotes	on
T4383	7459-7462	NN	denotes	day
T4384	7463-7465	CD	denotes	35
T4385	7466-7471	IN	denotes	after
T4386	7472-7484	NN	denotes	immunisation
T4387	7484-7485	.	denotes	.
T4388	7485-7556	sentence	denotes	The mice in the CA group were sacrificed on day 95 after immunisation.
T4389	7486-7489	DT	denotes	The
T4390	7490-7494	NNS	denotes	mice
T4392	7495-7497	IN	denotes	in
T4393	7498-7501	DT	denotes	the
T4395	7502-7504	NN	denotes	CA
T4394	7505-7510	NN	denotes	group
T4396	7511-7515	VBD	denotes	were
T4391	7516-7526	VBN	denotes	sacrificed
T4397	7527-7529	IN	denotes	on
T4398	7530-7533	NN	denotes	day
T4399	7534-7536	CD	denotes	95
T4400	7537-7542	IN	denotes	after
T4401	7543-7555	NN	denotes	immunisation
T4402	7555-7556	.	denotes	.
T4403	7556-7707	sentence	denotes	Three non-arthritic FVB/N mice and three DBA/1 mice that had developed arthritis for at least two months were sacrificed on day 95 after immunisation.
T4404	7557-7562	CD	denotes	Three
T4406	7563-7576	JJ	denotes	non-arthritic
T4407	7577-7580	NN	denotes	FVB
T4409	7580-7581	HYPH	denotes	/
T4408	7581-7582	NN	denotes	N
T4405	7583-7587	NNS	denotes	mice
T4411	7588-7591	CC	denotes	and
T4412	7592-7597	CD	denotes	three
T4414	7598-7601	NN	denotes	DBA
T4415	7601-7602	HYPH	denotes	/
T4416	7602-7603	CD	denotes	1
T4413	7604-7608	NNS	denotes	mice
T4417	7609-7613	WDT	denotes	that
T4419	7614-7617	VBD	denotes	had
T4418	7618-7627	VBN	denotes	developed
T4420	7628-7637	NN	denotes	arthritis
T4421	7638-7641	IN	denotes	for
T4422	7642-7644	RB	denotes	at
T4424	7645-7650	RBS	denotes	least
T4423	7651-7654	CD	denotes	two
T4425	7655-7661	NNS	denotes	months
T4426	7662-7666	VBD	denotes	were
T4410	7667-7677	VBN	denotes	sacrificed
T4427	7678-7680	IN	denotes	on
T4428	7681-7684	NN	denotes	day
T4429	7685-7687	CD	denotes	95
T4430	7688-7693	IN	denotes	after
T4431	7694-7706	NN	denotes	immunisation
T4432	7706-7707	.	denotes	.
T4628	7709-7716	NN	denotes	Linkage
T4629	7717-7725	NN	denotes	analysis
T4630	7725-7817	sentence	denotes	Detailed information on genotyping of the genome screen has been described previously [10].
T4631	7726-7734	JJ	denotes	Detailed
T4632	7735-7746	NN	denotes	information
T4634	7747-7749	IN	denotes	on
T4635	7750-7760	NN	denotes	genotyping
T4636	7761-7763	IN	denotes	of
T4637	7764-7767	DT	denotes	the
T4639	7768-7774	NN	denotes	genome
T4638	7775-7781	NN	denotes	screen
T4640	7782-7785	VBZ	denotes	has
T4641	7786-7790	VBN	denotes	been
T4633	7791-7800	VBN	denotes	described
T4642	7801-7811	RB	denotes	previously
T4643	7812-7813	-LRB-	denotes	[
T4644	7813-7815	CD	denotes	10
T4645	7815-7816	-RRB-	denotes	]
T4646	7816-7817	.	denotes	.
T4647	7817-7986	sentence	denotes	In short, we genotyped 290 F2 mice using 126 informative microsatellite markers covering the genome with an average inter-marker distance of 11.5 cM for 290 F2 progeny.
T4648	7818-7820	IN	denotes	In
T4650	7821-7826	JJ	denotes	short
T4651	7826-7828	,	denotes	,
T4652	7828-7830	PRP	denotes	we
T4649	7831-7840	VBD	denotes	genotyped
T4653	7841-7844	CD	denotes	290
T4655	7845-7847	NN	denotes	F2
T4654	7848-7852	NNS	denotes	mice
T4656	7853-7858	VBG	denotes	using
T4657	7859-7862	CD	denotes	126
T4659	7863-7874	JJ	denotes	informative
T4660	7875-7889	NN	denotes	microsatellite
T4658	7890-7897	NNS	denotes	markers
T4661	7898-7906	VBG	denotes	covering
T4662	7907-7910	DT	denotes	the
T4663	7911-7917	NN	denotes	genome
T4664	7918-7922	IN	denotes	with
T4665	7923-7925	DT	denotes	an
T4667	7926-7933	JJ	denotes	average
T4668	7934-7946	JJ	denotes	inter-marker
T4666	7947-7955	NN	denotes	distance
T4669	7956-7958	IN	denotes	of
T4670	7959-7963	CD	denotes	11.5
T4671	7964-7966	NN	denotes	cM
T4672	7967-7970	IN	denotes	for
T4673	7971-7974	CD	denotes	290
T4675	7975-7977	NN	denotes	F2
T4674	7978-7985	NN	denotes	progeny
T4676	7985-7986	.	denotes	.
T4677	7986-8058	sentence	denotes	All linkage analyses were performed with QTX Map manager software [23].
T4678	7987-7990	DT	denotes	All
T4680	7991-7998	NN	denotes	linkage
T4679	7999-8007	NNS	denotes	analyses
T4682	8008-8012	VBD	denotes	were
T4681	8013-8022	VBN	denotes	performed
T4683	8023-8027	IN	denotes	with
T4684	8028-8031	NN	denotes	QTX
T4686	8032-8035	NN	denotes	Map
T4687	8036-8043	NN	denotes	manager
T4685	8044-8052	NN	denotes	software
T4688	8053-8054	-LRB-	denotes	[
T4689	8054-8056	CD	denotes	23
T4690	8056-8057	-RRB-	denotes	]
T4691	8057-8058	.	denotes	.
T4692	8058-8138	sentence	denotes	The main clinical phenotype of CIA, arthritis severity, was taken as phenotype.
T4693	8059-8062	DT	denotes	The
T4695	8063-8067	JJ	denotes	main
T4696	8068-8076	JJ	denotes	clinical
T4694	8077-8086	NN	denotes	phenotype
T4698	8087-8089	IN	denotes	of
T4699	8090-8093	NN	denotes	CIA
T4700	8093-8095	,	denotes	,
T4701	8095-8104	NN	denotes	arthritis
T4702	8105-8113	NN	denotes	severity
T4703	8113-8115	,	denotes	,
T4704	8115-8118	VBD	denotes	was
T4697	8119-8124	VBN	denotes	taken
T4705	8125-8127	IN	denotes	as
T4706	8128-8137	NN	denotes	phenotype
T4707	8137-8138	.	denotes	.
T4708	8138-8240	sentence	denotes	To detect the small-effect QTL, the threshold value of linkage was set as P = 0.05 (Chi-square test).
T4709	8139-8141	TO	denotes	To
T4710	8142-8148	VB	denotes	detect
T4712	8149-8152	DT	denotes	the
T4714	8153-8158	JJ	denotes	small
T4716	8158-8159	HYPH	denotes	-
T4715	8159-8165	NN	denotes	effect
T4713	8166-8169	NN	denotes	QTL
T4717	8169-8171	,	denotes	,
T4718	8171-8174	DT	denotes	the
T4720	8175-8184	NN	denotes	threshold
T4719	8185-8190	NN	denotes	value
T4721	8191-8193	IN	denotes	of
T4722	8194-8201	NN	denotes	linkage
T4723	8202-8205	VBD	denotes	was
T4711	8206-8209	VBN	denotes	set
T4724	8210-8212	IN	denotes	as
T4725	8213-8214	NN	denotes	P
T4727	8215-8216	SYM	denotes	=
T4726	8217-8221	CD	denotes	0.05
T4728	8222-8223	-LRB-	denotes	(
T4730	8223-8226	NN	denotes	Chi
T4732	8226-8227	HYPH	denotes	-
T4731	8227-8233	NN	denotes	square
T4729	8234-8238	NN	denotes	test
T4733	8238-8239	-RRB-	denotes	)
T4734	8239-8240	.	denotes	.
T5000	8242-8248	NN	denotes	Sample
T5001	8249-8260	NN	denotes	preparation
T5002	8261-8264	CC	denotes	and
T5003	8265-8275	NN	denotes	microarray
T5004	8276-8289	NN	denotes	hybridisation
T5005	8289-8375	sentence	denotes	Lymph nodes (LNs) draining the immunisation site were used for total RNA preparation.
T5006	8290-8295	NN	denotes	Lymph
T5007	8296-8301	NNS	denotes	nodes
T5009	8302-8303	-LRB-	denotes	(
T5010	8303-8306	NNS	denotes	LNs
T5011	8306-8307	-RRB-	denotes	)
T5012	8308-8316	VBG	denotes	draining
T5013	8317-8320	DT	denotes	the
T5015	8321-8333	NN	denotes	immunisation
T5014	8334-8338	NN	denotes	site
T5016	8339-8343	VBD	denotes	were
T5008	8344-8348	VBN	denotes	used
T5017	8349-8352	IN	denotes	for
T5018	8353-8358	JJ	denotes	total
T5020	8359-8362	NN	denotes	RNA
T5019	8363-8374	NN	denotes	preparation
T5021	8374-8375	.	denotes	.
T5022	8375-8521	sentence	denotes	The total RNA was extracted from the tissue homogenates using a commercial kit in accordance with the provided protocol (QIGEN, Hilden, Germany).
T5023	8376-8379	DT	denotes	The
T5025	8380-8385	JJ	denotes	total
T5024	8386-8389	NN	denotes	RNA
T5027	8390-8393	VBD	denotes	was
T5026	8394-8403	VBN	denotes	extracted
T5028	8404-8408	IN	denotes	from
T5029	8409-8412	DT	denotes	the
T5031	8413-8419	NN	denotes	tissue
T5030	8420-8431	NNS	denotes	homogenates
T5032	8432-8437	VBG	denotes	using
T5033	8438-8439	DT	denotes	a
T5035	8440-8450	JJ	denotes	commercial
T5034	8451-8454	NN	denotes	kit
T5036	8455-8457	IN	denotes	in
T5037	8458-8468	NN	denotes	accordance
T5038	8469-8473	IN	denotes	with
T5039	8474-8477	DT	denotes	the
T5041	8478-8486	VBN	denotes	provided
T5040	8487-8495	NN	denotes	protocol
T5042	8496-8497	-LRB-	denotes	(
T5043	8497-8502	NNP	denotes	QIGEN
T5044	8502-8504	,	denotes	,
T5045	8504-8510	NNP	denotes	Hilden
T5046	8510-8512	,	denotes	,
T5047	8512-8519	NNP	denotes	Germany
T5048	8519-8520	-RRB-	denotes	)
T5049	8520-8521	.	denotes	.
T5050	8521-8656	sentence	denotes	Analysis of gene expression was conducted using a U430A array (Affymetrix, Santa Clara, CA, USA) interrogating more than 22,000 genes.
T5051	8522-8530	NN	denotes	Analysis
T5053	8531-8533	IN	denotes	of
T5054	8534-8538	NN	denotes	gene
T5055	8539-8549	NN	denotes	expression
T5056	8550-8553	VBD	denotes	was
T5052	8554-8563	VBN	denotes	conducted
T5057	8564-8569	VBG	denotes	using
T5058	8570-8571	DT	denotes	a
T5060	8572-8577	NN	denotes	U430A
T5059	8578-8583	NN	denotes	array
T5061	8584-8585	-LRB-	denotes	(
T5062	8585-8595	NNP	denotes	Affymetrix
T5063	8595-8597	,	denotes	,
T5064	8597-8602	NNP	denotes	Santa
T5065	8603-8608	NNP	denotes	Clara
T5066	8608-8610	,	denotes	,
T5067	8610-8612	NNP	denotes	CA
T5068	8612-8614	,	denotes	,
T5069	8614-8617	NNP	denotes	USA
T5070	8617-8618	-RRB-	denotes	)
T5071	8619-8632	VBG	denotes	interrogating
T5072	8633-8637	JJR	denotes	more
T5074	8638-8642	IN	denotes	than
T5073	8643-8649	CD	denotes	22,000
T5075	8650-8655	NNS	denotes	genes
T5076	8655-8656	.	denotes	.
T5077	8656-8733	sentence	denotes	RNA probes were labelled in accordance with the manufacturer's instructions.
T5078	8657-8660	NN	denotes	RNA
T5079	8661-8667	NNS	denotes	probes
T5081	8668-8672	VBD	denotes	were
T5080	8673-8681	VBN	denotes	labelled
T5082	8682-8684	IN	denotes	in
T5083	8685-8695	NN	denotes	accordance
T5084	8696-8700	IN	denotes	with
T5085	8701-8704	DT	denotes	the
T5086	8705-8717	NN	denotes	manufacturer
T5088	8717-8719	POS	denotes	's
T5087	8720-8732	NNS	denotes	instructions
T5089	8732-8733	.	denotes	.
T5090	8733-8802	sentence	denotes	Samples from individual mice were hybridised onto individual arrays.
T5091	8734-8741	NNS	denotes	Samples
T5093	8742-8746	IN	denotes	from
T5094	8747-8757	JJ	denotes	individual
T5095	8758-8762	NNS	denotes	mice
T5096	8763-8767	VBD	denotes	were
T5092	8768-8778	VBN	denotes	hybridised
T5097	8779-8783	IN	denotes	onto
T5098	8784-8794	JJ	denotes	individual
T5099	8795-8801	NNS	denotes	arrays
T5100	8801-8802	.	denotes	.
T5101	8802-8882	sentence	denotes	Hybridisation and washing of gene chips were done as previously described [16].
T5102	8803-8816	NN	denotes	Hybridisation
T5104	8817-8820	CC	denotes	and
T5105	8821-8828	NN	denotes	washing
T5106	8829-8831	IN	denotes	of
T5107	8832-8836	NN	denotes	gene
T5108	8837-8842	NNS	denotes	chips
T5109	8843-8847	VBD	denotes	were
T5103	8848-8852	VBN	denotes	done
T5110	8853-8855	IN	denotes	as
T5112	8856-8866	RB	denotes	previously
T5111	8867-8876	VBN	denotes	described
T5113	8877-8878	-LRB-	denotes	[
T5114	8878-8880	CD	denotes	16
T5115	8880-8881	-RRB-	denotes	]
T5116	8881-8882	.	denotes	.
T5117	8882-8963	sentence	denotes	Fluorescent signals were collected by laser scan (Hewlett-Packard Gene Scanner).
T5118	8883-8894	JJ	denotes	Fluorescent
T5119	8895-8902	NNS	denotes	signals
T5121	8903-8907	VBD	denotes	were
T5120	8908-8917	VBN	denotes	collected
T5122	8918-8920	IN	denotes	by
T5123	8921-8926	NN	denotes	laser
T5124	8927-8931	NN	denotes	scan
T5125	8932-8933	-LRB-	denotes	(
T5127	8933-8940	NNP	denotes	Hewlett
T5129	8940-8941	HYPH	denotes	-
T5128	8941-8948	NNP	denotes	Packard
T5130	8949-8953	NNP	denotes	Gene
T5126	8954-8961	NNP	denotes	Scanner
T5131	8961-8962	-RRB-	denotes	)
T5132	8962-8963	.	denotes	.
T5603	8965-8975	NN	denotes	Microarray
T5604	8976-8984	NN	denotes	analysis
T5605	8984-9144	sentence	denotes	Normalisation of the expression level was done using Affymetrix software MAS 5, which is based on global scaling of total gene expression level per microarray.
T5606	8985-8998	NN	denotes	Normalisation
T5608	8999-9001	IN	denotes	of
T5609	9002-9005	DT	denotes	the
T5611	9006-9016	NN	denotes	expression
T5610	9017-9022	NN	denotes	level
T5612	9023-9026	VBD	denotes	was
T5607	9027-9031	VBN	denotes	done
T5613	9032-9037	VBG	denotes	using
T5614	9038-9048	NNP	denotes	Affymetrix
T5616	9049-9057	NN	denotes	software
T5615	9058-9061	NN	denotes	MAS
T5617	9062-9063	CD	denotes	5
T5618	9063-9065	,	denotes	,
T5619	9065-9070	WDT	denotes	which
T5621	9071-9073	VBZ	denotes	is
T5620	9074-9079	VBN	denotes	based
T5622	9080-9082	IN	denotes	on
T5623	9083-9089	JJ	denotes	global
T5624	9090-9097	NN	denotes	scaling
T5625	9098-9100	IN	denotes	of
T5626	9101-9106	JJ	denotes	total
T5628	9107-9111	NN	denotes	gene
T5629	9112-9122	NN	denotes	expression
T5627	9123-9128	NN	denotes	level
T5630	9129-9132	IN	denotes	per
T5631	9133-9143	NN	denotes	microarray
T5632	9143-9144	.	denotes	.
T5633	9144-9222	sentence	denotes	The normalised expression values were imported to and analysed by dCHIP [24].
T5634	9145-9148	DT	denotes	The
T5636	9149-9159	JJ	denotes	normalised
T5637	9160-9170	NN	denotes	expression
T5635	9171-9177	NNS	denotes	values
T5639	9178-9182	VBD	denotes	were
T5638	9183-9191	VBN	denotes	imported
T5640	9192-9194	IN	denotes	to
T5641	9195-9198	CC	denotes	and
T5642	9199-9207	VBN	denotes	analysed
T5643	9208-9210	IN	denotes	by
T5644	9211-9216	NN	denotes	dCHIP
T5645	9217-9218	-LRB-	denotes	[
T5646	9218-9220	CD	denotes	24
T5647	9220-9221	-RRB-	denotes	]
T5648	9221-9222	.	denotes	.
T5649	9222-9545	sentence	denotes	Differentially expressed genes were identified by defining the appropriate filtering criteria in the dCHIP software as: lower 90% confidence boundary of fold change between the group means exceeded twofold; the absolute difference between the two groups exceeded 100; the P value threshold of the unpaired t-test was 0.05.
T5650	9223-9237	RB	denotes	Differentially
T5651	9238-9247	VBN	denotes	expressed
T5652	9248-9253	NNS	denotes	genes
T5654	9254-9258	VBD	denotes	were
T5653	9259-9269	VBN	denotes	identified
T5655	9270-9272	IN	denotes	by
T5656	9273-9281	VBG	denotes	defining
T5657	9282-9285	DT	denotes	the
T5659	9286-9297	JJ	denotes	appropriate
T5660	9298-9307	NN	denotes	filtering
T5658	9308-9316	NNS	denotes	criteria
T5661	9317-9319	IN	denotes	in
T5662	9320-9323	DT	denotes	the
T5664	9324-9329	NN	denotes	dCHIP
T5663	9330-9338	NN	denotes	software
T5665	9339-9341	IN	denotes	as
T5666	9341-9343	:	denotes	:
T5667	9343-9348	JJ	denotes	lower
T5669	9349-9351	CD	denotes	90
T5668	9351-9352	NN	denotes	%
T5671	9353-9363	NN	denotes	confidence
T5670	9364-9372	NN	denotes	boundary
T5673	9373-9375	IN	denotes	of
T5674	9376-9380	NN	denotes	fold
T5675	9381-9387	NN	denotes	change
T5676	9388-9395	IN	denotes	between
T5677	9396-9399	DT	denotes	the
T5679	9400-9405	NN	denotes	group
T5678	9406-9411	NNS	denotes	means
T5672	9412-9420	VBN	denotes	exceeded
T5681	9421-9428	RB	denotes	twofold
T5682	9428-9429	:	denotes	;
T5683	9430-9433	DT	denotes	the
T5685	9434-9442	JJ	denotes	absolute
T5684	9443-9453	NN	denotes	difference
T5687	9454-9461	IN	denotes	between
T5688	9462-9465	DT	denotes	the
T5690	9466-9469	CD	denotes	two
T5689	9470-9476	NNS	denotes	groups
T5686	9477-9485	VBD	denotes	exceeded
T5691	9486-9489	CD	denotes	100
T5692	9489-9490	:	denotes	;
T5693	9491-9494	DT	denotes	the
T5695	9495-9496	NN	denotes	P
T5696	9497-9502	NN	denotes	value
T5694	9503-9512	NN	denotes	threshold
T5697	9513-9515	IN	denotes	of
T5698	9516-9519	DT	denotes	the
T5700	9520-9528	JJ	denotes	unpaired
T5701	9529-9530	NN	denotes	t
T5702	9530-9531	HYPH	denotes	-
T5699	9531-9535	NN	denotes	test
T5680	9536-9539	VBD	denotes	was
T5703	9540-9544	CD	denotes	0.05
T5704	9544-9545	.	denotes	.
T5705	9545-9691	sentence	denotes	The false discovery rate was established with a permutation test for each pairwise comparison to estimate the proportion of false-positive genes.
T5706	9546-9549	DT	denotes	The
T5708	9550-9555	JJ	denotes	false
T5709	9556-9565	NN	denotes	discovery
T5707	9566-9570	NN	denotes	rate
T5711	9571-9574	VBD	denotes	was
T5710	9575-9586	VBN	denotes	established
T5712	9587-9591	IN	denotes	with
T5713	9592-9593	DT	denotes	a
T5715	9594-9605	NN	denotes	permutation
T5714	9606-9610	NN	denotes	test
T5716	9611-9614	IN	denotes	for
T5717	9615-9619	DT	denotes	each
T5719	9620-9628	JJ	denotes	pairwise
T5718	9629-9639	NN	denotes	comparison
T5720	9640-9642	TO	denotes	to
T5721	9643-9651	VB	denotes	estimate
T5722	9652-9655	DT	denotes	the
T5723	9656-9666	NN	denotes	proportion
T5724	9667-9669	IN	denotes	of
T5725	9670-9675	JJ	denotes	false
T5727	9675-9676	HYPH	denotes	-
T5726	9676-9684	JJ	denotes	positive
T5728	9685-9690	NNS	denotes	genes
T5729	9690-9691	.	denotes	.
T5730	9691-9802	sentence	denotes	Hierarchical gene clustering was performed with dCHIP to characterise the gene expression patterns during CIA.
T5731	9692-9704	JJ	denotes	Hierarchical
T5733	9705-9709	NN	denotes	gene
T5732	9710-9720	NN	denotes	clustering
T5735	9721-9724	VBD	denotes	was
T5734	9725-9734	VBN	denotes	performed
T5736	9735-9739	IN	denotes	with
T5737	9740-9745	NN	denotes	dCHIP
T5738	9746-9748	TO	denotes	to
T5739	9749-9761	VB	denotes	characterise
T5740	9762-9765	DT	denotes	the
T5742	9766-9770	NN	denotes	gene
T5743	9771-9781	NN	denotes	expression
T5741	9782-9790	NNS	denotes	patterns
T5744	9791-9797	IN	denotes	during
T5745	9798-9801	NN	denotes	CIA
T5746	9801-9802	.	denotes	.
T5747	9802-10044	sentence	denotes	The default clustering algorithm of genes was as follows: the distance between two genes is defined as 1 – r, where r is the Pearson correlation coefficient between the standardised expression values of the two genes across the samples used.
T5748	9803-9806	DT	denotes	The
T5750	9807-9814	NN	denotes	default
T5751	9815-9825	NN	denotes	clustering
T5749	9826-9835	NN	denotes	algorithm
T5753	9836-9838	IN	denotes	of
T5754	9839-9844	NNS	denotes	genes
T5752	9845-9848	VBD	denotes	was
T5756	9849-9851	IN	denotes	as
T5757	9852-9859	VBZ	denotes	follows
T5758	9859-9861	:	denotes	:
T5759	9861-9864	DT	denotes	the
T5760	9865-9873	NN	denotes	distance
T5761	9874-9881	IN	denotes	between
T5762	9882-9885	CD	denotes	two
T5763	9886-9891	NNS	denotes	genes
T5764	9892-9894	VBZ	denotes	is
T5755	9895-9902	VBN	denotes	defined
T5765	9903-9905	IN	denotes	as
T5766	9906-9907	CD	denotes	1
T5768	9908-9909	HYPH	denotes	–
T5767	9910-9911	NN	denotes	r
T5769	9911-9913	,	denotes	,
T5770	9913-9918	WRB	denotes	where
T5772	9919-9920	NN	denotes	r
T5771	9921-9923	VBZ	denotes	is
T5773	9924-9927	DT	denotes	the
T5775	9928-9935	NNP	denotes	Pearson
T5776	9936-9947	NN	denotes	correlation
T5774	9948-9959	NN	denotes	coefficient
T5777	9960-9967	IN	denotes	between
T5778	9968-9971	DT	denotes	the
T5780	9972-9984	VBN	denotes	standardised
T5781	9985-9995	NN	denotes	expression
T5779	9996-10002	NNS	denotes	values
T5782	10003-10005	IN	denotes	of
T5783	10006-10009	DT	denotes	the
T5785	10010-10013	CD	denotes	two
T5784	10014-10019	NNS	denotes	genes
T5786	10020-10026	IN	denotes	across
T5787	10027-10030	DT	denotes	the
T5788	10031-10038	NNS	denotes	samples
T5789	10039-10043	VBN	denotes	used
T5790	10043-10044	.	denotes	.
T5791	10044-10216	sentence	denotes	To characterise the functional relationship between differentially expressed genes, Gene Ontology (GO) term classification incorporated in DNA-Chip Analyzer was performed.
T5792	10045-10047	TO	denotes	To
T5793	10048-10060	VB	denotes	characterise
T5795	10061-10064	DT	denotes	the
T5797	10065-10075	JJ	denotes	functional
T5796	10076-10088	NN	denotes	relationship
T5798	10089-10096	IN	denotes	between
T5799	10097-10111	RB	denotes	differentially
T5801	10112-10121	VBN	denotes	expressed
T5800	10122-10127	NNS	denotes	genes
T5802	10127-10129	,	denotes	,
T5803	10129-10133	NN	denotes	Gene
T5804	10134-10142	NN	denotes	Ontology
T5806	10143-10144	-LRB-	denotes	(
T5807	10144-10146	NN	denotes	GO
T5808	10146-10147	-RRB-	denotes	)
T5809	10148-10152	NN	denotes	term
T5805	10153-10167	NN	denotes	classification
T5810	10168-10180	VBN	denotes	incorporated
T5811	10181-10183	IN	denotes	in
T5812	10184-10187	NNP	denotes	DNA
T5814	10187-10188	HYPH	denotes	-
T5813	10188-10192	NNP	denotes	Chip
T5815	10193-10201	NNP	denotes	Analyzer
T5816	10202-10205	VBD	denotes	was
T5794	10206-10215	VBN	denotes	performed
T5817	10215-10216	.	denotes	.
T5818	10216-10334	sentence	denotes	The significant level for a function cluster was set at P < 0.005, and the minimum size of a cluster was three genes.
T5819	10217-10220	DT	denotes	The
T5821	10221-10232	JJ	denotes	significant
T5820	10233-10238	NN	denotes	level
T5823	10239-10242	IN	denotes	for
T5824	10243-10244	DT	denotes	a
T5826	10245-10253	NN	denotes	function
T5825	10254-10261	NN	denotes	cluster
T5827	10262-10265	VBD	denotes	was
T5822	10266-10269	VBN	denotes	set
T5828	10270-10272	IN	denotes	at
T5829	10273-10274	NN	denotes	P
T5830	10275-10276	SYM	denotes	<
T5831	10277-10282	CD	denotes	0.005
T5832	10282-10284	,	denotes	,
T5833	10284-10287	CC	denotes	and
T5834	10288-10291	DT	denotes	the
T5836	10292-10299	JJ	denotes	minimum
T5835	10300-10304	NN	denotes	size
T5838	10305-10307	IN	denotes	of
T5839	10308-10309	DT	denotes	a
T5840	10310-10317	NN	denotes	cluster
T5837	10318-10321	VBD	denotes	was
T5841	10322-10327	CD	denotes	three
T5842	10328-10333	NNS	denotes	genes
T5843	10333-10334	.	denotes	.
T7078	10345-10350	JJ	denotes	Small
T7080	10350-10351	HYPH	denotes	-
T7079	10351-10357	NN	denotes	effect
T7081	10358-10361	NNS	denotes	QTL
T7082	10362-10364	IN	denotes	of
T7083	10365-10368	NN	denotes	CIA
T7084	10369-10371	IN	denotes	in
T7085	10372-10373	-LRB-	denotes	(
T7086	10373-10376	NN	denotes	DBA
T7088	10376-10377	HYPH	denotes	/
T7089	10377-10378	CD	denotes	1
T7090	10379-10380	SYM	denotes	×
T7091	10381-10384	NN	denotes	FVB
T7093	10384-10385	HYPH	denotes	/
T7092	10385-10386	NN	denotes	N
T7094	10386-10387	-RRB-	denotes	)
T7095	10388-10390	NN	denotes	F2
T7087	10391-10398	NN	denotes	progeny
T7096	10398-10528	sentence	denotes	In a previous study, we carried out a genome screen to identify QTL controlling CIA susceptibility in (DBA/1 × FVB/N) F2 progeny.
T7097	10399-10401	IN	denotes	In
T7099	10402-10403	DT	denotes	a
T7101	10404-10412	JJ	denotes	previous
T7100	10413-10418	NN	denotes	study
T7102	10418-10420	,	denotes	,
T7103	10420-10422	PRP	denotes	we
T7098	10423-10430	VBD	denotes	carried
T7104	10431-10434	RP	denotes	out
T7105	10435-10436	DT	denotes	a
T7107	10437-10443	NN	denotes	genome
T7106	10444-10450	NN	denotes	screen
T7108	10451-10453	TO	denotes	to
T7109	10454-10462	VB	denotes	identify
T7110	10463-10466	NN	denotes	QTL
T7111	10467-10478	VBG	denotes	controlling
T7112	10479-10482	NN	denotes	CIA
T7113	10483-10497	NN	denotes	susceptibility
T7114	10498-10500	IN	denotes	in
T7115	10501-10502	-LRB-	denotes	(
T7116	10502-10505	NN	denotes	DBA
T7118	10505-10506	HYPH	denotes	/
T7119	10506-10507	CD	denotes	1
T7120	10508-10509	SYM	denotes	×
T7122	10510-10513	NN	denotes	FVB
T7123	10513-10514	HYPH	denotes	/
T7121	10514-10515	NN	denotes	N
T7124	10515-10516	-RRB-	denotes	)
T7125	10517-10519	NN	denotes	F2
T7117	10520-10527	NN	denotes	progeny
T7126	10527-10528	.	denotes	.
T7127	10528-10677	sentence	denotes	For the phenotype of arthritis severity, only one QTL, Cia2, was identified, with a highly significant logarithm of the odds (LOD) score of 12 [10].
T7128	10529-10532	IN	denotes	For
T7130	10533-10536	DT	denotes	the
T7131	10537-10546	NN	denotes	phenotype
T7132	10547-10549	IN	denotes	of
T7133	10550-10559	NN	denotes	arthritis
T7134	10560-10568	NN	denotes	severity
T7135	10568-10570	,	denotes	,
T7136	10570-10574	RB	denotes	only
T7138	10575-10578	CD	denotes	one
T7137	10579-10582	NN	denotes	QTL
T7139	10582-10584	,	denotes	,
T7140	10584-10588	NN	denotes	Cia2
T7141	10588-10590	,	denotes	,
T7142	10590-10593	VBD	denotes	was
T7129	10594-10604	VBN	denotes	identified
T7143	10604-10606	,	denotes	,
T7144	10606-10610	IN	denotes	with
T7145	10611-10612	DT	denotes	a
T7147	10613-10619	RB	denotes	highly
T7148	10620-10631	JJ	denotes	significant
T7149	10632-10641	NN	denotes	logarithm
T7150	10642-10644	IN	denotes	of
T7151	10645-10648	DT	denotes	the
T7152	10649-10653	NNS	denotes	odds
T7153	10654-10655	-LRB-	denotes	(
T7154	10655-10658	NN	denotes	LOD
T7155	10658-10659	-RRB-	denotes	)
T7146	10660-10665	NN	denotes	score
T7156	10666-10668	IN	denotes	of
T7157	10669-10671	CD	denotes	12
T7158	10672-10673	-LRB-	denotes	[
T7159	10673-10675	CD	denotes	10
T7160	10675-10676	-RRB-	denotes	]
T7161	10676-10677	.	denotes	.
T7162	10677-10898	sentence	denotes	However, Cia2 contributed to only 16% of the phenotype variations, indicating that there should be some small-effect QTL whose contributions to CIA were not big enough to reach the significant threshold value of linkage.
T7163	10678-10685	RB	denotes	However
T7165	10685-10687	,	denotes	,
T7166	10687-10691	NN	denotes	Cia2
T7164	10692-10703	VBD	denotes	contributed
T7167	10704-10706	IN	denotes	to
T7168	10707-10711	RB	denotes	only
T7170	10712-10714	CD	denotes	16
T7169	10714-10715	NN	denotes	%
T7171	10716-10718	IN	denotes	of
T7172	10719-10722	DT	denotes	the
T7174	10723-10732	NN	denotes	phenotype
T7173	10733-10743	NNS	denotes	variations
T7175	10743-10745	,	denotes	,
T7176	10745-10755	VBG	denotes	indicating
T7177	10756-10760	IN	denotes	that
T7179	10761-10766	EX	denotes	there
T7180	10767-10773	MD	denotes	should
T7178	10774-10776	VB	denotes	be
T7181	10777-10781	DT	denotes	some
T7183	10782-10787	JJ	denotes	small
T7185	10787-10788	HYPH	denotes	-
T7184	10788-10794	NN	denotes	effect
T7182	10795-10798	NNS	denotes	QTL
T7186	10799-10804	WP$	denotes	whose
T7187	10805-10818	NNS	denotes	contributions
T7189	10819-10821	IN	denotes	to
T7190	10822-10825	NN	denotes	CIA
T7188	10826-10830	VBD	denotes	were
T7191	10831-10834	RB	denotes	not
T7192	10835-10838	JJ	denotes	big
T7193	10839-10845	RB	denotes	enough
T7194	10846-10848	TO	denotes	to
T7195	10849-10854	VB	denotes	reach
T7196	10855-10858	DT	denotes	the
T7198	10859-10870	JJ	denotes	significant
T7199	10871-10880	NN	denotes	threshold
T7197	10881-10886	NN	denotes	value
T7200	10887-10889	IN	denotes	of
T7201	10890-10897	NN	denotes	linkage
T7202	10897-10898	.	denotes	.
T7203	10898-11020	sentence	denotes	To identify these potential small-effect QTL, we reanalyzed the data using a lower threshold value of linkage (P = 0.05).
T7204	10899-10901	TO	denotes	To
T7205	10902-10910	VB	denotes	identify
T7207	10911-10916	DT	denotes	these
T7209	10917-10926	JJ	denotes	potential
T7210	10927-10932	JJ	denotes	small
T7212	10932-10933	HYPH	denotes	-
T7211	10933-10939	NN	denotes	effect
T7208	10940-10943	NNS	denotes	QTL
T7213	10943-10945	,	denotes	,
T7214	10945-10947	PRP	denotes	we
T7206	10948-10958	VBD	denotes	reanalyzed
T7215	10959-10962	DT	denotes	the
T7216	10963-10967	NNS	denotes	data
T7217	10968-10973	VBG	denotes	using
T7218	10974-10975	DT	denotes	a
T7220	10976-10981	JJR	denotes	lower
T7221	10982-10991	NN	denotes	threshold
T7219	10992-10997	NN	denotes	value
T7222	10998-11000	IN	denotes	of
T7223	11001-11008	NN	denotes	linkage
T7224	11009-11010	-LRB-	denotes	(
T7226	11010-11011	NN	denotes	P
T7227	11012-11013	SYM	denotes	=
T7225	11014-11018	CD	denotes	0.05
T7228	11018-11019	-RRB-	denotes	)
T7229	11019-11020	.	denotes	.
T7230	11020-11254	sentence	denotes	We reasoned that since the main candidate gene of Cia2, complement component C5 (Hc), was proven to be essential for CIA development and because the FVB/N strain is C5 deficient [10,25], some small-effect QTL might be masked by Cia2.
T7231	11021-11023	PRP	denotes	We
T7232	11024-11032	VBD	denotes	reasoned
T7233	11033-11037	IN	denotes	that
T7235	11038-11043	IN	denotes	since
T7237	11044-11047	DT	denotes	the
T7239	11048-11052	JJ	denotes	main
T7240	11053-11062	NN	denotes	candidate
T7238	11063-11067	NN	denotes	gene
T7241	11068-11070	IN	denotes	of
T7242	11071-11075	NN	denotes	Cia2
T7243	11075-11077	,	denotes	,
T7244	11077-11087	NN	denotes	complement
T7246	11088-11097	NN	denotes	component
T7245	11098-11100	NN	denotes	C5
T7247	11101-11102	-LRB-	denotes	(
T7248	11102-11104	NN	denotes	Hc
T7249	11104-11105	-RRB-	denotes	)
T7250	11105-11107	,	denotes	,
T7251	11107-11110	VBD	denotes	was
T7236	11111-11117	VBN	denotes	proven
T7252	11118-11120	TO	denotes	to
T7253	11121-11123	VB	denotes	be
T7254	11124-11133	JJ	denotes	essential
T7255	11134-11137	IN	denotes	for
T7256	11138-11141	NN	denotes	CIA
T7257	11142-11153	NN	denotes	development
T7258	11154-11157	CC	denotes	and
T7259	11158-11165	IN	denotes	because
T7261	11166-11169	DT	denotes	the
T7263	11170-11173	NN	denotes	FVB
T7265	11173-11174	HYPH	denotes	/
T7264	11174-11175	NN	denotes	N
T7262	11176-11182	NN	denotes	strain
T7260	11183-11185	VBZ	denotes	is
T7266	11186-11188	NN	denotes	C5
T7267	11189-11198	JJ	denotes	deficient
T7268	11199-11200	-LRB-	denotes	[
T7270	11200-11202	CD	denotes	10
T7271	11202-11203	,	denotes	,
T7269	11203-11205	CD	denotes	25
T7272	11205-11206	-RRB-	denotes	]
T7273	11206-11208	,	denotes	,
T7274	11208-11212	DT	denotes	some
T7276	11213-11218	JJ	denotes	small
T7278	11218-11219	HYPH	denotes	-
T7277	11219-11225	NN	denotes	effect
T7275	11226-11229	NNS	denotes	QTL
T7279	11230-11235	MD	denotes	might
T7280	11236-11238	VB	denotes	be
T7234	11239-11245	VBN	denotes	masked
T7281	11246-11248	IN	denotes	by
T7282	11249-11253	NN	denotes	Cia2
T7283	11253-11254	.	denotes	.
T7284	11254-11446	sentence	denotes	To exclude the masking effect of C5, we performed linkage analysis with 3 datasets, the first containing all 290 F2 progeny, the second 77 C5+/+ F2 progeny and the third 133 C5+/- F2 progeny.
T7285	11255-11257	TO	denotes	To
T7286	11258-11265	VB	denotes	exclude
T7288	11266-11269	DT	denotes	the
T7290	11270-11277	NN	denotes	masking
T7289	11278-11284	NN	denotes	effect
T7291	11285-11287	IN	denotes	of
T7292	11288-11290	NN	denotes	C5
T7293	11290-11292	,	denotes	,
T7294	11292-11294	PRP	denotes	we
T7287	11295-11304	VBD	denotes	performed
T7295	11305-11312	NN	denotes	linkage
T7296	11313-11321	NN	denotes	analysis
T7297	11322-11326	IN	denotes	with
T7298	11327-11328	CD	denotes	3
T7299	11329-11337	NNS	denotes	datasets
T7300	11337-11339	,	denotes	,
T7301	11339-11342	DT	denotes	the
T7302	11343-11348	JJ	denotes	first
T7303	11349-11359	VBG	denotes	containing
T7304	11360-11363	DT	denotes	all
T7306	11364-11367	CD	denotes	290
T7307	11368-11370	NN	denotes	F2
T7305	11371-11378	NN	denotes	progeny
T7308	11378-11380	,	denotes	,
T7309	11380-11383	DT	denotes	the
T7310	11384-11390	JJ	denotes	second
T7312	11391-11393	CD	denotes	77
T7313	11394-11397	NN	denotes	C5+
T7314	11397-11398	HYPH	denotes	/
T7315	11398-11399	SYM	denotes	+
T7316	11400-11402	NN	denotes	F2
T7311	11403-11410	NN	denotes	progeny
T7317	11411-11414	CC	denotes	and
T7318	11415-11418	DT	denotes	the
T7319	11419-11424	JJ	denotes	third
T7321	11425-11428	CD	denotes	133
T7322	11429-11432	NN	denotes	C5+
T7323	11432-11433	HYPH	denotes	/
T7324	11433-11434	SYM	denotes	-
T7325	11435-11437	NN	denotes	F2
T7320	11438-11445	NN	denotes	progeny
T7326	11445-11446	.	denotes	.
T7327	11446-11584	sentence	denotes	Eight genomic regions were linked to the phenotype of CIA severity (loci 1 to 8, Table 2), with P values varying between 0.043 and 0.003.
T7328	11447-11452	CD	denotes	Eight
T7330	11453-11460	JJ	denotes	genomic
T7329	11461-11468	NNS	denotes	regions
T7332	11469-11473	VBD	denotes	were
T7331	11474-11480	VBN	denotes	linked
T7333	11481-11483	IN	denotes	to
T7334	11484-11487	DT	denotes	the
T7335	11488-11497	NN	denotes	phenotype
T7336	11498-11500	IN	denotes	of
T7337	11501-11504	NN	denotes	CIA
T7338	11505-11513	NN	denotes	severity
T7339	11514-11515	-LRB-	denotes	(
T7341	11515-11519	NNS	denotes	loci
T7342	11520-11521	CD	denotes	1
T7343	11522-11524	IN	denotes	to
T7344	11525-11526	CD	denotes	8
T7345	11526-11528	,	denotes	,
T7340	11528-11533	NN	denotes	Table
T7346	11534-11535	CD	denotes	2
T7347	11535-11536	-RRB-	denotes	)
T7348	11536-11538	,	denotes	,
T7349	11538-11542	IN	denotes	with
T7351	11543-11544	NN	denotes	P
T7352	11545-11551	NNS	denotes	values
T7350	11552-11559	VBG	denotes	varying
T7353	11560-11567	IN	denotes	between
T7354	11568-11573	CD	denotes	0.043
T7355	11574-11577	CC	denotes	and
T7356	11578-11583	CD	denotes	0.003
T7357	11583-11584	.	denotes	.
T7358	11584-11670	sentence	denotes	These eight small-effect QTL were located on chromosomes 5, 6, 7, 10, 11, 16, and 17.
T7359	11585-11590	DT	denotes	These
T7361	11591-11596	CD	denotes	eight
T7362	11597-11602	JJ	denotes	small
T7364	11602-11603	HYPH	denotes	-
T7363	11603-11609	NN	denotes	effect
T7360	11610-11613	NNS	denotes	QTL
T7366	11614-11618	VBD	denotes	were
T7365	11619-11626	VBN	denotes	located
T7367	11627-11629	IN	denotes	on
T7368	11630-11641	NNS	denotes	chromosomes
T7369	11642-11643	CD	denotes	5
T7370	11643-11645	,	denotes	,
T7371	11645-11646	CD	denotes	6
T7372	11646-11648	,	denotes	,
T7373	11648-11649	CD	denotes	7
T7374	11649-11651	,	denotes	,
T7375	11651-11653	CD	denotes	10
T7376	11653-11655	,	denotes	,
T7377	11655-11657	CD	denotes	11
T7378	11657-11659	,	denotes	,
T7379	11659-11661	CD	denotes	16
T7380	11661-11663	,	denotes	,
T7381	11663-11666	CC	denotes	and
T7382	11667-11669	CD	denotes	17
T7383	11669-11670	.	denotes	.
T7384	11670-11722	sentence	denotes	Five loci were identified in at least two datasets.
T7385	11671-11675	CD	denotes	Five
T7386	11676-11680	NNS	denotes	loci
T7388	11681-11685	VBD	denotes	were
T7387	11686-11696	VBN	denotes	identified
T7389	11697-11699	IN	denotes	in
T7390	11700-11702	RB	denotes	at
T7392	11703-11708	RBS	denotes	least
T7391	11709-11712	CD	denotes	two
T7393	11713-11721	NNS	denotes	datasets
T7394	11721-11722	.	denotes	.
T7395	11722-11836	sentence	denotes	Of the eight loci, five had DBA/1 as the susceptibility allele, and three had FVB/N as the susceptibility allele.
T7396	11723-11725	IN	denotes	Of
T7398	11726-11729	DT	denotes	the
T7400	11730-11735	CD	denotes	eight
T7399	11736-11740	NNS	denotes	loci
T7401	11740-11742	,	denotes	,
T7402	11742-11746	CD	denotes	five
T7397	11747-11750	VBD	denotes	had
T7403	11751-11754	NN	denotes	DBA
T7404	11754-11755	HYPH	denotes	/
T7405	11755-11756	CD	denotes	1
T7406	11757-11759	IN	denotes	as
T7407	11760-11763	DT	denotes	the
T7409	11764-11778	NN	denotes	susceptibility
T7408	11779-11785	NN	denotes	allele
T7410	11785-11787	,	denotes	,
T7411	11787-11790	CC	denotes	and
T7412	11791-11796	CD	denotes	three
T7413	11797-11800	VBD	denotes	had
T7414	11801-11804	NN	denotes	FVB
T7416	11804-11805	HYPH	denotes	/
T7415	11805-11806	NN	denotes	N
T7417	11807-11809	IN	denotes	as
T7418	11810-11813	DT	denotes	the
T7420	11814-11828	NN	denotes	susceptibility
T7419	11829-11835	NN	denotes	allele
T7421	11835-11836	.	denotes	.
T7422	11836-12078	sentence	denotes	Lander and Botstein [26] suggested a LOD score of between 2 and 3 to ensure an overall false positive rate of 5%, which means that using a lower threshold value will prevent false negative QTL at the expense of increasing false positive QTL.
T7423	11837-11843	NNP	denotes	Lander
T7425	11844-11847	CC	denotes	and
T7426	11848-11856	NNP	denotes	Botstein
T7427	11857-11858	-LRB-	denotes	[
T7428	11858-11860	CD	denotes	26
T7429	11860-11861	-RRB-	denotes	]
T7424	11862-11871	VBD	denotes	suggested
T7430	11872-11873	DT	denotes	a
T7432	11874-11877	NN	denotes	LOD
T7431	11878-11883	NN	denotes	score
T7433	11884-11886	IN	denotes	of
T7434	11887-11894	IN	denotes	between
T7435	11895-11896	CD	denotes	2
T7436	11897-11900	CC	denotes	and
T7437	11901-11902	CD	denotes	3
T7438	11903-11905	TO	denotes	to
T7439	11906-11912	VB	denotes	ensure
T7440	11913-11915	DT	denotes	an
T7442	11916-11923	JJ	denotes	overall
T7443	11924-11929	JJ	denotes	false
T7444	11930-11938	JJ	denotes	positive
T7441	11939-11943	NN	denotes	rate
T7445	11944-11946	IN	denotes	of
T7446	11947-11948	CD	denotes	5
T7447	11948-11949	NN	denotes	%
T7448	11949-11951	,	denotes	,
T7449	11951-11956	WDT	denotes	which
T7450	11957-11962	VBZ	denotes	means
T7451	11963-11967	IN	denotes	that
T7453	11968-11973	VBG	denotes	using
T7454	11974-11975	DT	denotes	a
T7456	11976-11981	JJR	denotes	lower
T7457	11982-11991	NN	denotes	threshold
T7455	11992-11997	NN	denotes	value
T7458	11998-12002	MD	denotes	will
T7452	12003-12010	VB	denotes	prevent
T7459	12011-12016	JJ	denotes	false
T7460	12017-12025	JJ	denotes	negative
T7461	12026-12029	NNS	denotes	QTL
T7462	12030-12032	IN	denotes	at
T7463	12033-12036	DT	denotes	the
T7464	12037-12044	NN	denotes	expense
T7465	12045-12047	IN	denotes	of
T7466	12048-12058	VBG	denotes	increasing
T7467	12059-12064	JJ	denotes	false
T7468	12065-12073	JJ	denotes	positive
T7469	12074-12077	NNS	denotes	QTL
T7470	12077-12078	.	denotes	.
T7471	12078-12254	sentence	denotes	Being aware of this, we examined these genomic regions to search whether they, or their syntenic genomic regions on the human genome, have been previously linked to arthritis.
T7472	12079-12084	VBG	denotes	Being
T7474	12085-12090	JJ	denotes	aware
T7475	12091-12093	IN	denotes	of
T7476	12094-12098	DT	denotes	this
T7477	12098-12100	,	denotes	,
T7478	12100-12102	PRP	denotes	we
T7473	12103-12111	VBD	denotes	examined
T7479	12112-12117	DT	denotes	these
T7481	12118-12125	JJ	denotes	genomic
T7480	12126-12133	NNS	denotes	regions
T7482	12134-12136	TO	denotes	to
T7483	12137-12143	VB	denotes	search
T7484	12144-12151	IN	denotes	whether
T7486	12152-12156	PRP	denotes	they
T7487	12156-12158	,	denotes	,
T7488	12158-12160	CC	denotes	or
T7489	12161-12166	PRP$	denotes	their
T7491	12167-12175	JJ	denotes	syntenic
T7492	12176-12183	JJ	denotes	genomic
T7490	12184-12191	NNS	denotes	regions
T7493	12192-12194	IN	denotes	on
T7494	12195-12198	DT	denotes	the
T7496	12199-12204	JJ	denotes	human
T7495	12205-12211	NN	denotes	genome
T7497	12211-12213	,	denotes	,
T7498	12213-12217	VBP	denotes	have
T7499	12218-12222	VBN	denotes	been
T7500	12223-12233	RB	denotes	previously
T7485	12234-12240	VBN	denotes	linked
T7501	12241-12243	IN	denotes	to
T7502	12244-12253	NN	denotes	arthritis
T7503	12253-12254	.	denotes	.
T7504	12254-12349	sentence	denotes	Four small-effect QTL overlapped with arthritis QTL on the mouse genome identified previously.
T7505	12255-12259	CD	denotes	Four
T7507	12260-12265	JJ	denotes	small
T7509	12265-12266	HYPH	denotes	-
T7508	12266-12272	NN	denotes	effect
T7506	12273-12276	NNS	denotes	QTL
T7510	12277-12287	VBD	denotes	overlapped
T7511	12288-12292	IN	denotes	with
T7512	12293-12302	NN	denotes	arthritis
T7513	12303-12306	NNS	denotes	QTL
T7514	12307-12309	IN	denotes	on
T7515	12310-12313	DT	denotes	the
T7517	12314-12319	NN	denotes	mouse
T7516	12320-12326	NN	denotes	genome
T7518	12327-12337	VBN	denotes	identified
T7519	12338-12348	RB	denotes	previously
T7520	12348-12349	.	denotes	.
T7521	12349-12460	sentence	denotes	Locus 1 and 2 overlap with Cia13 and Cia14, which control severity of CIA in (DBA/1 × BALB/C) F2 progeny [27].
T7522	12350-12355	NN	denotes	Locus
T7523	12356-12357	CD	denotes	1
T7525	12358-12361	CC	denotes	and
T7526	12362-12363	CD	denotes	2
T7524	12364-12371	VBP	denotes	overlap
T7527	12372-12376	IN	denotes	with
T7528	12377-12382	NN	denotes	Cia13
T7529	12383-12386	CC	denotes	and
T7530	12387-12392	NN	denotes	Cia14
T7531	12392-12394	,	denotes	,
T7532	12394-12399	WDT	denotes	which
T7533	12400-12407	VBP	denotes	control
T7534	12408-12416	NN	denotes	severity
T7535	12417-12419	IN	denotes	of
T7536	12420-12423	NN	denotes	CIA
T7537	12424-12426	IN	denotes	in
T7538	12427-12428	-LRB-	denotes	(
T7539	12428-12431	NN	denotes	DBA
T7541	12431-12432	HYPH	denotes	/
T7542	12432-12433	CD	denotes	1
T7543	12434-12435	SYM	denotes	×
T7544	12436-12440	NN	denotes	BALB
T7546	12440-12441	HYPH	denotes	/
T7545	12441-12442	NN	denotes	C
T7547	12442-12443	-RRB-	denotes	)
T7548	12444-12446	NN	denotes	F2
T7540	12447-12454	NN	denotes	progeny
T7549	12455-12456	-LRB-	denotes	[
T7550	12456-12458	CD	denotes	27
T7551	12458-12459	-RRB-	denotes	]
T7552	12459-12460	.	denotes	.
T7553	12460-12570	sentence	denotes	Locus 5 located on chromosome 10 overlaps with Cia8, which was identified in (DBA/1 × B10.Q) F2 progeny [28].
T7554	12461-12466	NN	denotes	Locus
T7556	12467-12468	CD	denotes	5
T7557	12469-12476	VBN	denotes	located
T7558	12477-12479	IN	denotes	on
T7559	12480-12490	NN	denotes	chromosome
T7560	12491-12493	CD	denotes	10
T7555	12494-12502	VBZ	denotes	overlaps
T7561	12503-12507	IN	denotes	with
T7562	12508-12512	NN	denotes	Cia8
T7563	12512-12514	,	denotes	,
T7564	12514-12519	WDT	denotes	which
T7566	12520-12523	VBD	denotes	was
T7565	12524-12534	VBN	denotes	identified
T7567	12535-12537	IN	denotes	in
T7568	12538-12539	-LRB-	denotes	(
T7569	12539-12542	NN	denotes	DBA
T7571	12542-12543	HYPH	denotes	/
T7572	12543-12544	CD	denotes	1
T7573	12545-12546	SYM	denotes	×
T7574	12547-12552	NN	denotes	B10.Q
T7575	12552-12553	-RRB-	denotes	)
T7576	12554-12556	NN	denotes	F2
T7570	12557-12564	NN	denotes	progeny
T7577	12565-12566	-LRB-	denotes	[
T7578	12566-12568	CD	denotes	28
T7579	12568-12569	-RRB-	denotes	]
T7580	12569-12570	.	denotes	.
T7581	12570-12726	sentence	denotes	Locus 6 overlaps with Pgia7, which controls susceptibility to proteoglycan-induced arthritis (PGIA) and was identified in (BALB/C × DBA/2) F2 progeny [29].
T7582	12571-12576	NN	denotes	Locus
T7584	12577-12578	CD	denotes	6
T7583	12579-12587	VBZ	denotes	overlaps
T7585	12588-12592	IN	denotes	with
T7586	12593-12598	NN	denotes	Pgia7
T7587	12598-12600	,	denotes	,
T7588	12600-12605	WDT	denotes	which
T7589	12606-12614	VBZ	denotes	controls
T7590	12615-12629	NN	denotes	susceptibility
T7591	12630-12632	IN	denotes	to
T7592	12633-12645	NN	denotes	proteoglycan
T7594	12645-12646	HYPH	denotes	-
T7593	12646-12653	VBN	denotes	induced
T7595	12654-12663	NN	denotes	arthritis
T7596	12664-12665	-LRB-	denotes	(
T7597	12665-12669	NN	denotes	PGIA
T7598	12669-12670	-RRB-	denotes	)
T7599	12671-12674	CC	denotes	and
T7600	12675-12678	VBD	denotes	was
T7601	12679-12689	VBN	denotes	identified
T7602	12690-12692	IN	denotes	in
T7603	12693-12694	-LRB-	denotes	(
T7605	12694-12698	NN	denotes	BALB
T7606	12698-12699	HYPH	denotes	/
T7604	12699-12700	NN	denotes	C
T7608	12701-12702	SYM	denotes	×
T7609	12703-12706	NN	denotes	DBA
T7610	12706-12707	HYPH	denotes	/
T7611	12707-12708	CD	denotes	2
T7612	12708-12709	-RRB-	denotes	)
T7613	12710-12712	NN	denotes	F2
T7607	12713-12720	NN	denotes	progeny
T7614	12721-12722	-LRB-	denotes	[
T7615	12722-12724	CD	denotes	29
T7616	12724-12725	-RRB-	denotes	]
T7617	12725-12726	.	denotes	.
T7618	12726-12839	sentence	denotes	The syntenic genomic regions of five small-effect QTL on the human genome have been reported to be linked to RA.
T7619	12727-12730	DT	denotes	The
T7621	12731-12739	JJ	denotes	syntenic
T7622	12740-12747	JJ	denotes	genomic
T7620	12748-12755	NNS	denotes	regions
T7624	12756-12758	IN	denotes	of
T7625	12759-12763	CD	denotes	five
T7627	12764-12769	JJ	denotes	small
T7629	12769-12770	HYPH	denotes	-
T7628	12770-12776	NN	denotes	effect
T7626	12777-12780	NNS	denotes	QTL
T7630	12781-12783	IN	denotes	on
T7631	12784-12787	DT	denotes	the
T7633	12788-12793	JJ	denotes	human
T7632	12794-12800	NN	denotes	genome
T7634	12801-12805	VBP	denotes	have
T7635	12806-12810	VBN	denotes	been
T7623	12811-12819	VBN	denotes	reported
T7636	12820-12822	TO	denotes	to
T7638	12823-12825	VB	denotes	be
T7637	12826-12832	VBN	denotes	linked
T7639	12833-12835	IN	denotes	to
T7640	12836-12838	NN	denotes	RA
T7641	12838-12839	.	denotes	.
T7642	12839-13198	sentence	denotes	These are genomic regions 22q11 and 12p13-q24 on chromosome 22 and 12 (the counterparts of locus 2), 12p13-pter on chromosome 12 (the counterpart of locus 3), 21q22-qter and 10q22-23 on chromosome 21 and 10 (the counterparts of locus 5), 17q21-25 on chromosome 17 (the counterpart of locus 6) and 3q29-qter on chromosome 3 (the counterpart of locus 7) [2,4].
T7643	12840-12845	DT	denotes	These
T7644	12846-12849	VBP	denotes	are
T7645	12850-12857	JJ	denotes	genomic
T7646	12858-12865	NNS	denotes	regions
T7647	12866-12871	NN	denotes	22q11
T7648	12872-12875	CC	denotes	and
T7649	12876-12881	NN	denotes	12p13
T7651	12881-12882	HYPH	denotes	-
T7650	12882-12885	NN	denotes	q24
T7652	12886-12888	IN	denotes	on
T7653	12889-12899	NN	denotes	chromosome
T7654	12900-12902	CD	denotes	22
T7655	12903-12906	CC	denotes	and
T7656	12907-12909	CD	denotes	12
T7657	12910-12911	-LRB-	denotes	(
T7659	12911-12914	DT	denotes	the
T7658	12915-12927	NNS	denotes	counterparts
T7660	12928-12930	IN	denotes	of
T7661	12931-12936	NN	denotes	locus
T7662	12937-12938	CD	denotes	2
T7663	12938-12939	-RRB-	denotes	)
T7664	12939-12941	,	denotes	,
T7665	12941-12946	NN	denotes	12p13
T7667	12946-12947	HYPH	denotes	-
T7666	12947-12951	NN	denotes	pter
T7668	12952-12954	IN	denotes	on
T7669	12955-12965	NN	denotes	chromosome
T7670	12966-12968	CD	denotes	12
T7671	12969-12970	-LRB-	denotes	(
T7673	12970-12973	DT	denotes	the
T7672	12974-12985	NN	denotes	counterpart
T7674	12986-12988	IN	denotes	of
T7675	12989-12994	NN	denotes	locus
T7676	12995-12996	CD	denotes	3
T7677	12996-12997	-RRB-	denotes	)
T7678	12997-12999	,	denotes	,
T7679	12999-13004	NN	denotes	21q22
T7681	13004-13005	HYPH	denotes	-
T7680	13005-13009	NN	denotes	qter
T7682	13010-13013	CC	denotes	and
T7683	13014-13019	NN	denotes	10q22
T7684	13019-13020	HYPH	denotes	-
T7685	13020-13022	CD	denotes	23
T7686	13023-13025	IN	denotes	on
T7687	13026-13036	NN	denotes	chromosome
T7688	13037-13039	CD	denotes	21
T7689	13040-13043	CC	denotes	and
T7690	13044-13046	CD	denotes	10
T7691	13047-13048	-LRB-	denotes	(
T7693	13048-13051	DT	denotes	the
T7692	13052-13064	NNS	denotes	counterparts
T7694	13065-13067	IN	denotes	of
T7695	13068-13073	NN	denotes	locus
T7696	13074-13075	CD	denotes	5
T7697	13075-13076	-RRB-	denotes	)
T7698	13076-13078	,	denotes	,
T7699	13078-13083	NN	denotes	17q21
T7700	13083-13084	HYPH	denotes	-
T7701	13084-13086	CD	denotes	25
T7702	13087-13089	IN	denotes	on
T7703	13090-13100	NN	denotes	chromosome
T7704	13101-13103	CD	denotes	17
T7705	13104-13105	-LRB-	denotes	(
T7707	13105-13108	DT	denotes	the
T7706	13109-13120	NN	denotes	counterpart
T7708	13121-13123	IN	denotes	of
T7709	13124-13129	NN	denotes	locus
T7710	13130-13131	CD	denotes	6
T7711	13131-13132	-RRB-	denotes	)
T7712	13133-13136	CC	denotes	and
T7713	13137-13141	NN	denotes	3q29
T7715	13141-13142	HYPH	denotes	-
T7714	13142-13146	NN	denotes	qter
T7716	13147-13149	IN	denotes	on
T7717	13150-13160	NN	denotes	chromosome
T7718	13161-13162	CD	denotes	3
T7719	13163-13164	-LRB-	denotes	(
T7721	13164-13167	DT	denotes	the
T7720	13168-13179	NN	denotes	counterpart
T7722	13180-13182	IN	denotes	of
T7723	13183-13188	NN	denotes	locus
T7724	13189-13190	CD	denotes	7
T7725	13190-13191	-RRB-	denotes	)
T7726	13192-13193	-LRB-	denotes	[
T7728	13193-13194	CD	denotes	2
T7729	13194-13195	,	denotes	,
T7727	13195-13196	CD	denotes	4
T7730	13196-13197	-RRB-	denotes	]
T7731	13197-13198	.	denotes	.
T8314	13200-13206	NN	denotes	Strain
T8316	13206-13207	HYPH	denotes	-
T8315	13207-13215	JJ	denotes	specific
T8318	13216-13230	RB	denotes	differentially
T8319	13231-13240	VBN	denotes	expressed
T8317	13241-13246	NNS	denotes	genes
T8320	13246-13340	sentence	denotes	We detected the gene expression profiles using three mice per group, which is a small number.
T8321	13247-13249	PRP	denotes	We
T8322	13250-13258	VBD	denotes	detected
T8323	13259-13262	DT	denotes	the
T8325	13263-13267	NN	denotes	gene
T8326	13268-13278	NN	denotes	expression
T8324	13279-13287	NNS	denotes	profiles
T8327	13288-13293	VBG	denotes	using
T8328	13294-13299	CD	denotes	three
T8329	13300-13304	NNS	denotes	mice
T8330	13305-13308	IN	denotes	per
T8331	13309-13314	NN	denotes	group
T8332	13314-13316	,	denotes	,
T8333	13316-13321	WDT	denotes	which
T8334	13322-13324	VBZ	denotes	is
T8335	13325-13326	DT	denotes	a
T8337	13327-13332	JJ	denotes	small
T8336	13333-13339	NN	denotes	number
T8338	13339-13340	.	denotes	.
T8339	13340-13472	sentence	denotes	Being aware of the importance of data reproducibility, we determined the coefficient of variation (CV) to measure data variability.
T8340	13341-13346	VBG	denotes	Being
T8342	13347-13352	JJ	denotes	aware
T8343	13353-13355	IN	denotes	of
T8344	13356-13359	DT	denotes	the
T8345	13360-13370	NN	denotes	importance
T8346	13371-13373	IN	denotes	of
T8347	13374-13378	NNS	denotes	data
T8348	13379-13394	NN	denotes	reproducibility
T8349	13394-13396	,	denotes	,
T8350	13396-13398	PRP	denotes	we
T8341	13399-13409	VBD	denotes	determined
T8351	13410-13413	DT	denotes	the
T8352	13414-13425	NN	denotes	coefficient
T8353	13426-13428	IN	denotes	of
T8354	13429-13438	NN	denotes	variation
T8355	13439-13440	-LRB-	denotes	(
T8356	13440-13442	NN	denotes	CV
T8357	13442-13443	-RRB-	denotes	)
T8358	13444-13446	TO	denotes	to
T8359	13447-13454	VB	denotes	measure
T8360	13455-13459	NNS	denotes	data
T8361	13460-13471	NN	denotes	variability
T8362	13471-13472	.	denotes	.
T8363	13472-13563	sentence	denotes	The CV for each gene on the chip and the mean CV for the entire probe set were calculated.
T8364	13473-13476	DT	denotes	The
T8365	13477-13479	NN	denotes	CV
T8367	13480-13483	IN	denotes	for
T8368	13484-13488	DT	denotes	each
T8369	13489-13493	NN	denotes	gene
T8370	13494-13496	IN	denotes	on
T8371	13497-13500	DT	denotes	the
T8372	13501-13505	NN	denotes	chip
T8373	13506-13509	CC	denotes	and
T8374	13510-13513	DT	denotes	the
T8376	13514-13518	JJ	denotes	mean
T8375	13519-13521	NN	denotes	CV
T8377	13522-13525	IN	denotes	for
T8378	13526-13529	DT	denotes	the
T8380	13530-13536	JJ	denotes	entire
T8379	13537-13542	NN	denotes	probe
T8381	13543-13546	VBN	denotes	set
T8382	13547-13551	VBD	denotes	were
T8366	13552-13562	VBN	denotes	calculated
T8383	13562-13563	.	denotes	.
T8384	13563-13734	sentence	denotes	The mean CV ranged between 18.4% and 25.8% for all experimental groups, and this relatively low CV indicated that these data could be used for further analysis (Table 1).
T8385	13564-13567	DT	denotes	The
T8387	13568-13572	JJ	denotes	mean
T8386	13573-13575	NN	denotes	CV
T8388	13576-13582	VBD	denotes	ranged
T8389	13583-13590	IN	denotes	between
T8390	13591-13595	CD	denotes	18.4
T8391	13595-13596	NN	denotes	%
T8392	13597-13600	CC	denotes	and
T8393	13601-13605	CD	denotes	25.8
T8394	13605-13606	NN	denotes	%
T8395	13607-13610	IN	denotes	for
T8396	13611-13614	DT	denotes	all
T8398	13615-13627	JJ	denotes	experimental
T8397	13628-13634	NNS	denotes	groups
T8399	13634-13636	,	denotes	,
T8400	13636-13639	CC	denotes	and
T8401	13640-13644	DT	denotes	this
T8403	13645-13655	RB	denotes	relatively
T8404	13656-13659	JJ	denotes	low
T8402	13660-13662	NN	denotes	CV
T8405	13663-13672	VBD	denotes	indicated
T8406	13673-13677	IN	denotes	that
T8408	13678-13683	DT	denotes	these
T8409	13684-13688	NNS	denotes	data
T8410	13689-13694	MD	denotes	could
T8411	13695-13697	VB	denotes	be
T8407	13698-13702	VBN	denotes	used
T8412	13703-13706	IN	denotes	for
T8413	13707-13714	JJ	denotes	further
T8414	13715-13723	NN	denotes	analysis
T8415	13724-13725	-LRB-	denotes	(
T8416	13725-13730	NN	denotes	Table
T8417	13731-13732	CD	denotes	1
T8418	13732-13733	-RRB-	denotes	)
T8419	13733-13734	.	denotes	.
T8420	13734-13932	sentence	denotes	To search for strain-specific differentially expressed genes, we performed comparisons of gene expression between the DBA/1 and FVB/N strains at all four phases of CIA, including NC, PI, OA and CA.
T8421	13735-13737	TO	denotes	To
T8422	13738-13744	VB	denotes	search
T8424	13745-13748	IN	denotes	for
T8425	13749-13755	NN	denotes	strain
T8427	13755-13756	HYPH	denotes	-
T8426	13756-13764	JJ	denotes	specific
T8429	13765-13779	RB	denotes	differentially
T8430	13780-13789	VBN	denotes	expressed
T8428	13790-13795	NNS	denotes	genes
T8431	13795-13797	,	denotes	,
T8432	13797-13799	PRP	denotes	we
T8423	13800-13809	VBD	denotes	performed
T8433	13810-13821	NNS	denotes	comparisons
T8434	13822-13824	IN	denotes	of
T8435	13825-13829	NN	denotes	gene
T8436	13830-13840	NN	denotes	expression
T8437	13841-13848	IN	denotes	between
T8438	13849-13852	DT	denotes	the
T8440	13853-13856	NN	denotes	DBA
T8441	13856-13857	HYPH	denotes	/
T8442	13857-13858	CD	denotes	1
T8443	13859-13862	CC	denotes	and
T8444	13863-13866	NN	denotes	FVB
T8446	13866-13867	HYPH	denotes	/
T8445	13867-13868	NN	denotes	N
T8439	13869-13876	NNS	denotes	strains
T8447	13877-13879	IN	denotes	at
T8448	13880-13883	DT	denotes	all
T8450	13884-13888	CD	denotes	four
T8449	13889-13895	NNS	denotes	phases
T8451	13896-13898	IN	denotes	of
T8452	13899-13902	NN	denotes	CIA
T8453	13902-13904	,	denotes	,
T8454	13904-13913	VBG	denotes	including
T8455	13914-13916	NN	denotes	NC
T8456	13916-13918	,	denotes	,
T8457	13918-13920	NN	denotes	PI
T8458	13920-13922	,	denotes	,
T8459	13922-13924	NN	denotes	OA
T8460	13925-13928	CC	denotes	and
T8461	13929-13931	NN	denotes	CA
T8462	13931-13932	.	denotes	.
T8463	13932-14038	sentence	denotes	For the naive mice without immunisation, 361 genes were differentially expressed between the two strains.
T8464	13933-13936	IN	denotes	For
T8466	13937-13940	DT	denotes	the
T8468	13941-13946	JJ	denotes	naive
T8467	13947-13951	NNS	denotes	mice
T8469	13952-13959	IN	denotes	without
T8470	13960-13972	NN	denotes	immunisation
T8471	13972-13974	,	denotes	,
T8472	13974-13977	CD	denotes	361
T8473	13978-13983	NNS	denotes	genes
T8474	13984-13988	VBD	denotes	were
T8475	13989-14003	RB	denotes	differentially
T8465	14004-14013	VBN	denotes	expressed
T8476	14014-14021	IN	denotes	between
T8477	14022-14025	DT	denotes	the
T8479	14026-14029	CD	denotes	two
T8478	14030-14037	NNS	denotes	strains
T8480	14037-14038	.	denotes	.
T8481	14038-14165	sentence	denotes	On day 10 after immunisation, when both strains did not show any sign of the disease, 141 genes were differentially expressed.
T8482	14039-14041	IN	denotes	On
T8484	14042-14045	NN	denotes	day
T8485	14046-14048	CD	denotes	10
T8486	14049-14054	IN	denotes	after
T8487	14055-14067	NN	denotes	immunisation
T8488	14067-14069	,	denotes	,
T8489	14069-14073	WRB	denotes	when
T8491	14074-14078	DT	denotes	both
T8492	14079-14086	NNS	denotes	strains
T8493	14087-14090	VBD	denotes	did
T8494	14091-14094	RB	denotes	not
T8490	14095-14099	VB	denotes	show
T8495	14100-14103	DT	denotes	any
T8496	14104-14108	NN	denotes	sign
T8497	14109-14111	IN	denotes	of
T8498	14112-14115	DT	denotes	the
T8499	14116-14123	NN	denotes	disease
T8500	14123-14125	,	denotes	,
T8501	14125-14128	CD	denotes	141
T8502	14129-14134	NNS	denotes	genes
T8503	14135-14139	VBD	denotes	were
T8504	14140-14154	RB	denotes	differentially
T8483	14155-14164	VBN	denotes	expressed
T8505	14164-14165	.	denotes	.
T8506	14165-14328	sentence	denotes	After DBA/1 mice developed CIA, 184 and 85 differentially expressed genes were identified between these two strains at the onset and chronic phases, respectively.
T8507	14166-14171	IN	denotes	After
T8509	14172-14175	NN	denotes	DBA
T8511	14175-14176	HYPH	denotes	/
T8512	14176-14177	CD	denotes	1
T8510	14178-14182	NNS	denotes	mice
T8508	14183-14192	VBD	denotes	developed
T8514	14193-14196	NN	denotes	CIA
T8515	14196-14198	,	denotes	,
T8516	14198-14201	CD	denotes	184
T8518	14202-14205	CC	denotes	and
T8519	14206-14208	CD	denotes	85
T8520	14209-14223	RB	denotes	differentially
T8521	14224-14233	VBN	denotes	expressed
T8517	14234-14239	NNS	denotes	genes
T8522	14240-14244	VBD	denotes	were
T8513	14245-14255	VBN	denotes	identified
T8523	14256-14263	IN	denotes	between
T8524	14264-14269	DT	denotes	these
T8526	14270-14273	CD	denotes	two
T8525	14274-14281	NNS	denotes	strains
T8527	14282-14284	IN	denotes	at
T8528	14285-14288	DT	denotes	the
T8530	14289-14294	NN	denotes	onset
T8531	14295-14298	CC	denotes	and
T8532	14299-14306	JJ	denotes	chronic
T8529	14307-14313	NNS	denotes	phases
T8533	14313-14315	,	denotes	,
T8534	14315-14327	RB	denotes	respectively
T8535	14327-14328	.	denotes	.
T8536	14328-14496	sentence	denotes	When the lists of the differentially expressed genes at the four phases were merged and overlapping genes were excluded, 509 genes were identified (Additional file 1).
T8537	14329-14333	WRB	denotes	When
T8539	14334-14337	DT	denotes	the
T8540	14338-14343	NNS	denotes	lists
T8541	14344-14346	IN	denotes	of
T8542	14347-14350	DT	denotes	the
T8544	14351-14365	RB	denotes	differentially
T8545	14366-14375	VBN	denotes	expressed
T8543	14376-14381	NNS	denotes	genes
T8546	14382-14384	IN	denotes	at
T8547	14385-14388	DT	denotes	the
T8549	14389-14393	CD	denotes	four
T8548	14394-14400	NNS	denotes	phases
T8550	14401-14405	VBD	denotes	were
T8538	14406-14412	VBN	denotes	merged
T8552	14413-14416	CC	denotes	and
T8553	14417-14428	VBG	denotes	overlapping
T8554	14429-14434	NNS	denotes	genes
T8556	14435-14439	VBD	denotes	were
T8555	14440-14448	VBN	denotes	excluded
T8557	14448-14450	,	denotes	,
T8558	14450-14453	CD	denotes	509
T8559	14454-14459	NNS	denotes	genes
T8560	14460-14464	VBD	denotes	were
T8551	14465-14475	VBN	denotes	identified
T8561	14476-14477	-LRB-	denotes	(
T8563	14477-14487	JJ	denotes	Additional
T8562	14488-14492	NN	denotes	file
T8564	14493-14494	CD	denotes	1
T8565	14494-14495	-RRB-	denotes	)
T8566	14495-14496	.	denotes	.
T8567	14496-14596	sentence	denotes	Twenty-one genes consistently showed differential expression between the two strains at all phases.
T8568	14497-14503	CD	denotes	Twenty
T8570	14503-14504	HYPH	denotes	-
T8569	14504-14507	CD	denotes	one
T8571	14508-14513	NNS	denotes	genes
T8573	14514-14526	RB	denotes	consistently
T8572	14527-14533	VBD	denotes	showed
T8574	14534-14546	JJ	denotes	differential
T8575	14547-14557	NN	denotes	expression
T8576	14558-14565	IN	denotes	between
T8577	14566-14569	DT	denotes	the
T8579	14570-14573	CD	denotes	two
T8578	14574-14581	NNS	denotes	strains
T8580	14582-14584	IN	denotes	at
T8581	14585-14588	DT	denotes	all
T8582	14589-14595	NNS	denotes	phases
T8583	14595-14596	.	denotes	.
T8584	14596-14757	sentence	denotes	Besides these 21 genes, only 3 additional genes were strain-specific differentially expressed during the 3 phases after CIA induction (PI, OA and CA; Figure 1).
T8585	14597-14604	IN	denotes	Besides
T8587	14605-14610	DT	denotes	these
T8589	14611-14613	CD	denotes	21
T8588	14614-14619	NNS	denotes	genes
T8590	14619-14621	,	denotes	,
T8591	14621-14625	RB	denotes	only
T8593	14626-14627	CD	denotes	3
T8594	14628-14638	JJ	denotes	additional
T8592	14639-14644	NNS	denotes	genes
T8595	14645-14649	VBD	denotes	were
T8596	14650-14656	NN	denotes	strain
T8598	14656-14657	HYPH	denotes	-
T8597	14657-14665	RB	denotes	specific
T8599	14666-14680	RB	denotes	differentially
T8586	14681-14690	VBN	denotes	expressed
T8600	14691-14697	IN	denotes	during
T8601	14698-14701	DT	denotes	the
T8603	14702-14703	CD	denotes	3
T8602	14704-14710	NNS	denotes	phases
T8604	14711-14716	IN	denotes	after
T8605	14717-14720	NN	denotes	CIA
T8606	14721-14730	NN	denotes	induction
T8607	14731-14732	-LRB-	denotes	(
T8609	14732-14734	NN	denotes	PI
T8610	14734-14736	,	denotes	,
T8611	14736-14738	NN	denotes	OA
T8612	14739-14742	CC	denotes	and
T8613	14743-14745	NN	denotes	CA
T8614	14745-14746	:	denotes	;
T8608	14747-14753	NN	denotes	Figure
T8615	14754-14755	CD	denotes	1
T8616	14755-14756	-RRB-	denotes	)
T8617	14756-14757	.	denotes	.
T9552	14759-14766	NN	denotes	Disease
T9554	14766-14767	HYPH	denotes	-
T9553	14767-14775	JJ	denotes	specific
T9556	14776-14790	RB	denotes	differentially
T9557	14791-14800	VBN	denotes	expressed
T9555	14801-14806	NNS	denotes	genes
T9558	14806-14980	sentence	denotes	To identify the disease-specific differentially expressed genes in CIA, we detected the genes that were differentially expressed in LNs during CIA in the susceptible strain.
T9559	14807-14809	TO	denotes	To
T9560	14810-14818	VB	denotes	identify
T9562	14819-14822	DT	denotes	the
T9564	14823-14830	NN	denotes	disease
T9566	14830-14831	HYPH	denotes	-
T9565	14831-14839	JJ	denotes	specific
T9567	14840-14854	RB	denotes	differentially
T9568	14855-14864	VBN	denotes	expressed
T9563	14865-14870	NNS	denotes	genes
T9569	14871-14873	IN	denotes	in
T9570	14874-14877	NN	denotes	CIA
T9571	14877-14879	,	denotes	,
T9572	14879-14881	PRP	denotes	we
T9561	14882-14890	VBD	denotes	detected
T9573	14891-14894	DT	denotes	the
T9574	14895-14900	NNS	denotes	genes
T9575	14901-14905	WDT	denotes	that
T9577	14906-14910	VBD	denotes	were
T9578	14911-14925	RB	denotes	differentially
T9576	14926-14935	VBN	denotes	expressed
T9579	14936-14938	IN	denotes	in
T9580	14939-14942	NNS	denotes	LNs
T9581	14943-14949	IN	denotes	during
T9582	14950-14953	NN	denotes	CIA
T9583	14954-14956	IN	denotes	in
T9584	14957-14960	DT	denotes	the
T9586	14961-14972	JJ	denotes	susceptible
T9585	14973-14979	NN	denotes	strain
T9587	14979-14980	.	denotes	.
T9588	14980-15059	sentence	denotes	Three experimental conditions, PI, OA and CA, were compared with the NC group.
T9589	14981-14986	CD	denotes	Three
T9591	14987-14999	JJ	denotes	experimental
T9590	15000-15010	NNS	denotes	conditions
T9593	15010-15012	,	denotes	,
T9594	15012-15014	NN	denotes	PI
T9595	15014-15016	,	denotes	,
T9596	15016-15018	NN	denotes	OA
T9597	15019-15022	CC	denotes	and
T9598	15023-15025	NN	denotes	CA
T9599	15025-15027	,	denotes	,
T9600	15027-15031	VBD	denotes	were
T9592	15032-15040	VBN	denotes	compared
T9601	15041-15045	IN	denotes	with
T9602	15046-15049	DT	denotes	the
T9604	15050-15052	NN	denotes	NC
T9603	15053-15058	NN	denotes	group
T9605	15058-15059	.	denotes	.
T9606	15059-15265	sentence	denotes	On day 10 after immunisation, 102 genes were differentially expressed – most of them were upregulated (78 out of 102) – while at the onset phase of the disease, only 26 genes were differentially expressed.
T9607	15060-15062	IN	denotes	On
T9609	15063-15066	NN	denotes	day
T9610	15067-15069	CD	denotes	10
T9611	15070-15075	IN	denotes	after
T9612	15076-15088	NN	denotes	immunisation
T9613	15088-15090	,	denotes	,
T9614	15090-15093	CD	denotes	102
T9615	15094-15099	NNS	denotes	genes
T9617	15100-15104	VBD	denotes	were
T9618	15105-15119	RB	denotes	differentially
T9616	15120-15129	VBN	denotes	expressed
T9619	15130-15131	,	denotes	–
T9620	15132-15136	JJS	denotes	most
T9621	15137-15139	IN	denotes	of
T9622	15140-15144	PRP	denotes	them
T9623	15145-15149	VBD	denotes	were
T9608	15150-15161	VBN	denotes	upregulated
T9624	15162-15163	-LRB-	denotes	(
T9626	15163-15165	CD	denotes	78
T9627	15166-15169	IN	denotes	out
T9628	15170-15172	IN	denotes	of
T9625	15173-15176	CD	denotes	102
T9629	15176-15177	-RRB-	denotes	)
T9630	15178-15179	,	denotes	–
T9631	15180-15185	IN	denotes	while
T9633	15186-15188	IN	denotes	at
T9634	15189-15192	DT	denotes	the
T9636	15193-15198	NN	denotes	onset
T9635	15199-15204	NN	denotes	phase
T9637	15205-15207	IN	denotes	of
T9638	15208-15211	DT	denotes	the
T9639	15212-15219	NN	denotes	disease
T9640	15219-15221	,	denotes	,
T9641	15221-15225	RB	denotes	only
T9643	15226-15228	CD	denotes	26
T9642	15229-15234	NNS	denotes	genes
T9644	15235-15239	VBD	denotes	were
T9645	15240-15254	RB	denotes	differentially
T9632	15255-15264	VBN	denotes	expressed
T9646	15264-15265	.	denotes	.
T9647	15265-15384	sentence	denotes	At the chronic phase of the disease, 184 differentially expressed genes were identified, with 156 downregulated genes.
T9648	15266-15268	IN	denotes	At
T9650	15269-15272	DT	denotes	the
T9652	15273-15280	JJ	denotes	chronic
T9651	15281-15286	NN	denotes	phase
T9653	15287-15289	IN	denotes	of
T9654	15290-15293	DT	denotes	the
T9655	15294-15301	NN	denotes	disease
T9656	15301-15303	,	denotes	,
T9657	15303-15306	CD	denotes	184
T9659	15307-15321	RB	denotes	differentially
T9660	15322-15331	VBN	denotes	expressed
T9658	15332-15337	NNS	denotes	genes
T9661	15338-15342	VBD	denotes	were
T9649	15343-15353	VBN	denotes	identified
T9662	15353-15355	,	denotes	,
T9663	15355-15359	IN	denotes	with
T9664	15360-15363	CD	denotes	156
T9666	15364-15377	VBN	denotes	downregulated
T9665	15378-15383	NNS	denotes	genes
T9667	15383-15384	.	denotes	.
T9668	15384-15455	sentence	denotes	Only one gene was differentially expressed at all three phases of CIA.
T9669	15385-15389	RB	denotes	Only
T9671	15390-15393	CD	denotes	one
T9670	15394-15398	NN	denotes	gene
T9673	15399-15402	VBD	denotes	was
T9674	15403-15417	RB	denotes	differentially
T9672	15418-15427	VBN	denotes	expressed
T9675	15428-15430	IN	denotes	at
T9676	15431-15434	DT	denotes	all
T9678	15435-15440	CD	denotes	three
T9677	15441-15447	NNS	denotes	phases
T9679	15448-15450	IN	denotes	of
T9680	15451-15454	NN	denotes	CIA
T9681	15454-15455	.	denotes	.
T9682	15455-15603	sentence	denotes	Besides this gene, five, one and six differentially expressed genes were shared by PI with OA, PI with CA and OA with CA, respectively (Figure 2a).
T9683	15456-15463	IN	denotes	Besides
T9685	15464-15468	DT	denotes	this
T9686	15469-15473	NN	denotes	gene
T9687	15473-15475	,	denotes	,
T9688	15475-15479	CD	denotes	five
T9690	15479-15481	,	denotes	,
T9691	15481-15484	CD	denotes	one
T9692	15485-15488	CC	denotes	and
T9693	15489-15492	CD	denotes	six
T9694	15493-15507	RB	denotes	differentially
T9695	15508-15517	VBN	denotes	expressed
T9689	15518-15523	NNS	denotes	genes
T9696	15524-15528	VBD	denotes	were
T9684	15529-15535	VBN	denotes	shared
T9697	15536-15538	IN	denotes	by
T9698	15539-15541	NN	denotes	PI
T9699	15542-15546	IN	denotes	with
T9700	15547-15549	NN	denotes	OA
T9701	15549-15551	,	denotes	,
T9702	15551-15553	NN	denotes	PI
T9703	15554-15558	IN	denotes	with
T9704	15559-15561	NN	denotes	CA
T9705	15562-15565	CC	denotes	and
T9706	15566-15568	NN	denotes	OA
T9707	15569-15573	IN	denotes	with
T9708	15574-15576	NN	denotes	CA
T9709	15576-15578	,	denotes	,
T9710	15578-15590	RB	denotes	respectively
T9711	15591-15592	-LRB-	denotes	(
T9713	15592-15598	NN	denotes	Figure
T9712	15599-15601	NN	denotes	2a
T9714	15601-15602	-RRB-	denotes	)
T9715	15602-15603	.	denotes	.
T9716	15603-15747	sentence	denotes	Taken together, 310 disease-specific differentially expressed genes were differentially regulated during CIA in DBA/1 mice (Additional file 2).
T9717	15604-15609	VBN	denotes	Taken
T9719	15610-15618	RB	denotes	together
T9720	15618-15620	,	denotes	,
T9721	15620-15623	CD	denotes	310
T9723	15624-15631	NN	denotes	disease
T9725	15631-15632	HYPH	denotes	-
T9724	15632-15640	JJ	denotes	specific
T9726	15641-15655	RB	denotes	differentially
T9727	15656-15665	VBN	denotes	expressed
T9722	15666-15671	NNS	denotes	genes
T9728	15672-15676	VBD	denotes	were
T9729	15677-15691	RB	denotes	differentially
T9718	15692-15701	VBN	denotes	regulated
T9730	15702-15708	IN	denotes	during
T9731	15709-15712	NN	denotes	CIA
T9732	15713-15715	IN	denotes	in
T9733	15716-15719	NN	denotes	DBA
T9735	15719-15720	HYPH	denotes	/
T9736	15720-15721	CD	denotes	1
T9734	15722-15726	NNS	denotes	mice
T9737	15727-15728	-LRB-	denotes	(
T9739	15728-15738	JJ	denotes	Additional
T9738	15739-15743	NN	denotes	file
T9740	15744-15745	CD	denotes	2
T9741	15745-15746	-RRB-	denotes	)
T9742	15746-15747	.	denotes	.
T9743	15747-15875	sentence	denotes	To further characterise the gene expression pattern during CIA, we performed hierarchical cluster analysis for these 310 genes.
T9744	15748-15750	TO	denotes	To
T9746	15751-15758	RB	denotes	further
T9745	15759-15771	VB	denotes	characterise
T9748	15772-15775	DT	denotes	the
T9750	15776-15780	NN	denotes	gene
T9751	15781-15791	NN	denotes	expression
T9749	15792-15799	NN	denotes	pattern
T9752	15800-15806	IN	denotes	during
T9753	15807-15810	NN	denotes	CIA
T9754	15810-15812	,	denotes	,
T9755	15812-15814	PRP	denotes	we
T9747	15815-15824	VBD	denotes	performed
T9756	15825-15837	JJ	denotes	hierarchical
T9758	15838-15845	NN	denotes	cluster
T9757	15846-15854	NN	denotes	analysis
T9759	15855-15858	IN	denotes	for
T9760	15859-15864	DT	denotes	these
T9762	15865-15868	CD	denotes	310
T9761	15869-15874	NNS	denotes	genes
T9763	15874-15875	.	denotes	.
T9764	15875-15997	sentence	denotes	Six gene clusters were identified (clusters I to VI, Figure 2b), each with a distinct gene expression pattern during CIA.
T9765	15876-15879	CD	denotes	Six
T9767	15880-15884	NN	denotes	gene
T9766	15885-15893	NNS	denotes	clusters
T9769	15894-15898	VBD	denotes	were
T9768	15899-15909	VBN	denotes	identified
T9770	15910-15911	-LRB-	denotes	(
T9772	15911-15919	NNS	denotes	clusters
T9771	15920-15921	CD	denotes	I
T9773	15922-15924	IN	denotes	to
T9774	15925-15927	CD	denotes	VI
T9775	15927-15929	,	denotes	,
T9776	15929-15935	NN	denotes	Figure
T9777	15936-15938	NN	denotes	2b
T9778	15938-15939	-RRB-	denotes	)
T9779	15939-15941	,	denotes	,
T9780	15941-15945	DT	denotes	each
T9781	15946-15950	IN	denotes	with
T9782	15951-15952	DT	denotes	a
T9784	15953-15961	JJ	denotes	distinct
T9785	15962-15966	NN	denotes	gene
T9786	15967-15977	NN	denotes	expression
T9783	15978-15985	NN	denotes	pattern
T9787	15986-15992	IN	denotes	during
T9788	15993-15996	NN	denotes	CIA
T9789	15996-15997	.	denotes	.
T9790	15997-16091	sentence	denotes	Cluster I contains 16 genes, representing genes that were upregulated after induction of CIA.
T9791	15998-16005	NN	denotes	Cluster
T9793	16006-16007	CD	denotes	I
T9792	16008-16016	VBZ	denotes	contains
T9794	16017-16019	CD	denotes	16
T9795	16020-16025	NNS	denotes	genes
T9796	16025-16027	,	denotes	,
T9797	16027-16039	VBG	denotes	representing
T9798	16040-16045	NNS	denotes	genes
T9799	16046-16050	WDT	denotes	that
T9801	16051-16055	VBD	denotes	were
T9800	16056-16067	VBN	denotes	upregulated
T9802	16068-16073	IN	denotes	after
T9803	16074-16083	NN	denotes	induction
T9804	16084-16086	IN	denotes	of
T9805	16087-16090	NN	denotes	CIA
T9806	16090-16091	.	denotes	.
T9807	16091-16259	sentence	denotes	The expression of these genes reached a peak at the onset phase of the disease and functional clustering results revealed that they are related to the immune response.
T9808	16092-16095	DT	denotes	The
T9809	16096-16106	NN	denotes	expression
T9811	16107-16109	IN	denotes	of
T9812	16110-16115	DT	denotes	these
T9813	16116-16121	NNS	denotes	genes
T9810	16122-16129	VBD	denotes	reached
T9814	16130-16131	DT	denotes	a
T9815	16132-16136	NN	denotes	peak
T9816	16137-16139	IN	denotes	at
T9817	16140-16143	DT	denotes	the
T9819	16144-16149	NN	denotes	onset
T9818	16150-16155	NN	denotes	phase
T9820	16156-16158	IN	denotes	of
T9821	16159-16162	DT	denotes	the
T9822	16163-16170	NN	denotes	disease
T9823	16171-16174	CC	denotes	and
T9824	16175-16185	JJ	denotes	functional
T9826	16186-16196	NN	denotes	clustering
T9825	16197-16204	NNS	denotes	results
T9827	16205-16213	VBD	denotes	revealed
T9828	16214-16218	IN	denotes	that
T9830	16219-16223	PRP	denotes	they
T9831	16224-16227	VBP	denotes	are
T9829	16228-16235	VBN	denotes	related
T9832	16236-16238	IN	denotes	to
T9833	16239-16242	DT	denotes	the
T9835	16243-16249	JJ	denotes	immune
T9834	16250-16258	NN	denotes	response
T9836	16258-16259	.	denotes	.
T9837	16259-16379	sentence	denotes	Cluster II contains 12 genes whose expression was gradually upregulated and reached a peak at the chronic phase of CIA.
T9838	16260-16267	NN	denotes	Cluster
T9840	16268-16270	CD	denotes	II
T9839	16271-16279	VBZ	denotes	contains
T9841	16280-16282	CD	denotes	12
T9842	16283-16288	NNS	denotes	genes
T9843	16289-16294	WP$	denotes	whose
T9844	16295-16305	NN	denotes	expression
T9846	16306-16309	VBD	denotes	was
T9847	16310-16319	RB	denotes	gradually
T9845	16320-16331	VBN	denotes	upregulated
T9848	16332-16335	CC	denotes	and
T9849	16336-16343	VBN	denotes	reached
T9850	16344-16345	DT	denotes	a
T9851	16346-16350	NN	denotes	peak
T9852	16351-16353	IN	denotes	at
T9853	16354-16357	DT	denotes	the
T9855	16358-16365	JJ	denotes	chronic
T9854	16366-16371	NN	denotes	phase
T9856	16372-16374	IN	denotes	of
T9857	16375-16378	NN	denotes	CIA
T9858	16378-16379	.	denotes	.
T9859	16379-16489	sentence	denotes	These genes are mainly related to the immune response, organelle membrane and extracellular region and space.
T9860	16380-16385	DT	denotes	These
T9861	16386-16391	NNS	denotes	genes
T9863	16392-16395	VBP	denotes	are
T9864	16396-16402	RB	denotes	mainly
T9862	16403-16410	VBN	denotes	related
T9865	16411-16413	IN	denotes	to
T9866	16414-16417	DT	denotes	the
T9868	16418-16424	JJ	denotes	immune
T9867	16425-16433	NN	denotes	response
T9869	16433-16435	,	denotes	,
T9870	16435-16444	NN	denotes	organelle
T9871	16445-16453	NN	denotes	membrane
T9872	16454-16457	CC	denotes	and
T9873	16458-16471	JJ	denotes	extracellular
T9874	16472-16478	NN	denotes	region
T9875	16479-16482	CC	denotes	and
T9876	16483-16488	NN	denotes	space
T9877	16488-16489	.	denotes	.
T9878	16489-16563	sentence	denotes	Cluster III contains 78 genes that were only upregulated at the PI phase.
T9879	16490-16497	NN	denotes	Cluster
T9881	16498-16501	CD	denotes	III
T9880	16502-16510	VBZ	denotes	contains
T9882	16511-16513	CD	denotes	78
T9883	16514-16519	NNS	denotes	genes
T9884	16520-16524	WDT	denotes	that
T9886	16525-16529	VBD	denotes	were
T9887	16530-16534	RB	denotes	only
T9885	16535-16546	VBN	denotes	upregulated
T9888	16547-16549	IN	denotes	at
T9889	16550-16553	DT	denotes	the
T9891	16554-16556	NN	denotes	PI
T9890	16557-16562	NN	denotes	phase
T9892	16562-16563	.	denotes	.
T9893	16563-16618	sentence	denotes	These genes are related to the intercellular junction.
T9894	16564-16569	DT	denotes	These
T9895	16570-16575	NNS	denotes	genes
T9897	16576-16579	VBP	denotes	are
T9896	16580-16587	VBN	denotes	related
T9898	16588-16590	IN	denotes	to
T9899	16591-16594	DT	denotes	the
T9901	16595-16608	JJ	denotes	intercellular
T9900	16609-16617	NN	denotes	junction
T9902	16617-16618	.	denotes	.
T9903	16618-16749	sentence	denotes	More than half of the genes (156 of 310) belong to cluster IV and represent genes specifically downregultaed at the chronic phase.
T9904	16619-16623	JJR	denotes	More
T9906	16624-16628	IN	denotes	than
T9905	16629-16633	NN	denotes	half
T9908	16634-16636	IN	denotes	of
T9909	16637-16640	DT	denotes	the
T9910	16641-16646	NNS	denotes	genes
T9911	16647-16648	-LRB-	denotes	(
T9913	16648-16651	CD	denotes	156
T9914	16652-16654	IN	denotes	of
T9912	16655-16658	CD	denotes	310
T9915	16658-16659	-RRB-	denotes	)
T9907	16660-16666	VBP	denotes	belong
T9916	16667-16669	IN	denotes	to
T9917	16670-16677	NN	denotes	cluster
T9918	16678-16680	CD	denotes	IV
T9919	16681-16684	CC	denotes	and
T9920	16685-16694	VBP	denotes	represent
T9921	16695-16700	NNS	denotes	genes
T9922	16701-16713	RB	denotes	specifically
T9923	16714-16727	VBN	denotes	downregultaed
T9924	16728-16730	IN	denotes	at
T9925	16731-16734	DT	denotes	the
T9927	16735-16742	JJ	denotes	chronic
T9926	16743-16748	NN	denotes	phase
T9928	16748-16749	.	denotes	.
T9929	16749-16887	sentence	denotes	These genes are functionally related to lymphocyte proliferation, T cell activation, protein binding as well as the notch signal pathway.
T9930	16750-16755	DT	denotes	These
T9931	16756-16761	NNS	denotes	genes
T9933	16762-16765	VBP	denotes	are
T9934	16766-16778	RB	denotes	functionally
T9932	16779-16786	VBN	denotes	related
T9935	16787-16789	IN	denotes	to
T9936	16790-16800	NN	denotes	lymphocyte
T9937	16801-16814	NN	denotes	proliferation
T9938	16814-16816	,	denotes	,
T9939	16816-16817	NN	denotes	T
T9940	16818-16822	NN	denotes	cell
T9941	16823-16833	NN	denotes	activation
T9942	16833-16835	,	denotes	,
T9943	16835-16842	NN	denotes	protein
T9944	16843-16850	NN	denotes	binding
T9945	16851-16853	RB	denotes	as
T9947	16854-16858	RB	denotes	well
T9946	16859-16861	IN	denotes	as
T9948	16862-16865	DT	denotes	the
T9950	16866-16871	NN	denotes	notch
T9951	16872-16878	NN	denotes	signal
T9949	16879-16886	NN	denotes	pathway
T9952	16886-16887	.	denotes	.
T9953	16887-16949	sentence	denotes	Cluster V contains eight genes downregulated at the PI phase.
T9954	16888-16895	NN	denotes	Cluster
T9956	16896-16897	CD	denotes	V
T9955	16898-16906	VBZ	denotes	contains
T9957	16907-16912	CD	denotes	eight
T9958	16913-16918	NNS	denotes	genes
T9959	16919-16932	VBN	denotes	downregulated
T9960	16933-16935	IN	denotes	at
T9961	16936-16939	DT	denotes	the
T9963	16940-16942	NN	denotes	PI
T9962	16943-16948	NN	denotes	phase
T9964	16948-16949	.	denotes	.
T9965	16949-17009	sentence	denotes	Cluster VI contains 18 genes downregulated at the OA phase.
T9966	16950-16957	NN	denotes	Cluster
T9968	16958-16960	CD	denotes	VI
T9967	16961-16969	VBZ	denotes	contains
T9969	16970-16972	CD	denotes	18
T9970	16973-16978	NNS	denotes	genes
T9971	16979-16992	VBN	denotes	downregulated
T9972	16993-16995	IN	denotes	at
T9973	16996-16999	DT	denotes	the
T9975	17000-17002	NN	denotes	OA
T9974	17003-17008	NN	denotes	phase
T9976	17008-17009	.	denotes	.
T9977	17009-17125	sentence	denotes	The GO term classification showed no functional cluster that was significantly enriched in these two gene clusters.
T9978	17010-17013	DT	denotes	The
T9980	17014-17016	NN	denotes	GO
T9981	17017-17021	NN	denotes	term
T9979	17022-17036	NN	denotes	classification
T9982	17037-17043	VBD	denotes	showed
T9983	17044-17046	DT	denotes	no
T9985	17047-17057	JJ	denotes	functional
T9984	17058-17065	NN	denotes	cluster
T9986	17066-17070	WDT	denotes	that
T9988	17071-17074	VBD	denotes	was
T9989	17075-17088	RB	denotes	significantly
T9987	17089-17097	VBN	denotes	enriched
T9990	17098-17100	IN	denotes	in
T9991	17101-17106	DT	denotes	these
T9993	17107-17110	CD	denotes	two
T9994	17111-17115	NN	denotes	gene
T9992	17116-17124	NNS	denotes	clusters
T9995	17124-17125	.	denotes	.
T10781	17127-17136	NN	denotes	Candidate
T10782	17137-17142	NNS	denotes	genes
T10783	17143-17146	IN	denotes	for
T10784	17147-17150	DT	denotes	the
T10786	17151-17156	JJ	denotes	small
T10788	17156-17157	HYPH	denotes	-
T10787	17157-17163	NN	denotes	effect
T10785	17164-17167	NNS	denotes	QTL
T10789	17168-17170	IN	denotes	of
T10790	17171-17174	NN	denotes	CIA
T10791	17174-17441	sentence	denotes	To identify candidate susceptibility genes for the CIA small-effect QTL, we compared the list of strain-specific differentially expressed genes with the list of disease-specific differentially expressed genes; 117 genes were shared by both lists (Additional file 3).
T10792	17175-17177	TO	denotes	To
T10793	17178-17186	VB	denotes	identify
T10795	17187-17196	NN	denotes	candidate
T10797	17197-17211	NN	denotes	susceptibility
T10796	17212-17217	NNS	denotes	genes
T10798	17218-17221	IN	denotes	for
T10799	17222-17225	DT	denotes	the
T10801	17226-17229	NN	denotes	CIA
T10802	17230-17235	JJ	denotes	small
T10804	17235-17236	HYPH	denotes	-
T10803	17236-17242	NN	denotes	effect
T10800	17243-17246	NNS	denotes	QTL
T10805	17246-17248	,	denotes	,
T10806	17248-17250	PRP	denotes	we
T10794	17251-17259	VBD	denotes	compared
T10808	17260-17263	DT	denotes	the
T10809	17264-17268	NN	denotes	list
T10810	17269-17271	IN	denotes	of
T10811	17272-17278	NN	denotes	strain
T10813	17278-17279	HYPH	denotes	-
T10812	17279-17287	JJ	denotes	specific
T10815	17288-17302	RB	denotes	differentially
T10816	17303-17312	VBN	denotes	expressed
T10814	17313-17318	NNS	denotes	genes
T10817	17319-17323	IN	denotes	with
T10818	17324-17327	DT	denotes	the
T10819	17328-17332	NN	denotes	list
T10820	17333-17335	IN	denotes	of
T10821	17336-17343	NN	denotes	disease
T10823	17343-17344	HYPH	denotes	-
T10822	17344-17352	JJ	denotes	specific
T10825	17353-17367	RB	denotes	differentially
T10826	17368-17377	VBN	denotes	expressed
T10824	17378-17383	NNS	denotes	genes
T10827	17383-17384	:	denotes	;
T10828	17385-17388	CD	denotes	117
T10829	17389-17394	NNS	denotes	genes
T10830	17395-17399	VBD	denotes	were
T10807	17400-17406	VBN	denotes	shared
T10831	17407-17409	IN	denotes	by
T10832	17410-17414	DT	denotes	both
T10833	17415-17420	NNS	denotes	lists
T10834	17421-17422	-LRB-	denotes	(
T10836	17422-17432	JJ	denotes	Additional
T10835	17433-17437	NN	denotes	file
T10837	17438-17439	CD	denotes	3
T10838	17439-17440	-RRB-	denotes	)
T10839	17440-17441	.	denotes	.
T10840	17441-17555	sentence	denotes	Figure 3 visualises positions of the 117 genes retrieved from Ensembl [30] in relation to the 8 small-effect QTL.
T10841	17442-17448	NN	denotes	Figure
T10843	17449-17450	CD	denotes	3
T10842	17451-17461	VBZ	denotes	visualises
T10844	17462-17471	NNS	denotes	positions
T10845	17472-17474	IN	denotes	of
T10846	17475-17478	DT	denotes	the
T10848	17479-17482	CD	denotes	117
T10847	17483-17488	NNS	denotes	genes
T10849	17489-17498	VBN	denotes	retrieved
T10850	17499-17503	IN	denotes	from
T10851	17504-17511	NNP	denotes	Ensembl
T10852	17512-17513	-LRB-	denotes	[
T10853	17513-17515	CD	denotes	30
T10854	17515-17516	-RRB-	denotes	]
T10855	17517-17519	IN	denotes	in
T10856	17520-17528	NN	denotes	relation
T10857	17529-17531	IN	denotes	to
T10858	17532-17535	DT	denotes	the
T10860	17536-17537	CD	denotes	8
T10861	17538-17543	JJ	denotes	small
T10863	17543-17544	HYPH	denotes	-
T10862	17544-17550	NN	denotes	effect
T10859	17551-17554	NNS	denotes	QTL
T10864	17554-17555	.	denotes	.
T10865	17555-17629	sentence	denotes	The eight loci were located on 7 chromosomes, 5, 6, 7, 10, 11, 16 and 17.
T10866	17556-17559	DT	denotes	The
T10868	17560-17565	CD	denotes	eight
T10867	17566-17570	NNS	denotes	loci
T10870	17571-17575	VBD	denotes	were
T10869	17576-17583	VBN	denotes	located
T10871	17584-17586	IN	denotes	on
T10872	17587-17588	CD	denotes	7
T10873	17589-17600	NNS	denotes	chromosomes
T10874	17600-17602	,	denotes	,
T10875	17602-17603	CD	denotes	5
T10876	17603-17605	,	denotes	,
T10877	17605-17606	CD	denotes	6
T10878	17606-17608	,	denotes	,
T10879	17608-17609	CD	denotes	7
T10880	17609-17611	,	denotes	,
T10881	17611-17613	CD	denotes	10
T10882	17613-17615	,	denotes	,
T10883	17615-17617	CD	denotes	11
T10884	17617-17619	,	denotes	,
T10885	17619-17621	CD	denotes	16
T10886	17622-17625	CC	denotes	and
T10887	17626-17628	CD	denotes	17
T10888	17628-17629	.	denotes	.
T10889	17629-17760	sentence	denotes	Since the confidence intervals of QTL in F2 progeny are around 20 cM [26], we used 40 Mb as the confidence intervals for all loci.
T10890	17630-17635	IN	denotes	Since
T10892	17636-17639	DT	denotes	the
T10894	17640-17650	NN	denotes	confidence
T10893	17651-17660	NNS	denotes	intervals
T10895	17661-17663	IN	denotes	of
T10896	17664-17667	NNS	denotes	QTL
T10897	17668-17670	IN	denotes	in
T10898	17671-17673	NN	denotes	F2
T10899	17674-17681	NN	denotes	progeny
T10891	17682-17685	VBP	denotes	are
T10901	17686-17692	IN	denotes	around
T10902	17693-17695	CD	denotes	20
T10903	17696-17698	NN	denotes	cM
T10904	17699-17700	-LRB-	denotes	[
T10905	17700-17702	CD	denotes	26
T10906	17702-17703	-RRB-	denotes	]
T10907	17703-17705	,	denotes	,
T10908	17705-17707	PRP	denotes	we
T10900	17708-17712	VBD	denotes	used
T10909	17713-17715	CD	denotes	40
T10910	17716-17718	NN	denotes	Mb
T10911	17719-17721	IN	denotes	as
T10912	17722-17725	DT	denotes	the
T10914	17726-17736	NN	denotes	confidence
T10913	17737-17746	NNS	denotes	intervals
T10915	17747-17750	IN	denotes	for
T10916	17751-17754	DT	denotes	all
T10917	17755-17759	NNS	denotes	loci
T10918	17759-17760	.	denotes	.
T10919	17760-17843	sentence	denotes	Twenty-one genes were located in the confidence intervals of six of the eight QTL.
T10920	17761-17767	CD	denotes	Twenty
T10922	17767-17768	HYPH	denotes	-
T10921	17768-17771	CD	denotes	one
T10923	17772-17777	NNS	denotes	genes
T10925	17778-17782	VBD	denotes	were
T10924	17783-17790	VBN	denotes	located
T10926	17791-17793	IN	denotes	in
T10927	17794-17797	DT	denotes	the
T10929	17798-17808	NN	denotes	confidence
T10928	17809-17818	NNS	denotes	intervals
T10930	17819-17821	IN	denotes	of
T10931	17822-17825	CD	denotes	six
T10933	17826-17828	IN	denotes	of
T10934	17829-17832	DT	denotes	the
T10932	17833-17838	CD	denotes	eight
T10935	17839-17842	NNS	denotes	QTL
T10936	17842-17843	.	denotes	.
T10937	17843-18032	sentence	denotes	We located 5, 4, 2, 1, 3 and 6 potential candidate genes within the confidence intervals of loci 1, 2, 3, 5, 6 and 8, respectively, while no candidate gene was identified for loci 4 and 7.
T10938	17844-17846	PRP	denotes	We
T10939	17847-17854	VBD	denotes	located
T10940	17855-17856	CD	denotes	5
T10942	17856-17858	,	denotes	,
T10943	17858-17859	CD	denotes	4
T10944	17859-17861	,	denotes	,
T10945	17861-17862	CD	denotes	2
T10946	17862-17864	,	denotes	,
T10947	17864-17865	CD	denotes	1
T10948	17865-17867	,	denotes	,
T10949	17867-17868	CD	denotes	3
T10950	17869-17872	CC	denotes	and
T10951	17873-17874	CD	denotes	6
T10952	17875-17884	JJ	denotes	potential
T10953	17885-17894	NN	denotes	candidate
T10941	17895-17900	NNS	denotes	genes
T10954	17901-17907	IN	denotes	within
T10955	17908-17911	DT	denotes	the
T10957	17912-17922	NN	denotes	confidence
T10956	17923-17932	NNS	denotes	intervals
T10958	17933-17935	IN	denotes	of
T10959	17936-17940	NNS	denotes	loci
T10960	17941-17942	CD	denotes	1
T10961	17942-17944	,	denotes	,
T10962	17944-17945	CD	denotes	2
T10963	17945-17947	,	denotes	,
T10964	17947-17948	CD	denotes	3
T10965	17948-17950	,	denotes	,
T10966	17950-17951	CD	denotes	5
T10967	17951-17953	,	denotes	,
T10968	17953-17954	CD	denotes	6
T10969	17955-17958	CC	denotes	and
T10970	17959-17960	CD	denotes	8
T10971	17960-17962	,	denotes	,
T10972	17962-17974	RB	denotes	respectively
T10973	17974-17976	,	denotes	,
T10974	17976-17981	IN	denotes	while
T10976	17982-17984	DT	denotes	no
T10978	17985-17994	NN	denotes	candidate
T10977	17995-17999	NN	denotes	gene
T10979	18000-18003	VBD	denotes	was
T10975	18004-18014	VBN	denotes	identified
T10980	18015-18018	IN	denotes	for
T10981	18019-18023	NNS	denotes	loci
T10982	18024-18025	CD	denotes	4
T10983	18026-18029	CC	denotes	and
T10984	18030-18031	CD	denotes	7
T10985	18031-18032	.	denotes	.
T10986	18032-18100	sentence	denotes	Table 3 summarises the 21 candidate genes identified in this study.
T10987	18033-18038	NN	denotes	Table
T10989	18039-18040	CD	denotes	3
T10988	18041-18051	VBZ	denotes	summarises
T10990	18052-18055	DT	denotes	the
T10992	18056-18058	CD	denotes	21
T10993	18059-18068	NN	denotes	candidate
T10991	18069-18074	NNS	denotes	genes
T10994	18075-18085	VBN	denotes	identified
T10995	18086-18088	IN	denotes	in
T10996	18089-18093	DT	denotes	this
T10997	18094-18099	NN	denotes	study
T10998	18099-18100	.	denotes	.
T10999	18100-18217	sentence	denotes	Two genes, hspa1a and Oas1a, were upregulated at the OA phase of CIA and Oas1a was also upregulated at the PI phase.
T11000	18101-18104	CD	denotes	Two
T11001	18105-18110	NNS	denotes	genes
T11003	18110-18112	,	denotes	,
T11004	18112-18118	NN	denotes	hspa1a
T11005	18119-18122	CC	denotes	and
T11006	18123-18128	NN	denotes	Oas1a
T11007	18128-18130	,	denotes	,
T11008	18130-18134	VBD	denotes	were
T11002	18135-18146	VBN	denotes	upregulated
T11009	18147-18149	IN	denotes	at
T11010	18150-18153	DT	denotes	the
T11012	18154-18156	NN	denotes	OA
T11011	18157-18162	NN	denotes	phase
T11013	18163-18165	IN	denotes	of
T11014	18166-18169	NN	denotes	CIA
T11015	18170-18173	CC	denotes	and
T11016	18174-18179	NN	denotes	Oas1a
T11018	18180-18183	VBD	denotes	was
T11019	18184-18188	RB	denotes	also
T11017	18189-18200	VBN	denotes	upregulated
T11020	18201-18203	IN	denotes	at
T11021	18204-18207	DT	denotes	the
T11023	18208-18210	NN	denotes	PI
T11022	18211-18216	NN	denotes	phase
T11024	18216-18217	.	denotes	.
T11025	18217-18312	sentence	denotes	Except for these two genes, all other 19 genes were downregulated at the chronic phase of CIA.
T11026	18218-18224	IN	denotes	Except
T11028	18225-18228	IN	denotes	for
T11029	18229-18234	DT	denotes	these
T11031	18235-18238	CD	denotes	two
T11030	18239-18244	NNS	denotes	genes
T11032	18244-18246	,	denotes	,
T11033	18246-18249	DT	denotes	all
T11035	18250-18255	JJ	denotes	other
T11036	18256-18258	CD	denotes	19
T11034	18259-18264	NNS	denotes	genes
T11037	18265-18269	VBD	denotes	were
T11027	18270-18283	VBN	denotes	downregulated
T11038	18284-18286	IN	denotes	at
T11039	18287-18290	DT	denotes	the
T11041	18291-18298	JJ	denotes	chronic
T11040	18299-18304	NN	denotes	phase
T11042	18305-18307	IN	denotes	of
T11043	18308-18311	NN	denotes	CIA
T11044	18311-18312	.	denotes	.
T11045	18312-18409	sentence	denotes	All genes, except hspa1a, showed expression differences between the two strains at the NC phase.
T11046	18313-18316	DT	denotes	All
T11047	18317-18322	NNS	denotes	genes
T11049	18322-18324	,	denotes	,
T11050	18324-18330	IN	denotes	except
T11051	18331-18337	NN	denotes	hspa1a
T11052	18337-18339	,	denotes	,
T11048	18339-18345	VBD	denotes	showed
T11053	18346-18356	NN	denotes	expression
T11054	18357-18368	NNS	denotes	differences
T11055	18369-18376	IN	denotes	between
T11056	18377-18380	DT	denotes	the
T11058	18381-18384	CD	denotes	two
T11057	18385-18392	NNS	denotes	strains
T11059	18393-18395	IN	denotes	at
T11060	18396-18399	DT	denotes	the
T11062	18400-18402	NN	denotes	NC
T11061	18403-18408	NN	denotes	phase
T11063	18408-18409	.	denotes	.
T11064	18409-18521	sentence	denotes	Five genes were differentially expressed at all phases of CIA, including H2-Q10, Mapk14, Pscd1, Kpnb1 and Wdr1.
T11065	18410-18414	CD	denotes	Five
T11066	18415-18420	NNS	denotes	genes
T11068	18421-18425	VBD	denotes	were
T11069	18426-18440	RB	denotes	differentially
T11067	18441-18450	VBN	denotes	expressed
T11070	18451-18453	IN	denotes	at
T11071	18454-18457	DT	denotes	all
T11072	18458-18464	NNS	denotes	phases
T11073	18465-18467	IN	denotes	of
T11074	18468-18471	NN	denotes	CIA
T11075	18471-18473	,	denotes	,
T11076	18473-18482	VBG	denotes	including
T11077	18483-18485	NN	denotes	H2
T11079	18485-18486	HYPH	denotes	-
T11078	18486-18489	NN	denotes	Q10
T11080	18489-18491	,	denotes	,
T11081	18491-18497	NN	denotes	Mapk14
T11082	18497-18499	,	denotes	,
T11083	18499-18504	NN	denotes	Pscd1
T11084	18504-18506	,	denotes	,
T11085	18506-18511	NN	denotes	Kpnb1
T11086	18512-18515	CC	denotes	and
T11087	18516-18520	NN	denotes	Wdr1
T11088	18520-18521	.	denotes	.
T11089	18521-18805	sentence	denotes	Among these five genes, H2-Q10 had a consistently higher expression in the DBA/1 than the FVB/N strain in all CIA phases, while the other four genes had a higher expression in the DBA/1 strain at the early stages, including NC, PI and OA, but a lower expression at the chronic phase.
T11090	18522-18527	IN	denotes	Among
T11092	18528-18533	DT	denotes	these
T11094	18534-18538	CD	denotes	five
T11093	18539-18544	NNS	denotes	genes
T11095	18544-18546	,	denotes	,
T11096	18546-18548	NN	denotes	H2
T11098	18548-18549	HYPH	denotes	-
T11097	18549-18552	NN	denotes	Q10
T11091	18553-18556	VBD	denotes	had
T11099	18557-18558	DT	denotes	a
T11101	18559-18571	RB	denotes	consistently
T11102	18572-18578	JJR	denotes	higher
T11100	18579-18589	NN	denotes	expression
T11103	18590-18592	IN	denotes	in
T11104	18593-18596	DT	denotes	the
T11105	18597-18600	NN	denotes	DBA
T11106	18600-18601	HYPH	denotes	/
T11107	18601-18602	CD	denotes	1
T11108	18603-18607	IN	denotes	than
T11109	18608-18611	DT	denotes	the
T11111	18612-18615	NN	denotes	FVB
T11113	18615-18616	HYPH	denotes	/
T11112	18616-18617	NN	denotes	N
T11110	18618-18624	NN	denotes	strain
T11114	18625-18627	IN	denotes	in
T11115	18628-18631	DT	denotes	all
T11117	18632-18635	NN	denotes	CIA
T11116	18636-18642	NNS	denotes	phases
T11118	18642-18644	,	denotes	,
T11119	18644-18649	IN	denotes	while
T11121	18650-18653	DT	denotes	the
T11123	18654-18659	JJ	denotes	other
T11124	18660-18664	CD	denotes	four
T11122	18665-18670	NNS	denotes	genes
T11120	18671-18674	VBD	denotes	had
T11125	18675-18676	DT	denotes	a
T11127	18677-18683	JJR	denotes	higher
T11126	18684-18694	NN	denotes	expression
T11128	18695-18697	IN	denotes	in
T11129	18698-18701	DT	denotes	the
T11131	18702-18705	NN	denotes	DBA
T11132	18705-18706	HYPH	denotes	/
T11133	18706-18707	CD	denotes	1
T11130	18708-18714	NN	denotes	strain
T11134	18715-18717	IN	denotes	at
T11135	18718-18721	DT	denotes	the
T11137	18722-18727	JJ	denotes	early
T11136	18728-18734	NNS	denotes	stages
T11138	18734-18736	,	denotes	,
T11139	18736-18745	VBG	denotes	including
T11140	18746-18748	NN	denotes	NC
T11141	18748-18750	,	denotes	,
T11142	18750-18752	NN	denotes	PI
T11143	18753-18756	CC	denotes	and
T11144	18757-18759	NN	denotes	OA
T11145	18759-18761	,	denotes	,
T11146	18761-18764	CC	denotes	but
T11147	18765-18766	DT	denotes	a
T11149	18767-18772	JJR	denotes	lower
T11148	18773-18783	NN	denotes	expression
T11150	18784-18786	IN	denotes	at
T11151	18787-18790	DT	denotes	the
T11153	18791-18798	JJ	denotes	chronic
T11152	18799-18804	NN	denotes	phase
T11154	18804-18805	.	denotes	.
T11155	18805-18954	sentence	denotes	GO term classification analysis revealed that the functional cluster of protein kinase cascade was significantly enriched in the 21 candidate genes.
T11156	18806-18808	NN	denotes	GO
T11158	18809-18813	NN	denotes	term
T11159	18814-18828	NN	denotes	classification
T11157	18829-18837	NN	denotes	analysis
T11160	18838-18846	VBD	denotes	revealed
T11161	18847-18851	IN	denotes	that
T11163	18852-18855	DT	denotes	the
T11165	18856-18866	JJ	denotes	functional
T11164	18867-18874	NN	denotes	cluster
T11166	18875-18877	IN	denotes	of
T11167	18878-18885	NN	denotes	protein
T11169	18886-18892	NN	denotes	kinase
T11168	18893-18900	NN	denotes	cascade
T11170	18901-18904	VBD	denotes	was
T11171	18905-18918	RB	denotes	significantly
T11162	18919-18927	VBN	denotes	enriched
T11172	18928-18930	IN	denotes	in
T11173	18931-18934	DT	denotes	the
T11175	18935-18937	CD	denotes	21
T11176	18938-18947	NN	denotes	candidate
T11174	18948-18953	NNS	denotes	genes
T11177	18953-18954	.	denotes	.
T11178	18954-19046	sentence	denotes	This functional cluster contained four genes, including Mapk14, Mapk8ip3, Stat5a and Gna12.
T11179	18955-18959	DT	denotes	This
T11181	18960-18970	JJ	denotes	functional
T11180	18971-18978	NN	denotes	cluster
T11182	18979-18988	VBD	denotes	contained
T11183	18989-18993	CD	denotes	four
T11184	18994-18999	NNS	denotes	genes
T11185	18999-19001	,	denotes	,
T11186	19001-19010	VBG	denotes	including
T11187	19011-19017	NN	denotes	Mapk14
T11188	19017-19019	,	denotes	,
T11189	19019-19027	NN	denotes	Mapk8ip3
T11190	19027-19029	,	denotes	,
T11191	19029-19035	NN	denotes	Stat5a
T11192	19036-19039	CC	denotes	and
T11193	19040-19045	NN	denotes	Gna12
T11194	19045-19046	.	denotes	.
T13481	19059-19061	IN	denotes	In
T13483	19062-19066	DT	denotes	this
T13484	19067-19072	NN	denotes	study
T13485	19072-19074	,	denotes	,
T13486	19074-19076	PRP	denotes	we
T13482	19077-19086	VBD	denotes	attempted
T13487	19087-19090	IN	denotes	for
T13488	19091-19094	DT	denotes	the
T13490	19095-19100	JJ	denotes	first
T13489	19101-19105	NN	denotes	time
T13491	19106-19108	TO	denotes	to
T13492	19109-19117	VB	denotes	identify
T13493	19118-19123	JJ	denotes	small
T13495	19123-19124	HYPH	denotes	-
T13494	19124-19130	NN	denotes	effect
T13496	19131-19134	NNS	denotes	QTL
T13497	19135-19137	IN	denotes	in
T13498	19138-19140	DT	denotes	an
T13500	19141-19143	NN	denotes	F2
T13499	19144-19151	NN	denotes	progeny
T13501	19151-19152	.	denotes	.
T13502	19152-19325	sentence	denotes	Small-effect QTL are defined as those reaching the threshold value of P = 0.05 but that did not reach the significant threshold value suggested by Lander and Botstein [26].
T13503	19153-19158	JJ	denotes	Small
T13505	19158-19159	HYPH	denotes	-
T13504	19159-19165	NN	denotes	effect
T13506	19166-19169	NNS	denotes	QTL
T13508	19170-19173	VBP	denotes	are
T13507	19174-19181	VBN	denotes	defined
T13509	19182-19184	IN	denotes	as
T13510	19185-19190	DT	denotes	those
T13511	19191-19199	VBG	denotes	reaching
T13512	19200-19203	DT	denotes	the
T13514	19204-19213	NN	denotes	threshold
T13513	19214-19219	NN	denotes	value
T13515	19220-19222	IN	denotes	of
T13516	19223-19224	NN	denotes	P
T13518	19225-19226	SYM	denotes	=
T13517	19227-19231	CD	denotes	0.05
T13519	19232-19235	CC	denotes	but
T13520	19236-19240	DT	denotes	that
T13522	19241-19244	VBD	denotes	did
T13523	19245-19248	RB	denotes	not
T13521	19249-19254	VB	denotes	reach
T13524	19255-19258	DT	denotes	the
T13526	19259-19270	JJ	denotes	significant
T13527	19271-19280	NN	denotes	threshold
T13525	19281-19286	NN	denotes	value
T13528	19287-19296	VBN	denotes	suggested
T13529	19297-19299	IN	denotes	by
T13530	19300-19306	NNP	denotes	Lander
T13531	19307-19310	CC	denotes	and
T13532	19311-19319	NNP	denotes	Botstein
T13533	19320-19321	-LRB-	denotes	[
T13534	19321-19323	CD	denotes	26
T13535	19323-19324	-RRB-	denotes	]
T13536	19324-19325	.	denotes	.
T13537	19325-19454	sentence	denotes	Although not significant, there is evidence that most of the eight small-effect QTL likely contain susceptibility genes for CIA.
T13538	19326-19334	IN	denotes	Although
T13540	19335-19338	RB	denotes	not
T13539	19339-19350	JJ	denotes	significant
T13542	19350-19352	,	denotes	,
T13543	19352-19357	EX	denotes	there
T13541	19358-19360	VBZ	denotes	is
T13544	19361-19369	NN	denotes	evidence
T13545	19370-19374	IN	denotes	that
T13547	19375-19379	JJS	denotes	most
T13548	19380-19382	IN	denotes	of
T13549	19383-19386	DT	denotes	the
T13551	19387-19392	CD	denotes	eight
T13552	19393-19398	JJ	denotes	small
T13554	19398-19399	HYPH	denotes	-
T13553	19399-19405	NN	denotes	effect
T13550	19406-19409	NNS	denotes	QTL
T13555	19410-19416	RB	denotes	likely
T13546	19417-19424	VBP	denotes	contain
T13556	19425-19439	NN	denotes	susceptibility
T13557	19440-19445	NNS	denotes	genes
T13558	19446-19449	IN	denotes	for
T13559	19450-19453	NN	denotes	CIA
T13560	19453-19454	.	denotes	.
T13561	19454-19589	sentence	denotes	First, we performed the linkage analysis in three datasets, including all 290 F progeny, 76 C5+/+ F2 progeny and 133 C5+/- F2 progeny.
T13562	19455-19460	RB	denotes	First
T13564	19460-19462	,	denotes	,
T13565	19462-19464	PRP	denotes	we
T13563	19465-19474	VBD	denotes	performed
T13566	19475-19478	DT	denotes	the
T13568	19479-19486	NN	denotes	linkage
T13567	19487-19495	NN	denotes	analysis
T13569	19496-19498	IN	denotes	in
T13570	19499-19504	CD	denotes	three
T13571	19505-19513	NNS	denotes	datasets
T13572	19513-19515	,	denotes	,
T13573	19515-19524	VBG	denotes	including
T13574	19525-19528	DT	denotes	all
T13576	19529-19532	CD	denotes	290
T13577	19533-19534	NN	denotes	F
T13575	19535-19542	NN	denotes	progeny
T13578	19542-19544	,	denotes	,
T13579	19544-19546	CD	denotes	76
T13581	19547-19550	NN	denotes	C5+
T13582	19550-19551	HYPH	denotes	/
T13583	19551-19552	SYM	denotes	+
T13584	19553-19555	NN	denotes	F2
T13580	19556-19563	NN	denotes	progeny
T13585	19564-19567	CC	denotes	and
T13586	19568-19571	CD	denotes	133
T13588	19572-19575	NN	denotes	C5+
T13589	19575-19576	HYPH	denotes	/
T13590	19576-19577	SYM	denotes	-
T13591	19578-19580	NN	denotes	F2
T13587	19581-19588	NN	denotes	progeny
T13592	19588-19589	.	denotes	.
T13593	19589-19710	sentence	denotes	Five of the eight small-effect QTL were identified in at least two datasets, suggesting that these QTL are reproducible.
T13594	19590-19594	CD	denotes	Five
T13596	19595-19597	IN	denotes	of
T13597	19598-19601	DT	denotes	the
T13595	19602-19607	CD	denotes	eight
T13599	19608-19613	JJ	denotes	small
T13601	19613-19614	HYPH	denotes	-
T13600	19614-19620	NN	denotes	effect
T13598	19621-19624	NNS	denotes	QTL
T13603	19625-19629	VBD	denotes	were
T13602	19630-19640	VBN	denotes	identified
T13604	19641-19643	IN	denotes	in
T13605	19644-19646	RB	denotes	at
T13607	19647-19652	RBS	denotes	least
T13606	19653-19656	CD	denotes	two
T13608	19657-19665	NNS	denotes	datasets
T13609	19665-19667	,	denotes	,
T13610	19667-19677	VBG	denotes	suggesting
T13611	19678-19682	IN	denotes	that
T13613	19683-19688	DT	denotes	these
T13614	19689-19692	NNS	denotes	QTL
T13612	19693-19696	VBP	denotes	are
T13615	19697-19709	JJ	denotes	reproducible
T13616	19709-19710	.	denotes	.
T13617	19710-19839	sentence	denotes	Second, many QTL identified in the present study overlap with arthritis QTL previously identified, including loci 1, 2, 5 and 6.
T13618	19711-19717	RB	denotes	Second
T13620	19717-19719	,	denotes	,
T13621	19719-19723	JJ	denotes	many
T13622	19724-19727	NNS	denotes	QTL
T13623	19728-19738	VBN	denotes	identified
T13624	19739-19741	IN	denotes	in
T13625	19742-19745	DT	denotes	the
T13627	19746-19753	JJ	denotes	present
T13626	19754-19759	NN	denotes	study
T13619	19760-19767	VBP	denotes	overlap
T13628	19768-19772	IN	denotes	with
T13629	19773-19782	NN	denotes	arthritis
T13630	19783-19786	NNS	denotes	QTL
T13631	19787-19797	RB	denotes	previously
T13632	19798-19808	VBN	denotes	identified
T13633	19808-19810	,	denotes	,
T13634	19810-19819	VBG	denotes	including
T13635	19820-19824	NNS	denotes	loci
T13636	19825-19826	CD	denotes	1
T13637	19826-19828	,	denotes	,
T13638	19828-19829	CD	denotes	2
T13639	19829-19831	,	denotes	,
T13640	19831-19832	CD	denotes	5
T13641	19833-19836	CC	denotes	and
T13642	19837-19838	CD	denotes	6
T13643	19838-19839	.	denotes	.
T13644	19839-19981	sentence	denotes	In addition, syntenic analysis revealed that the counterpart genomic regions on the human genome of many of these eight QTL are linked to RA.
T13645	19840-19842	IN	denotes	In
T13647	19843-19851	NN	denotes	addition
T13648	19851-19853	,	denotes	,
T13649	19853-19861	JJ	denotes	syntenic
T13650	19862-19870	NN	denotes	analysis
T13646	19871-19879	VBD	denotes	revealed
T13651	19880-19884	IN	denotes	that
T13653	19885-19888	DT	denotes	the
T13655	19889-19900	NN	denotes	counterpart
T13656	19901-19908	JJ	denotes	genomic
T13654	19909-19916	NNS	denotes	regions
T13657	19917-19919	IN	denotes	on
T13658	19920-19923	DT	denotes	the
T13660	19924-19929	JJ	denotes	human
T13659	19930-19936	NN	denotes	genome
T13661	19937-19939	IN	denotes	of
T13662	19940-19944	JJ	denotes	many
T13663	19945-19947	IN	denotes	of
T13664	19948-19953	DT	denotes	these
T13666	19954-19959	CD	denotes	eight
T13665	19960-19963	NNS	denotes	QTL
T13667	19964-19967	VBP	denotes	are
T13652	19968-19974	VBN	denotes	linked
T13668	19975-19977	IN	denotes	to
T13669	19978-19980	NN	denotes	RA
T13670	19980-19981	.	denotes	.
T13671	19981-20238	sentence	denotes	For five of the eight small-effect QTL the DBA/1 alleles are the arthritis-enhancing alleles, while the FVBN alleles are the arthritis-enhancing alleles in the other three QTL, indicating that some susceptibility genes could come from the resistant strain.
T13672	19982-19985	IN	denotes	For
T13674	19986-19990	CD	denotes	five
T13676	19991-19993	IN	denotes	of
T13677	19994-19997	DT	denotes	the
T13675	19998-20003	CD	denotes	eight
T13679	20004-20009	JJ	denotes	small
T13681	20009-20010	HYPH	denotes	-
T13680	20010-20016	NN	denotes	effect
T13678	20017-20020	NNS	denotes	QTL
T13682	20021-20024	DT	denotes	the
T13684	20025-20028	NN	denotes	DBA
T13685	20028-20029	HYPH	denotes	/
T13686	20029-20030	CD	denotes	1
T13683	20031-20038	NNS	denotes	alleles
T13673	20039-20042	VBP	denotes	are
T13687	20043-20046	DT	denotes	the
T13689	20047-20056	NN	denotes	arthritis
T13691	20056-20057	HYPH	denotes	-
T13690	20057-20066	VBG	denotes	enhancing
T13688	20067-20074	NNS	denotes	alleles
T13692	20074-20076	,	denotes	,
T13693	20076-20081	IN	denotes	while
T13695	20082-20085	DT	denotes	the
T13697	20086-20090	NN	denotes	FVBN
T13696	20091-20098	NNS	denotes	alleles
T13694	20099-20102	VBP	denotes	are
T13698	20103-20106	DT	denotes	the
T13700	20107-20116	NN	denotes	arthritis
T13702	20116-20117	HYPH	denotes	-
T13701	20117-20126	VBG	denotes	enhancing
T13699	20127-20134	NNS	denotes	alleles
T13703	20135-20137	IN	denotes	in
T13704	20138-20141	DT	denotes	the
T13706	20142-20147	JJ	denotes	other
T13707	20148-20153	CD	denotes	three
T13705	20154-20157	NNS	denotes	QTL
T13708	20157-20159	,	denotes	,
T13709	20159-20169	VBG	denotes	indicating
T13710	20170-20174	IN	denotes	that
T13712	20175-20179	DT	denotes	some
T13714	20180-20194	NN	denotes	susceptibility
T13713	20195-20200	NNS	denotes	genes
T13715	20201-20206	MD	denotes	could
T13711	20207-20211	VB	denotes	come
T13716	20212-20216	IN	denotes	from
T13717	20217-20220	DT	denotes	the
T13719	20221-20230	JJ	denotes	resistant
T13718	20231-20237	NN	denotes	strain
T13720	20237-20238	.	denotes	.
T13721	20238-20361	sentence	denotes	Interestingly, loci 2 and 7 partially overlap with two arthritis-related QTL identified by us in the same F2 progeny [10].
T13722	20239-20252	RB	denotes	Interestingly
T13724	20252-20254	,	denotes	,
T13725	20254-20258	NNS	denotes	loci
T13726	20259-20260	CD	denotes	2
T13727	20261-20264	CC	denotes	and
T13728	20265-20266	CD	denotes	7
T13729	20267-20276	RB	denotes	partially
T13723	20277-20284	VBP	denotes	overlap
T13730	20285-20289	IN	denotes	with
T13731	20290-20293	CD	denotes	two
T13733	20294-20303	NN	denotes	arthritis
T13735	20303-20304	HYPH	denotes	-
T13734	20304-20311	VBN	denotes	related
T13732	20312-20315	NNS	denotes	QTL
T13736	20316-20326	VBN	denotes	identified
T13737	20327-20329	IN	denotes	by
T13738	20330-20332	PRP	denotes	us
T13739	20333-20335	IN	denotes	in
T13740	20336-20339	DT	denotes	the
T13742	20340-20344	JJ	denotes	same
T13743	20345-20347	NN	denotes	F2
T13741	20348-20355	NN	denotes	progeny
T13744	20356-20357	-LRB-	denotes	[
T13745	20357-20359	CD	denotes	10
T13746	20359-20360	-RRB-	denotes	]
T13747	20360-20361	.	denotes	.
T13748	20361-20474	sentence	denotes	Locus 2 was located at the same genomic region as Cia27, a QTL controlling IgG2a antibody levels to collagen II.
T13749	20362-20367	NN	denotes	Locus
T13751	20368-20369	CD	denotes	2
T13752	20370-20373	VBD	denotes	was
T13750	20374-20381	VBN	denotes	located
T13753	20382-20384	IN	denotes	at
T13754	20385-20388	DT	denotes	the
T13756	20389-20393	JJ	denotes	same
T13757	20394-20401	JJ	denotes	genomic
T13755	20402-20408	NN	denotes	region
T13758	20409-20411	IN	denotes	as
T13759	20412-20417	NN	denotes	Cia27
T13760	20417-20419	,	denotes	,
T13761	20419-20420	DT	denotes	a
T13762	20421-20424	NN	denotes	QTL
T13763	20425-20436	VBG	denotes	controlling
T13764	20437-20442	NN	denotes	IgG2a
T13766	20443-20451	NN	denotes	antibody
T13765	20452-20458	NNS	denotes	levels
T13767	20459-20461	IN	denotes	to
T13768	20462-20470	NN	denotes	collagen
T13769	20471-20473	CD	denotes	II
T13770	20473-20474	.	denotes	.
T13771	20474-20665	sentence	denotes	Recently, we have refined this QTL into a 4.1 Mb genomic region and showed that a gene within this region regulates CIA severity by controlling the IgG2a antibody levels to collagen II [31].
T13772	20475-20483	RB	denotes	Recently
T13774	20483-20485	,	denotes	,
T13775	20485-20487	PRP	denotes	we
T13776	20488-20492	VBP	denotes	have
T13773	20493-20500	VBN	denotes	refined
T13777	20501-20505	DT	denotes	this
T13778	20506-20509	NN	denotes	QTL
T13779	20510-20514	IN	denotes	into
T13780	20515-20516	DT	denotes	a
T13782	20517-20520	CD	denotes	4.1
T13783	20521-20523	NN	denotes	Mb
T13784	20524-20531	JJ	denotes	genomic
T13781	20532-20538	NN	denotes	region
T13785	20539-20542	CC	denotes	and
T13786	20543-20549	VBD	denotes	showed
T13787	20550-20554	IN	denotes	that
T13789	20555-20556	DT	denotes	a
T13790	20557-20561	NN	denotes	gene
T13791	20562-20568	IN	denotes	within
T13792	20569-20573	DT	denotes	this
T13793	20574-20580	NN	denotes	region
T13788	20581-20590	VBZ	denotes	regulates
T13794	20591-20594	NN	denotes	CIA
T13795	20595-20603	NN	denotes	severity
T13796	20604-20606	IN	denotes	by
T13797	20607-20618	VBG	denotes	controlling
T13798	20619-20622	DT	denotes	the
T13800	20623-20628	NN	denotes	IgG2a
T13801	20629-20637	NN	denotes	antibody
T13799	20638-20644	NNS	denotes	levels
T13802	20645-20647	IN	denotes	to
T13803	20648-20656	NN	denotes	collagen
T13804	20657-20659	CD	denotes	II
T13805	20660-20661	-LRB-	denotes	[
T13806	20661-20663	CD	denotes	31
T13807	20663-20664	-RRB-	denotes	]
T13808	20664-20665	.	denotes	.
T13809	20665-20750	sentence	denotes	Locus 7 on chromosome 16 overlaps with Lp1, which controls lymphocyte proliferation.
T13810	20666-20671	NN	denotes	Locus
T13812	20672-20673	CD	denotes	7
T13813	20674-20676	IN	denotes	on
T13814	20677-20687	NN	denotes	chromosome
T13815	20688-20690	CD	denotes	16
T13811	20691-20699	VBZ	denotes	overlaps
T13816	20700-20704	IN	denotes	with
T13817	20705-20708	NN	denotes	Lp1
T13818	20708-20710	,	denotes	,
T13819	20710-20715	WDT	denotes	which
T13820	20716-20724	VBZ	denotes	controls
T13821	20725-20735	NN	denotes	lymphocyte
T13822	20736-20749	NN	denotes	proliferation
T13823	20749-20750	.	denotes	.
T13824	20750-20879	sentence	denotes	Furthermore, according to our unpublished data, loci 8 on chromosome 17 controls lymphocyte adherence during development of CIA.
T13825	20751-20762	RB	denotes	Furthermore
T13827	20762-20764	,	denotes	,
T13828	20764-20773	VBG	denotes	according
T13829	20774-20776	IN	denotes	to
T13830	20777-20780	PRP$	denotes	our
T13832	20781-20792	JJ	denotes	unpublished
T13831	20793-20797	NNS	denotes	data
T13833	20797-20799	,	denotes	,
T13834	20799-20803	NNS	denotes	loci
T13835	20804-20805	CD	denotes	8
T13836	20806-20808	IN	denotes	on
T13837	20809-20819	NN	denotes	chromosome
T13838	20820-20822	CD	denotes	17
T13826	20823-20831	VBZ	denotes	controls
T13839	20832-20842	NN	denotes	lymphocyte
T13840	20843-20852	NN	denotes	adherence
T13841	20853-20859	IN	denotes	during
T13842	20860-20871	NN	denotes	development
T13843	20872-20874	IN	denotes	of
T13844	20875-20878	NN	denotes	CIA
T13845	20878-20879	.	denotes	.
T13846	20879-21003	sentence	denotes	Therefore, the gene within the small-effect QTL could affect CIA severity through controlling arthritis-related phenotypes.
T13847	20880-20889	RB	denotes	Therefore
T13849	20889-20891	,	denotes	,
T13850	20891-20894	DT	denotes	the
T13851	20895-20899	NN	denotes	gene
T13852	20900-20906	IN	denotes	within
T13853	20907-20910	DT	denotes	the
T13855	20911-20916	JJ	denotes	small
T13857	20916-20917	HYPH	denotes	-
T13856	20917-20923	NN	denotes	effect
T13854	20924-20927	NNS	denotes	QTL
T13858	20928-20933	MD	denotes	could
T13848	20934-20940	VB	denotes	affect
T13859	20941-20944	NN	denotes	CIA
T13860	20945-20953	NN	denotes	severity
T13861	20954-20961	IN	denotes	through
T13862	20962-20973	VBG	denotes	controlling
T13863	20974-20983	NN	denotes	arthritis
T13865	20983-20984	HYPH	denotes	-
T13864	20984-20991	VBN	denotes	related
T13866	20992-21002	NNS	denotes	phenotypes
T13867	21002-21003	.	denotes	.
T13868	21003-21140	sentence	denotes	Several studies have been carried out to detect gene expression during CIA, all of which used joints as the target tissue [15,16,21,22].
T13869	21004-21011	JJ	denotes	Several
T13870	21012-21019	NNS	denotes	studies
T13872	21020-21024	VBP	denotes	have
T13873	21025-21029	VBN	denotes	been
T13871	21030-21037	VBN	denotes	carried
T13874	21038-21041	RP	denotes	out
T13875	21042-21044	TO	denotes	to
T13876	21045-21051	VB	denotes	detect
T13877	21052-21056	NN	denotes	gene
T13878	21057-21067	NN	denotes	expression
T13879	21068-21074	IN	denotes	during
T13880	21075-21078	NN	denotes	CIA
T13881	21078-21080	,	denotes	,
T13882	21080-21083	DT	denotes	all
T13884	21084-21086	IN	denotes	of
T13885	21087-21092	WDT	denotes	which
T13883	21093-21097	VBD	denotes	used
T13886	21098-21104	NNS	denotes	joints
T13887	21105-21107	IN	denotes	as
T13888	21108-21111	DT	denotes	the
T13890	21112-21118	NN	denotes	target
T13889	21119-21125	NN	denotes	tissue
T13891	21126-21127	-LRB-	denotes	[
T13893	21127-21129	CD	denotes	15
T13894	21129-21130	,	denotes	,
T13895	21130-21132	CD	denotes	16
T13896	21132-21133	,	denotes	,
T13897	21133-21135	CD	denotes	21
T13898	21135-21136	,	denotes	,
T13892	21136-21138	CD	denotes	22
T13899	21138-21139	-RRB-	denotes	]
T13900	21139-21140	.	denotes	.
T13901	21140-21216	sentence	denotes	This study, for the first time, detected gene expression in LNs during CIA.
T13902	21141-21145	DT	denotes	This
T13903	21146-21151	NN	denotes	study
T13905	21151-21153	,	denotes	,
T13906	21153-21156	IN	denotes	for
T13907	21157-21160	DT	denotes	the
T13909	21161-21166	JJ	denotes	first
T13908	21167-21171	NN	denotes	time
T13910	21171-21173	,	denotes	,
T13904	21173-21181	VBD	denotes	detected
T13911	21182-21186	NN	denotes	gene
T13912	21187-21197	NN	denotes	expression
T13913	21198-21200	IN	denotes	in
T13914	21201-21204	NNS	denotes	LNs
T13915	21205-21211	IN	denotes	during
T13916	21212-21215	NN	denotes	CIA
T13917	21215-21216	.	denotes	.
T13918	21216-21368	sentence	denotes	We present an extensive study of gene expression patterns in LNs of both genetically susceptible and resistant strains at four different phases of CIA.
T13919	21217-21219	PRP	denotes	We
T13920	21220-21227	VBP	denotes	present
T13921	21228-21230	DT	denotes	an
T13923	21231-21240	JJ	denotes	extensive
T13922	21241-21246	NN	denotes	study
T13924	21247-21249	IN	denotes	of
T13925	21250-21254	NN	denotes	gene
T13927	21255-21265	NN	denotes	expression
T13926	21266-21274	NNS	denotes	patterns
T13928	21275-21277	IN	denotes	in
T13929	21278-21281	NNS	denotes	LNs
T13930	21282-21284	IN	denotes	of
T13931	21285-21289	CC	denotes	both
T13933	21290-21301	RB	denotes	genetically
T13934	21302-21313	JJ	denotes	susceptible
T13935	21314-21317	CC	denotes	and
T13936	21318-21327	JJ	denotes	resistant
T13932	21328-21335	NNS	denotes	strains
T13937	21336-21338	IN	denotes	at
T13938	21339-21343	CD	denotes	four
T13940	21344-21353	JJ	denotes	different
T13939	21354-21360	NNS	denotes	phases
T13941	21361-21363	IN	denotes	of
T13942	21364-21367	NN	denotes	CIA
T13943	21367-21368	.	denotes	.
T13944	21368-21553	sentence	denotes	In both strains, differentially regulated genes were highly concentrated at the PI and CA phases, and only a small number of genes were differentially expressed in two or three phases.
T13945	21369-21371	IN	denotes	In
T13947	21372-21376	DT	denotes	both
T13948	21377-21384	NNS	denotes	strains
T13949	21384-21386	,	denotes	,
T13950	21386-21400	RB	denotes	differentially
T13951	21401-21410	VBN	denotes	regulated
T13952	21411-21416	NNS	denotes	genes
T13946	21417-21421	VBD	denotes	were
T13953	21422-21428	RB	denotes	highly
T13954	21429-21441	JJ	denotes	concentrated
T13955	21442-21444	IN	denotes	at
T13956	21445-21448	DT	denotes	the
T13958	21449-21451	NN	denotes	PI
T13959	21452-21455	CC	denotes	and
T13960	21456-21458	NN	denotes	CA
T13957	21459-21465	NNS	denotes	phases
T13961	21465-21467	,	denotes	,
T13962	21467-21470	CC	denotes	and
T13963	21471-21475	RB	denotes	only
T13965	21476-21477	DT	denotes	a
T13966	21478-21483	JJ	denotes	small
T13964	21484-21490	NN	denotes	number
T13968	21491-21493	IN	denotes	of
T13969	21494-21499	NNS	denotes	genes
T13970	21500-21504	VBD	denotes	were
T13971	21505-21519	RB	denotes	differentially
T13967	21520-21529	VBN	denotes	expressed
T13972	21530-21532	IN	denotes	in
T13973	21533-21536	CD	denotes	two
T13975	21537-21539	CC	denotes	or
T13976	21540-21545	CD	denotes	three
T13974	21546-21552	NNS	denotes	phases
T13977	21552-21553	.	denotes	.
T13978	21553-21715	sentence	denotes	This indicates that biological responses in LNs were stronger in the PI and CA phases than in the OA phase, and the responses at different phases were different.
T13979	21554-21558	DT	denotes	This
T13980	21559-21568	VBZ	denotes	indicates
T13981	21569-21573	IN	denotes	that
T13983	21574-21584	JJ	denotes	biological
T13984	21585-21594	NNS	denotes	responses
T13985	21595-21597	IN	denotes	in
T13986	21598-21601	NNS	denotes	LNs
T13982	21602-21606	VBD	denotes	were
T13987	21607-21615	JJR	denotes	stronger
T13988	21616-21618	IN	denotes	in
T13989	21619-21622	DT	denotes	the
T13991	21623-21625	NN	denotes	PI
T13992	21626-21629	CC	denotes	and
T13993	21630-21632	NN	denotes	CA
T13990	21633-21639	NNS	denotes	phases
T13994	21640-21644	IN	denotes	than
T13995	21645-21647	IN	denotes	in
T13996	21648-21651	DT	denotes	the
T13998	21652-21654	NN	denotes	OA
T13997	21655-21660	NN	denotes	phase
T13999	21660-21662	,	denotes	,
T14000	21662-21665	CC	denotes	and
T14001	21666-21669	DT	denotes	the
T14002	21670-21679	NNS	denotes	responses
T14004	21680-21682	IN	denotes	at
T14005	21683-21692	JJ	denotes	different
T14006	21693-21699	NNS	denotes	phases
T14003	21700-21704	VBD	denotes	were
T14007	21705-21714	JJ	denotes	different
T14008	21714-21715	.	denotes	.
T14009	21715-21852	sentence	denotes	When comparing the susceptible to the resistant strain, the biggest difference was found in one cluster of genes (cluster IV, Figure 2).
T14010	21716-21720	WRB	denotes	When
T14011	21721-21730	VBG	denotes	comparing
T14013	21731-21734	DT	denotes	the
T14014	21735-21746	JJ	denotes	susceptible
T14015	21747-21749	IN	denotes	to
T14016	21750-21753	DT	denotes	the
T14017	21754-21763	JJ	denotes	resistant
T14018	21764-21770	NN	denotes	strain
T14019	21770-21772	,	denotes	,
T14020	21772-21775	DT	denotes	the
T14022	21776-21783	JJS	denotes	biggest
T14021	21784-21794	NN	denotes	difference
T14023	21795-21798	VBD	denotes	was
T14012	21799-21804	VBN	denotes	found
T14024	21805-21807	IN	denotes	in
T14025	21808-21811	CD	denotes	one
T14026	21812-21819	NN	denotes	cluster
T14027	21820-21822	IN	denotes	of
T14028	21823-21828	NNS	denotes	genes
T14029	21829-21830	-LRB-	denotes	(
T14030	21830-21837	NN	denotes	cluster
T14031	21838-21840	CD	denotes	IV
T14032	21840-21842	,	denotes	,
T14033	21842-21848	NN	denotes	Figure
T14034	21849-21850	CD	denotes	2
T14035	21850-21851	-RRB-	denotes	)
T14036	21851-21852	.	denotes	.
T14037	21852-22007	sentence	denotes	These genes had a higher expression in DBA/1 than in FVB/N at the early phases of CIA (NC, PI and OA) and the opposite expression pattern in the CA phase.
T14038	21853-21858	DT	denotes	These
T14039	21859-21864	NNS	denotes	genes
T14040	21865-21868	VBD	denotes	had
T14041	21869-21870	DT	denotes	a
T14043	21871-21877	JJR	denotes	higher
T14042	21878-21888	NN	denotes	expression
T14044	21889-21891	IN	denotes	in
T14045	21892-21895	NN	denotes	DBA
T14046	21895-21896	HYPH	denotes	/
T14047	21896-21897	CD	denotes	1
T14048	21898-21902	IN	denotes	than
T14049	21903-21905	IN	denotes	in
T14050	21906-21909	NN	denotes	FVB
T14052	21909-21910	HYPH	denotes	/
T14051	21910-21911	NN	denotes	N
T14053	21912-21914	IN	denotes	at
T14054	21915-21918	DT	denotes	the
T14056	21919-21924	JJ	denotes	early
T14055	21925-21931	NNS	denotes	phases
T14057	21932-21934	IN	denotes	of
T14058	21935-21938	NN	denotes	CIA
T14059	21939-21940	-LRB-	denotes	(
T14060	21940-21942	NN	denotes	NC
T14061	21942-21944	,	denotes	,
T14062	21944-21946	NN	denotes	PI
T14063	21947-21950	CC	denotes	and
T14064	21951-21953	NN	denotes	OA
T14065	21953-21954	-RRB-	denotes	)
T14066	21955-21958	CC	denotes	and
T14067	21959-21962	DT	denotes	the
T14069	21963-21971	JJ	denotes	opposite
T14070	21972-21982	NN	denotes	expression
T14068	21983-21990	NN	denotes	pattern
T14071	21991-21993	IN	denotes	in
T14072	21994-21997	DT	denotes	the
T14074	21998-22000	NN	denotes	CA
T14073	22001-22006	NN	denotes	phase
T14075	22006-22007	.	denotes	.
T14076	22007-22212	sentence	denotes	GO term classification revealed that these genes were related to lymphocyte proliferation and activation, suggesting that lymphocytes in the DBA/1 strain are more activated than those in the FVB/N strain.
T14077	22008-22010	NN	denotes	GO
T14079	22011-22015	NN	denotes	term
T14078	22016-22030	NN	denotes	classification
T14080	22031-22039	VBD	denotes	revealed
T14081	22040-22044	IN	denotes	that
T14083	22045-22050	DT	denotes	these
T14084	22051-22056	NNS	denotes	genes
T14085	22057-22061	VBD	denotes	were
T14082	22062-22069	VBN	denotes	related
T14086	22070-22072	IN	denotes	to
T14087	22073-22083	NN	denotes	lymphocyte
T14088	22084-22097	NN	denotes	proliferation
T14089	22098-22101	CC	denotes	and
T14090	22102-22112	NN	denotes	activation
T14091	22112-22114	,	denotes	,
T14092	22114-22124	VBG	denotes	suggesting
T14093	22125-22129	IN	denotes	that
T14095	22130-22141	NNS	denotes	lymphocytes
T14096	22142-22144	IN	denotes	in
T14097	22145-22148	DT	denotes	the
T14099	22149-22152	NN	denotes	DBA
T14100	22152-22153	HYPH	denotes	/
T14101	22153-22154	CD	denotes	1
T14098	22155-22161	NN	denotes	strain
T14094	22162-22165	VBP	denotes	are
T14102	22166-22170	RBR	denotes	more
T14103	22171-22180	JJ	denotes	activated
T14104	22181-22185	IN	denotes	than
T14105	22186-22191	DT	denotes	those
T14106	22192-22194	IN	denotes	in
T14107	22195-22198	DT	denotes	the
T14109	22199-22202	NN	denotes	FVB
T14111	22202-22203	HYPH	denotes	/
T14110	22203-22204	NN	denotes	N
T14108	22205-22211	NN	denotes	strain
T14112	22211-22212	.	denotes	.
T14113	22212-22353	sentence	denotes	However, this difference is not CIA specific because the expression difference between the two strains existed in mice without immunisation.
T14114	22213-22220	RB	denotes	However
T14116	22220-22222	,	denotes	,
T14117	22222-22226	DT	denotes	this
T14118	22227-22237	NN	denotes	difference
T14115	22238-22240	VBZ	denotes	is
T14119	22241-22244	RB	denotes	not
T14120	22245-22248	NN	denotes	CIA
T14121	22249-22257	JJ	denotes	specific
T14122	22258-22265	IN	denotes	because
T14124	22266-22269	DT	denotes	the
T14126	22270-22280	NN	denotes	expression
T14125	22281-22291	NN	denotes	difference
T14127	22292-22299	IN	denotes	between
T14128	22300-22303	DT	denotes	the
T14130	22304-22307	CD	denotes	two
T14129	22308-22315	NNS	denotes	strains
T14123	22316-22323	VBD	denotes	existed
T14131	22324-22326	IN	denotes	in
T14132	22327-22331	NNS	denotes	mice
T14133	22332-22339	IN	denotes	without
T14134	22340-22352	NN	denotes	immunisation
T14135	22352-22353	.	denotes	.
T14136	22353-22486	sentence	denotes	Additionally, some genes related to the immune response were upregulated in the DBA/1 strain but not in the FVB/N strain during CIA.
T14137	22354-22366	RB	denotes	Additionally
T14139	22366-22368	,	denotes	,
T14140	22368-22372	DT	denotes	some
T14141	22373-22378	NNS	denotes	genes
T14142	22379-22386	VBN	denotes	related
T14143	22387-22389	IN	denotes	to
T14144	22390-22393	DT	denotes	the
T14146	22394-22400	JJ	denotes	immune
T14145	22401-22409	NN	denotes	response
T14147	22410-22414	VBD	denotes	were
T14138	22415-22426	VBN	denotes	upregulated
T14148	22427-22429	IN	denotes	in
T14149	22430-22433	DT	denotes	the
T14151	22434-22437	NN	denotes	DBA
T14152	22437-22438	HYPH	denotes	/
T14153	22438-22439	CD	denotes	1
T14150	22440-22446	NN	denotes	strain
T14154	22447-22450	CC	denotes	but
T14155	22451-22454	RB	denotes	not
T14156	22455-22457	IN	denotes	in
T14157	22458-22461	DT	denotes	the
T14159	22462-22465	NN	denotes	FVB
T14161	22465-22466	HYPH	denotes	/
T14160	22466-22467	NN	denotes	N
T14158	22468-22474	NN	denotes	strain
T14162	22475-22481	IN	denotes	during
T14163	22482-22485	NN	denotes	CIA
T14164	22485-22486	.	denotes	.
T14165	22486-22717	sentence	denotes	These differences could explain why a higher antibody response to collagen II occurred in the DBA/1 strain compared to the FVB/N strain, and might partially explain the difference of the susceptibility to CIA between both strains.
T14166	22487-22492	DT	denotes	These
T14167	22493-22504	NNS	denotes	differences
T14169	22505-22510	MD	denotes	could
T14168	22511-22518	VB	denotes	explain
T14170	22519-22522	WRB	denotes	why
T14172	22523-22524	DT	denotes	a
T14174	22525-22531	JJR	denotes	higher
T14175	22532-22540	NN	denotes	antibody
T14173	22541-22549	NN	denotes	response
T14176	22550-22552	IN	denotes	to
T14177	22553-22561	NN	denotes	collagen
T14178	22562-22564	CD	denotes	II
T14171	22565-22573	VBD	denotes	occurred
T14179	22574-22576	IN	denotes	in
T14180	22577-22580	DT	denotes	the
T14182	22581-22584	NN	denotes	DBA
T14183	22584-22585	HYPH	denotes	/
T14184	22585-22586	CD	denotes	1
T14181	22587-22593	NN	denotes	strain
T14185	22594-22602	VBN	denotes	compared
T14186	22603-22605	IN	denotes	to
T14187	22606-22609	DT	denotes	the
T14189	22610-22613	NN	denotes	FVB
T14191	22613-22614	HYPH	denotes	/
T14190	22614-22615	NN	denotes	N
T14188	22616-22622	NN	denotes	strain
T14192	22622-22624	,	denotes	,
T14193	22624-22627	CC	denotes	and
T14194	22628-22633	MD	denotes	might
T14196	22634-22643	RB	denotes	partially
T14195	22644-22651	VB	denotes	explain
T14197	22652-22655	DT	denotes	the
T14198	22656-22666	NN	denotes	difference
T14199	22667-22669	IN	denotes	of
T14200	22670-22673	DT	denotes	the
T14201	22674-22688	NN	denotes	susceptibility
T14202	22689-22691	IN	denotes	to
T14203	22692-22695	NN	denotes	CIA
T14204	22696-22703	IN	denotes	between
T14205	22704-22708	DT	denotes	both
T14206	22709-22716	NNS	denotes	strains
T14207	22716-22717	.	denotes	.
T14208	22717-22901	sentence	denotes	Twenty-one genes were identified as potential candidate genes for six of the eight small-effect QTL according to their gene expression patterns during CIA and their genomic locations.
T14209	22718-22724	CD	denotes	Twenty
T14211	22724-22725	HYPH	denotes	-
T14210	22725-22728	CD	denotes	one
T14212	22729-22734	NNS	denotes	genes
T14214	22735-22739	VBD	denotes	were
T14213	22740-22750	VBN	denotes	identified
T14215	22751-22753	IN	denotes	as
T14216	22754-22763	JJ	denotes	potential
T14218	22764-22773	NN	denotes	candidate
T14217	22774-22779	NNS	denotes	genes
T14219	22780-22783	IN	denotes	for
T14220	22784-22787	CD	denotes	six
T14222	22788-22790	IN	denotes	of
T14223	22791-22794	DT	denotes	the
T14221	22795-22800	CD	denotes	eight
T14225	22801-22806	JJ	denotes	small
T14227	22806-22807	HYPH	denotes	-
T14226	22807-22813	NN	denotes	effect
T14224	22814-22817	NNS	denotes	QTL
T14228	22818-22827	VBG	denotes	according
T14229	22828-22830	IN	denotes	to
T14230	22831-22836	PRP$	denotes	their
T14232	22837-22841	NN	denotes	gene
T14233	22842-22852	NN	denotes	expression
T14231	22853-22861	NNS	denotes	patterns
T14234	22862-22868	IN	denotes	during
T14235	22869-22872	NN	denotes	CIA
T14236	22873-22876	CC	denotes	and
T14237	22877-22882	PRP$	denotes	their
T14239	22883-22890	JJ	denotes	genomic
T14238	22891-22900	NNS	denotes	locations
T14240	22900-22901	.	denotes	.
T14241	22901-23094	sentence	denotes	No candidate genes were located in QTL 4 and 7, suggesting that QTG polymorphisms of the susceptibility genes inside these two QTL might not affect the phenotype by regulating gene expression.
T14242	22902-22904	DT	denotes	No
T14244	22905-22914	NN	denotes	candidate
T14243	22915-22920	NNS	denotes	genes
T14246	22921-22925	VBD	denotes	were
T14245	22926-22933	VBN	denotes	located
T14247	22934-22936	IN	denotes	in
T14248	22937-22940	NNS	denotes	QTL
T14249	22941-22942	CD	denotes	4
T14250	22943-22946	CC	denotes	and
T14251	22947-22948	CD	denotes	7
T14252	22948-22950	,	denotes	,
T14253	22950-22960	VBG	denotes	suggesting
T14254	22961-22965	IN	denotes	that
T14256	22966-22969	NN	denotes	QTG
T14257	22970-22983	NNS	denotes	polymorphisms
T14258	22984-22986	IN	denotes	of
T14259	22987-22990	DT	denotes	the
T14261	22991-23005	NN	denotes	susceptibility
T14260	23006-23011	NNS	denotes	genes
T14262	23012-23018	IN	denotes	inside
T14263	23019-23024	DT	denotes	these
T14265	23025-23028	CD	denotes	two
T14264	23029-23032	NNS	denotes	QTL
T14266	23033-23038	MD	denotes	might
T14267	23039-23042	RB	denotes	not
T14255	23043-23049	VB	denotes	affect
T14268	23050-23053	DT	denotes	the
T14269	23054-23063	NN	denotes	phenotype
T14270	23064-23066	IN	denotes	by
T14271	23067-23077	VBG	denotes	regulating
T14272	23078-23082	NN	denotes	gene
T14273	23083-23093	NN	denotes	expression
T14274	23093-23094	.	denotes	.
T14275	23094-23167	sentence	denotes	Two of the 21 candidate genes were reported to be involved in arthritis.
T14276	23095-23098	CD	denotes	Two
T14278	23099-23101	IN	denotes	of
T14279	23102-23105	DT	denotes	the
T14277	23106-23108	CD	denotes	21
T14281	23109-23118	NN	denotes	candidate
T14280	23119-23124	NNS	denotes	genes
T14283	23125-23129	VBD	denotes	were
T14282	23130-23138	VBN	denotes	reported
T14284	23139-23141	TO	denotes	to
T14286	23142-23144	VB	denotes	be
T14285	23145-23153	VBN	denotes	involved
T14287	23154-23156	IN	denotes	in
T14288	23157-23166	NN	denotes	arthritis
T14289	23166-23167	.	denotes	.
T14290	23167-23385	sentence	denotes	Mapk14, a candidate gene for locus 8 and also called p38 mitogen-activated protein kinase (MAPK) alpha, regulates the production of arthritis-essential cytokines, such as tumour necrosis factor and interleukin-1 [32].
T14291	23168-23174	NN	denotes	Mapk14
T14293	23174-23176	,	denotes	,
T14294	23176-23177	DT	denotes	a
T14296	23178-23187	NN	denotes	candidate
T14295	23188-23192	NN	denotes	gene
T14297	23193-23196	IN	denotes	for
T14298	23197-23202	NN	denotes	locus
T14299	23203-23204	CD	denotes	8
T14300	23205-23208	CC	denotes	and
T14301	23209-23213	RB	denotes	also
T14302	23214-23220	VBN	denotes	called
T14303	23221-23224	NN	denotes	p38
T14305	23225-23232	NN	denotes	mitogen
T14307	23232-23233	HYPH	denotes	-
T14306	23233-23242	VBN	denotes	activated
T14308	23243-23250	NN	denotes	protein
T14304	23251-23257	NN	denotes	kinase
T14310	23258-23259	-LRB-	denotes	(
T14311	23259-23263	NN	denotes	MAPK
T14312	23263-23264	-RRB-	denotes	)
T14309	23265-23270	NN	denotes	alpha
T14313	23270-23272	,	denotes	,
T14292	23272-23281	VBZ	denotes	regulates
T14314	23282-23285	DT	denotes	the
T14315	23286-23296	NN	denotes	production
T14316	23297-23299	IN	denotes	of
T14317	23300-23309	NN	denotes	arthritis
T14319	23309-23310	HYPH	denotes	-
T14318	23310-23319	JJ	denotes	essential
T14320	23320-23329	NNS	denotes	cytokines
T14321	23329-23331	,	denotes	,
T14322	23331-23335	JJ	denotes	such
T14323	23336-23338	IN	denotes	as
T14324	23339-23345	NN	denotes	tumour
T14326	23346-23354	NN	denotes	necrosis
T14325	23355-23361	NN	denotes	factor
T14327	23362-23365	CC	denotes	and
T14328	23366-23377	NN	denotes	interleukin
T14329	23377-23378	HYPH	denotes	-
T14330	23378-23379	CD	denotes	1
T14331	23380-23381	-LRB-	denotes	[
T14332	23381-23383	CD	denotes	32
T14333	23383-23384	-RRB-	denotes	]
T14334	23384-23385	.	denotes	.
T14335	23385-23520	sentence	denotes	Moreover, inhibitors of p38 MAPK could attenuate CIA in rats [33], and p38 MAPK is becoming a potential therapeutic target in RA [32].
T14336	23386-23394	RB	denotes	Moreover
T14338	23394-23396	,	denotes	,
T14339	23396-23406	NNS	denotes	inhibitors
T14340	23407-23409	IN	denotes	of
T14341	23410-23413	NN	denotes	p38
T14342	23414-23418	NN	denotes	MAPK
T14343	23419-23424	MD	denotes	could
T14337	23425-23434	VB	denotes	attenuate
T14344	23435-23438	NN	denotes	CIA
T14345	23439-23441	IN	denotes	in
T14346	23442-23446	NNS	denotes	rats
T14347	23447-23448	-LRB-	denotes	[
T14348	23448-23450	CD	denotes	33
T14349	23450-23451	-RRB-	denotes	]
T14350	23451-23453	,	denotes	,
T14351	23453-23456	CC	denotes	and
T14352	23457-23460	NN	denotes	p38
T14353	23461-23465	NN	denotes	MAPK
T14355	23466-23468	VBZ	denotes	is
T14354	23469-23477	VBG	denotes	becoming
T14356	23478-23479	DT	denotes	a
T14358	23480-23489	JJ	denotes	potential
T14359	23490-23501	JJ	denotes	therapeutic
T14357	23502-23508	NN	denotes	target
T14360	23509-23511	IN	denotes	in
T14361	23512-23514	NN	denotes	RA
T14362	23515-23516	-LRB-	denotes	[
T14363	23516-23518	CD	denotes	32
T14364	23518-23519	-RRB-	denotes	]
T14365	23519-23520	.	denotes	.
T14366	23520-23633	sentence	denotes	Stat5a, a candidate gene for loci 6, is an essential molecule for lymphoid development and differentiation [34].
T14367	23521-23527	NN	denotes	Stat5a
T14369	23527-23529	,	denotes	,
T14370	23529-23530	DT	denotes	a
T14372	23531-23540	NN	denotes	candidate
T14371	23541-23545	NN	denotes	gene
T14373	23546-23549	IN	denotes	for
T14374	23550-23554	NNS	denotes	loci
T14375	23555-23556	CD	denotes	6
T14376	23556-23558	,	denotes	,
T14368	23558-23560	VBZ	denotes	is
T14377	23561-23563	DT	denotes	an
T14379	23564-23573	JJ	denotes	essential
T14378	23574-23582	NN	denotes	molecule
T14380	23583-23586	IN	denotes	for
T14381	23587-23595	NN	denotes	lymphoid
T14382	23596-23607	NN	denotes	development
T14383	23608-23611	CC	denotes	and
T14384	23612-23627	NN	denotes	differentiation
T14385	23628-23629	-LRB-	denotes	[
T14386	23629-23631	CD	denotes	34
T14387	23631-23632	-RRB-	denotes	]
T14388	23632-23633	.	denotes	.
T14389	23633-23741	sentence	denotes	Stat5a-deficient mice were reported to lose tolerance, resulting in the development of autoimmune diseases.
T14390	23634-23640	NN	denotes	Stat5a
T14392	23640-23641	HYPH	denotes	-
T14391	23641-23650	JJ	denotes	deficient
T14393	23651-23655	NNS	denotes	mice
T14395	23656-23660	VBD	denotes	were
T14394	23661-23669	VBN	denotes	reported
T14396	23670-23672	TO	denotes	to
T14397	23673-23677	VB	denotes	lose
T14398	23678-23687	NN	denotes	tolerance
T14399	23687-23689	,	denotes	,
T14400	23689-23698	VBG	denotes	resulting
T14401	23699-23701	IN	denotes	in
T14402	23702-23705	DT	denotes	the
T14403	23706-23717	NN	denotes	development
T14404	23718-23720	IN	denotes	of
T14405	23721-23731	JJ	denotes	autoimmune
T14406	23732-23740	NNS	denotes	diseases
T14407	23740-23741	.	denotes	.
T14408	23741-23860	sentence	denotes	Stat5a is suggested to contribute to tolerance through maintenance of the CD4+CD25+ regulatory T cell population [35].
T14409	23742-23748	NN	denotes	Stat5a
T14411	23749-23751	VBZ	denotes	is
T14410	23752-23761	VBN	denotes	suggested
T14412	23762-23764	TO	denotes	to
T14413	23765-23775	VB	denotes	contribute
T14414	23776-23778	IN	denotes	to
T14415	23779-23788	NN	denotes	tolerance
T14416	23789-23796	IN	denotes	through
T14417	23797-23808	NN	denotes	maintenance
T14418	23809-23811	IN	denotes	of
T14419	23812-23815	DT	denotes	the
T14421	23816-23825	NN	denotes	CD4+CD25+
T14422	23826-23836	JJ	denotes	regulatory
T14423	23837-23838	NN	denotes	T
T14424	23839-23843	NN	denotes	cell
T14420	23844-23854	NN	denotes	population
T14425	23855-23856	-LRB-	denotes	[
T14426	23856-23858	CD	denotes	35
T14427	23858-23859	-RRB-	denotes	]
T14428	23859-23860	.	denotes	.
T14429	23860-23983	sentence	denotes	Therefore, we have presented a strategy to identify small-effect QTL and search for potential candidate genes within them.
T14430	23861-23870	RB	denotes	Therefore
T14432	23870-23872	,	denotes	,
T14433	23872-23874	PRP	denotes	we
T14434	23875-23879	VBP	denotes	have
T14431	23880-23889	VBN	denotes	presented
T14435	23890-23891	DT	denotes	a
T14436	23892-23900	NN	denotes	strategy
T14437	23901-23903	TO	denotes	to
T14438	23904-23912	VB	denotes	identify
T14439	23913-23918	JJ	denotes	small
T14441	23918-23919	HYPH	denotes	-
T14440	23919-23925	NN	denotes	effect
T14442	23926-23929	NNS	denotes	QTL
T14443	23930-23933	CC	denotes	and
T14444	23934-23940	VB	denotes	search
T14445	23941-23944	IN	denotes	for
T14446	23945-23954	JJ	denotes	potential
T14448	23955-23964	NN	denotes	candidate
T14447	23965-23970	NNS	denotes	genes
T14449	23971-23977	IN	denotes	within
T14450	23978-23982	PRP	denotes	them
T14451	23982-23983	.	denotes	.
T14452	23983-24125	sentence	denotes	However, it is noteworthy that the low statistical threshold and small number of animals per group could lead to some false positive results.
T14453	23984-23991	RB	denotes	However
T14455	23991-23993	,	denotes	,
T14456	23993-23995	PRP	denotes	it
T14454	23996-23998	VBZ	denotes	is
T14457	23999-24009	JJ	denotes	noteworthy
T14458	24010-24014	IN	denotes	that
T14460	24015-24018	DT	denotes	the
T14462	24019-24022	JJ	denotes	low
T14463	24023-24034	JJ	denotes	statistical
T14461	24035-24044	NN	denotes	threshold
T14464	24045-24048	CC	denotes	and
T14465	24049-24054	JJ	denotes	small
T14466	24055-24061	NN	denotes	number
T14467	24062-24064	IN	denotes	of
T14468	24065-24072	NNS	denotes	animals
T14469	24073-24076	IN	denotes	per
T14470	24077-24082	NN	denotes	group
T14471	24083-24088	MD	denotes	could
T14459	24089-24093	VB	denotes	lead
T14472	24094-24096	IN	denotes	to
T14473	24097-24101	DT	denotes	some
T14475	24102-24107	JJ	denotes	false
T14476	24108-24116	JJ	denotes	positive
T14474	24117-24124	NNS	denotes	results
T14477	24124-24125	.	denotes	.
T14478	24125-24262	sentence	denotes	On the genome level, some of the eight small-effect QTL identified using a very low threshold value (P < 0.05) could be false positives.
T14479	24126-24128	IN	denotes	On
T14481	24129-24132	DT	denotes	the
T14483	24133-24139	NN	denotes	genome
T14482	24140-24145	NN	denotes	level
T14484	24145-24147	,	denotes	,
T14485	24147-24151	DT	denotes	some
T14486	24152-24154	IN	denotes	of
T14487	24155-24158	DT	denotes	the
T14489	24159-24164	CD	denotes	eight
T14490	24165-24170	JJ	denotes	small
T14492	24170-24171	HYPH	denotes	-
T14491	24171-24177	NN	denotes	effect
T14488	24178-24181	NNS	denotes	QTL
T14493	24182-24192	VBN	denotes	identified
T14494	24193-24198	VBG	denotes	using
T14495	24199-24200	DT	denotes	a
T14497	24201-24205	RB	denotes	very
T14498	24206-24209	JJ	denotes	low
T14499	24210-24219	NN	denotes	threshold
T14496	24220-24225	NN	denotes	value
T14500	24226-24227	-LRB-	denotes	(
T14502	24227-24228	NN	denotes	P
T14503	24229-24230	SYM	denotes	<
T14501	24231-24235	CD	denotes	0.05
T14504	24235-24236	-RRB-	denotes	)
T14505	24237-24242	MD	denotes	could
T14480	24243-24245	VB	denotes	be
T14506	24246-24251	JJ	denotes	false
T14507	24252-24261	NNS	denotes	positives
T14508	24261-24262	.	denotes	.
T14509	24262-24384	sentence	denotes	For example, locus 4 was identified with a low P value and does not overlap with any previously identified arthritis QTL.
T14510	24263-24266	IN	denotes	For
T14512	24267-24274	NN	denotes	example
T14513	24274-24276	,	denotes	,
T14514	24276-24281	NN	denotes	locus
T14515	24282-24283	CD	denotes	4
T14516	24284-24287	VBD	denotes	was
T14511	24288-24298	VBN	denotes	identified
T14517	24299-24303	IN	denotes	with
T14518	24304-24305	DT	denotes	a
T14520	24306-24309	JJ	denotes	low
T14521	24310-24311	NN	denotes	P
T14519	24312-24317	NN	denotes	value
T14522	24318-24321	CC	denotes	and
T14523	24322-24326	VBZ	denotes	does
T14525	24327-24330	RB	denotes	not
T14524	24331-24338	VB	denotes	overlap
T14526	24339-24343	IN	denotes	with
T14527	24344-24347	DT	denotes	any
T14529	24348-24358	RB	denotes	previously
T14530	24359-24369	VBN	denotes	identified
T14531	24370-24379	NN	denotes	arthritis
T14528	24380-24383	NNS	denotes	QTL
T14532	24383-24384	.	denotes	.
T14533	24384-24579	sentence	denotes	On the transcriptome level, the small number of animals per group and the low threshold used to detect gene expression could also result in false positives in the differentially expressed genes.
T14534	24385-24387	IN	denotes	On
T14536	24388-24391	DT	denotes	the
T14538	24392-24405	NN	denotes	transcriptome
T14537	24406-24411	NN	denotes	level
T14539	24411-24413	,	denotes	,
T14540	24413-24416	DT	denotes	the
T14542	24417-24422	JJ	denotes	small
T14541	24423-24429	NN	denotes	number
T14543	24430-24432	IN	denotes	of
T14544	24433-24440	NNS	denotes	animals
T14545	24441-24444	IN	denotes	per
T14546	24445-24450	NN	denotes	group
T14547	24451-24454	CC	denotes	and
T14548	24455-24458	DT	denotes	the
T14550	24459-24462	JJ	denotes	low
T14549	24463-24472	NN	denotes	threshold
T14551	24473-24477	VBN	denotes	used
T14552	24478-24480	TO	denotes	to
T14553	24481-24487	VB	denotes	detect
T14554	24488-24492	NN	denotes	gene
T14555	24493-24503	NN	denotes	expression
T14556	24504-24509	MD	denotes	could
T14557	24510-24514	RB	denotes	also
T14535	24515-24521	VB	denotes	result
T14558	24522-24524	IN	denotes	in
T14559	24525-24530	JJ	denotes	false
T14560	24531-24540	NNS	denotes	positives
T14561	24541-24543	IN	denotes	in
T14562	24544-24547	DT	denotes	the
T14564	24548-24562	RB	denotes	differentially
T14565	24563-24572	VBN	denotes	expressed
T14563	24573-24578	NNS	denotes	genes
T14566	24578-24579	.	denotes	.
T14567	24579-24725	sentence	denotes	Furthermore, the differential expression of a gene could result not only from allele difference between two strains, but also from other factors.
T14568	24580-24591	RB	denotes	Furthermore
T14570	24591-24593	,	denotes	,
T14571	24593-24596	DT	denotes	the
T14573	24597-24609	JJ	denotes	differential
T14572	24610-24620	NN	denotes	expression
T14574	24621-24623	IN	denotes	of
T14575	24624-24625	DT	denotes	a
T14576	24626-24630	NN	denotes	gene
T14577	24631-24636	MD	denotes	could
T14569	24637-24643	VB	denotes	result
T14578	24644-24647	RB	denotes	not
T14580	24648-24652	RB	denotes	only
T14579	24653-24657	IN	denotes	from
T14581	24658-24664	NN	denotes	allele
T14582	24665-24675	NN	denotes	difference
T14583	24676-24683	IN	denotes	between
T14584	24684-24687	CD	denotes	two
T14585	24688-24695	NNS	denotes	strains
T14586	24695-24697	,	denotes	,
T14587	24697-24700	CC	denotes	but
T14588	24701-24705	RB	denotes	also
T14589	24706-24710	IN	denotes	from
T14590	24711-24716	JJ	denotes	other
T14591	24717-24724	NNS	denotes	factors
T14592	24724-24725	.	denotes	.
T14593	24725-24788	sentence	denotes	Therefore, our findings should be confirmed in future studies.
T14594	24726-24735	RB	denotes	Therefore
T14596	24735-24737	,	denotes	,
T14597	24737-24740	PRP$	denotes	our
T14598	24741-24749	NNS	denotes	findings
T14599	24750-24756	MD	denotes	should
T14600	24757-24759	VB	denotes	be
T14595	24760-24769	VBN	denotes	confirmed
T14601	24770-24772	IN	denotes	in
T14602	24773-24779	JJ	denotes	future
T14603	24780-24787	NNS	denotes	studies
T14604	24787-24788	.	denotes	.
T14922	24801-24803	PRP	denotes	We
T14923	24804-24811	VBP	denotes	present
T14924	24812-24813	DT	denotes	a
T14925	24814-24822	NN	denotes	strategy
T14926	24823-24825	TO	denotes	to
T14927	24826-24832	VB	denotes	search
T14928	24833-24842	NN	denotes	candidate
T14929	24843-24848	NNS	denotes	genes
T14930	24849-24852	IN	denotes	for
T14931	24853-24858	JJ	denotes	small
T14933	24858-24859	HYPH	denotes	-
T14932	24859-24865	NN	denotes	effect
T14934	24866-24869	NNS	denotes	QTL
T14935	24869-24870	.	denotes	.
T14936	24870-24977	sentence	denotes	With this strategy, we identified 21 candidate genes for 8 small-effect QTL regulating CIA susceptibility.
T14937	24871-24875	IN	denotes	With
T14939	24876-24880	DT	denotes	this
T14940	24881-24889	NN	denotes	strategy
T14941	24889-24891	,	denotes	,
T14942	24891-24893	PRP	denotes	we
T14938	24894-24904	VBD	denotes	identified
T14943	24905-24907	CD	denotes	21
T14945	24908-24917	NN	denotes	candidate
T14944	24918-24923	NNS	denotes	genes
T14946	24924-24927	IN	denotes	for
T14947	24928-24929	CD	denotes	8
T14949	24930-24935	JJ	denotes	small
T14951	24935-24936	HYPH	denotes	-
T14950	24936-24942	NN	denotes	effect
T14952	24943-24946	NNS	denotes	QTL
T14953	24947-24957	VBG	denotes	regulating
T14954	24958-24961	NN	denotes	CIA
T14948	24962-24976	NN	denotes	susceptibility
T14955	24976-24977	.	denotes	.
T14956	24977-25038	sentence	denotes	Our future studies will be carried out using two approaches.
T14957	24978-24981	PRP$	denotes	Our
T14959	24982-24988	JJ	denotes	future
T14958	24989-24996	NNS	denotes	studies
T14961	24997-25001	MD	denotes	will
T14962	25002-25004	VB	denotes	be
T14960	25005-25012	VBN	denotes	carried
T14963	25013-25016	RP	denotes	out
T14964	25017-25022	VBG	denotes	using
T14965	25023-25026	CD	denotes	two
T14966	25027-25037	NNS	denotes	approaches
T14967	25037-25038	.	denotes	.
T14968	25038-25199	sentence	denotes	The first is generating congenic animals for promising small-effect QTL that have relatively high P values and overlap with previously-identified arthritis QTL.
T14969	25039-25042	DT	denotes	The
T14970	25043-25048	JJ	denotes	first
T14972	25049-25051	VBZ	denotes	is
T14971	25052-25062	VBG	denotes	generating
T14973	25063-25071	JJ	denotes	congenic
T14974	25072-25079	NNS	denotes	animals
T14975	25080-25083	IN	denotes	for
T14976	25084-25093	VBG	denotes	promising
T14978	25094-25099	JJ	denotes	small
T14980	25099-25100	HYPH	denotes	-
T14979	25100-25106	NN	denotes	effect
T14977	25107-25110	NNS	denotes	QTL
T14981	25111-25115	WDT	denotes	that
T14982	25116-25120	VBP	denotes	have
T14983	25121-25131	RB	denotes	relatively
T14984	25132-25136	JJ	denotes	high
T14986	25137-25138	NN	denotes	P
T14985	25139-25145	NNS	denotes	values
T14987	25146-25149	CC	denotes	and
T14988	25150-25157	VBP	denotes	overlap
T14989	25158-25162	IN	denotes	with
T14990	25163-25173	RB	denotes	previously
T14992	25173-25174	HYPH	denotes	-
T14991	25174-25184	VBN	denotes	identified
T14994	25185-25194	NN	denotes	arthritis
T14993	25195-25198	NNS	denotes	QTL
T14995	25198-25199	.	denotes	.
T14996	25199-25288	sentence	denotes	The second approach is investigating candidate genes using both mouse and human studies.
T14997	25200-25203	DT	denotes	The
T14999	25204-25210	JJ	denotes	second
T14998	25211-25219	NN	denotes	approach
T15000	25220-25222	VBZ	denotes	is
T15001	25223-25236	VBG	denotes	investigating
T15002	25237-25246	NN	denotes	candidate
T15003	25247-25252	NNS	denotes	genes
T15004	25253-25258	VBG	denotes	using
T15005	25259-25263	CC	denotes	both
T15006	25264-25269	NN	denotes	mouse
T15008	25270-25273	CC	denotes	and
T15009	25274-25279	JJ	denotes	human
T15007	25280-25287	NNS	denotes	studies
T15010	25287-25288	.	denotes	.
T15011	25288-25391	sentence	denotes	Candidate genes will be selected according to their function and polymorphism between the two strains.
T15012	25289-25298	NN	denotes	Candidate
T15013	25299-25304	NNS	denotes	genes
T15015	25305-25309	MD	denotes	will
T15016	25310-25312	VB	denotes	be
T15014	25313-25321	VBN	denotes	selected
T15017	25322-25331	VBG	denotes	according
T15018	25332-25334	IN	denotes	to
T15019	25335-25340	PRP$	denotes	their
T15020	25341-25349	NN	denotes	function
T15021	25350-25353	CC	denotes	and
T15022	25354-25366	NN	denotes	polymorphism
T15023	25367-25374	IN	denotes	between
T15024	25375-25378	DT	denotes	the
T15026	25379-25382	CD	denotes	two
T15025	25383-25390	NNS	denotes	strains
T15027	25390-25391	.	denotes	.
T15028	25391-25480	sentence	denotes	Thereafter, we will generate knock-out mice to investigate the role of the genes in CIA.
T15029	25392-25402	RB	denotes	Thereafter
T15031	25402-25404	,	denotes	,
T15032	25404-25406	PRP	denotes	we
T15033	25407-25411	MD	denotes	will
T15030	25412-25420	VB	denotes	generate
T15034	25421-25426	VB	denotes	knock
T15036	25426-25427	HYPH	denotes	-
T15037	25427-25430	RP	denotes	out
T15035	25431-25435	NNS	denotes	mice
T15038	25436-25438	TO	denotes	to
T15039	25439-25450	VB	denotes	investigate
T15040	25451-25454	DT	denotes	the
T15041	25455-25459	NN	denotes	role
T15042	25460-25462	IN	denotes	of
T15043	25463-25466	DT	denotes	the
T15044	25467-25472	NNS	denotes	genes
T15045	25473-25475	IN	denotes	in
T15046	25476-25479	NN	denotes	CIA
T15047	25479-25480	.	denotes	.
T15048	25480-25644	sentence	denotes	For the loci whose counterparts on the human genome are linked to RA, we will investigate the candidate genes using case-control association studies in RA cohorts.
T15049	25481-25484	IN	denotes	For
T15051	25485-25488	DT	denotes	the
T15052	25489-25493	NNS	denotes	loci
T15053	25494-25499	WP$	denotes	whose
T15054	25500-25512	NNS	denotes	counterparts
T15056	25513-25515	IN	denotes	on
T15057	25516-25519	DT	denotes	the
T15059	25520-25525	JJ	denotes	human
T15058	25526-25532	NN	denotes	genome
T15060	25533-25536	VBP	denotes	are
T15055	25537-25543	VBN	denotes	linked
T15061	25544-25546	IN	denotes	to
T15062	25547-25549	NN	denotes	RA
T15063	25549-25551	,	denotes	,
T15064	25551-25553	PRP	denotes	we
T15065	25554-25558	MD	denotes	will
T15050	25559-25570	VB	denotes	investigate
T15066	25571-25574	DT	denotes	the
T15068	25575-25584	NN	denotes	candidate
T15067	25585-25590	NNS	denotes	genes
T15069	25591-25596	VBG	denotes	using
T15070	25597-25601	NN	denotes	case
T15072	25601-25602	HYPH	denotes	-
T15071	25602-25609	NN	denotes	control
T15074	25610-25621	NN	denotes	association
T15073	25622-25629	NNS	denotes	studies
T15075	25630-25632	IN	denotes	in
T15076	25633-25635	NN	denotes	RA
T15077	25636-25643	NNS	denotes	cohorts
T15078	25643-25644	.	denotes	.
R1	T458	T459	amod	global,approaches
R10	T467	T466	compound	candidate,genes
R100	T565	T566	advmod	Second,detected
R1000	T3269	T3266	advmod	specific,expressed
R1001	T3270	T3269	punct	-,specific
R1002	T3271	T3266	advmod	differentially,expressed
R1003	T3272	T3266	prep	during,expressed
R1004	T3273	T3272	pobj	CIA,during
R1005	T3274	T3266	punct	;,expressed
R1006	T3275	T3266	cc	and,expressed
R1007	T3276	T3277	nsubjpass	they,expressed
R1008	T3277	T3266	conj	expressed,expressed
R1009	T3278	T3277	auxpass	are,expressed
R101	T567	T566	punct	", ",detected
R1010	T3279	T3280	npadvmod	strain,specific
R1011	T3280	T3277	advmod	specific,expressed
R1012	T3281	T3280	punct	-,specific
R1013	T3282	T3277	advmod	differentially,expressed
R1014	T3283	T3277	prep	between,expressed
R1015	T3284	T3285	det	the,strains
R1016	T3285	T3283	pobj	strains,between
R1017	T3286	T3285	nummod	two,strains
R1018	T3287	T3285	amod	parental,strains
R1019	T3288	T3277	prep	during,expressed
R102	T568	T566	nsubj	we,detected
R1020	T3289	T3288	pobj	CIA,during
R1021	T3290	T3249	punct	.,located
R1022	T4045	T4044	punct	", ",Animals
R1023	T4046	T4044	conj	immunisation,Animals
R1024	T4047	T4046	cc	and,immunisation
R1025	T4048	T4046	conj	assessment,immunisation
R1026	T4049	T4048	prep	of,assessment
R1027	T4050	T4049	pobj	arthritis,of
R1028	T4052	T4053	preconj	Both,DBA
R1029	T4053	T4054	nmod	DBA,mice
R103	T569	T570	compound	gene,expression
R1030	T4054	T4061	nsubjpass	mice,obtained
R1031	T4055	T4053	punct	/,DBA
R1032	T4056	T4053	nummod	1,DBA
R1033	T4057	T4053	cc	and,DBA
R1034	T4058	T4059	compound	FVB,N
R1035	T4059	T4053	conj	N,DBA
R1036	T4060	T4059	punct	/,N
R1037	T4062	T4054	acl	used,mice
R1038	T4063	T4062	prep	in,used
R1039	T4064	T4065	det	this,study
R104	T570	T571	compound	expression,patterns
R1040	T4065	T4063	pobj	study,in
R1041	T4066	T4061	auxpass	were,obtained
R1042	T4067	T4061	prep	from,obtained
R1043	T4068	T4069	det	the,Laboratory
R1044	T4069	T4067	pobj	Laboratory,from
R1045	T4070	T4069	compound	Jackson,Laboratory
R1046	T4071	T4061	cc	and,obtained
R1047	T4072	T4061	conj	kept,obtained
R1048	T4073	T4072	prep	in,kept
R1049	T4074	T4075	det	a,environment
R105	T571	T566	dobj	patterns,detected
R1050	T4075	T4073	pobj	environment,in
R1051	T4076	T4077	npadvmod	climate,controlled
R1052	T4077	T4075	amod	controlled,environment
R1053	T4078	T4077	punct	-,controlled
R1054	T4079	T4075	prep	with,environment
R1055	T4080	T4081	nummod	12,hour
R1056	T4081	T4082	compound	hour,cycles
R1057	T4082	T4079	pobj	cycles,with
R1058	T4083	T4084	compound	light,dark
R1059	T4084	T4082	compound	dark,cycles
R106	T572	T571	prep	of,patterns
R1060	T4085	T4084	punct	/,dark
R1061	T4086	T4075	prep	in,environment
R1062	T4087	T4088	det	the,facility
R1063	T4088	T4086	pobj	facility,in
R1064	T4089	T4088	compound	animal,facility
R1065	T4090	T4088	prep	at,facility
R1066	T4091	T4092	det	the,University
R1067	T4092	T4090	pobj	University,at
R1068	T4093	T4092	prep	of,University
R1069	T4094	T4093	pobj	Rostock,of
R107	T573	T574	det	both,strains
R1070	T4095	T4061	punct	.,obtained
R1071	T4097	T4098	det	All,experiments
R1072	T4098	T4100	nsubjpass	experiments,pre-approved
R1073	T4099	T4098	compound	animal,experiments
R1074	T4101	T4100	auxpass	were,pre-approved
R1075	T4102	T4100	agent	by,pre-approved
R1076	T4103	T4104	det	the,Committee
R1077	T4104	T4102	pobj	Committee,by
R1078	T4105	T4104	compound	State,Committee
R1079	T4106	T4107	compound	Animal,Care
R108	T574	T572	pobj	strains,of
R1080	T4107	T4104	compound	Care,Committee
R1081	T4108	T4100	punct	.,pre-approved
R1082	T4110	T4111	nsubjpass	CIA,induced
R1083	T4112	T4111	auxpass	was,induced
R1084	T4113	T4111	prep	in,induced
R1085	T4114	T4115	nmod	control,animals
R1086	T4115	T4113	pobj	animals,in
R1087	T4116	T4114	cc	and,control
R1088	T4117	T4114	conj	experimental,control
R1089	T4118	T4111	prep	according,induced
R109	T575	T566	prep	during,detected
R1090	T4119	T4118	prep	to,according
R1091	T4120	T4121	amod	established,protocols
R1092	T4121	T4119	pobj	protocols,to
R1093	T4122	T4121	acl	described,protocols
R1094	T4123	T4122	advmod	previously,described
R1095	T4124	T4125	punct	[,10
R1096	T4125	T4111	parataxis	10,induced
R1097	T4126	T4125	punct	],10
R1098	T4127	T4111	punct	.,induced
R1099	T4129	T4130	prep	In,immunised
R11	T468	T466	prep	of,genes
R110	T576	T575	pobj	CIA,during
R1100	T4131	T4129	pobj	brief,In
R1101	T4132	T4130	punct	", ",immunised
R1102	T4133	T4134	nmod	DBA,1J
R1103	T4134	T4136	nmod	1J,progeny
R1104	T4135	T4134	punct	/,1J
R1105	T4136	T4130	nsubjpass	progeny,immunised
R1106	T4137	T4134	punct	", ",1J
R1107	T4138	T4139	compound	FVB,N
R1108	T4139	T4134	conj	N,1J
R1109	T4140	T4139	punct	/,N
R111	T577	T566	punct	.,detected
R1110	T4141	T4139	cc	and,N
R1111	T4142	T4143	punct	(,1J
R1112	T4143	T4139	conj	1J,N
R1113	T4144	T4143	compound	DBA,1J
R1114	T4145	T4143	punct	/,1J
R1115	T4146	T4143	punct	×,1J
R1116	T4147	T4148	compound	FVB,N
R1117	T4148	T4143	appos	N,1J
R1118	T4149	T4148	punct	/,N
R1119	T4150	T4143	punct	),1J
R112	T579	T580	det	The,genes
R1120	T4151	T4136	compound	F2,progeny
R1121	T4152	T4130	auxpass	were,immunised
R1122	T4153	T4130	prep	at,immunised
R1123	T4154	T4155	quantmod	8,12
R1124	T4155	T4157	nummod	12,weeks
R1125	T4156	T4155	quantmod	to,12
R1126	T4157	T4153	pobj	weeks,at
R1127	T4158	T4130	prep	at,immunised
R1128	T4159	T4160	det	the,base
R1129	T4160	T4158	pobj	base,at
R113	T580	T582	nsubjpass	genes,identified
R1130	T4161	T4160	prep	of,base
R1131	T4162	T4163	det	the,tail
R1132	T4163	T4161	pobj	tail,of
R1133	T4164	T4130	prep	with,immunised
R1134	T4165	T4166	nummod	125,μg
R1135	T4166	T4164	pobj	μg,with
R1136	T4167	T4166	prep	of,μg
R1137	T4168	T4169	amod	bovine,Collagen
R1138	T4169	T4167	pobj	Collagen,of
R1139	T4170	T4169	nummod	II,Collagen
R114	T581	T580	compound	candidate,genes
R1140	T4171	T4172	punct	(,Chondrex
R1141	T4172	T4169	parataxis	Chondrex,Collagen
R1142	T4173	T4172	punct	", ",Chondrex
R1143	T4174	T4172	npadvmod	Redmond,Chondrex
R1144	T4175	T4172	punct	", ",Chondrex
R1145	T4176	T4172	npadvmod	WA,Chondrex
R1146	T4177	T4172	punct	", ",Chondrex
R1147	T4178	T4172	npadvmod	USA,Chondrex
R1148	T4179	T4172	punct	),Chondrex
R1149	T4180	T4169	acl	emulsified,Collagen
R115	T582	T584	ccomp	identified,located
R1150	T4181	T4180	prep	in,emulsified
R1151	T4182	T4181	pobj	CFA,in
R1152	T4183	T4184	punct	(,DIFCO
R1153	T4184	T4182	parataxis	DIFCO,CFA
R1154	T4185	T4184	punct	", ",DIFCO
R1155	T4186	T4184	npadvmod	Detroit,DIFCO
R1156	T4187	T4184	punct	", ",DIFCO
R1157	T4188	T4184	npadvmod	MI,DIFCO
R1158	T4189	T4184	punct	", ",DIFCO
R1159	T4190	T4184	npadvmod	USA,DIFCO
R116	T583	T582	auxpass	were,identified
R1160	T4191	T4184	punct	),DIFCO
R1161	T4192	T4130	punct	.,immunised
R1162	T4194	T4195	det	The,scoring
R1163	T4195	T4197	nsubj	scoring,commenced
R1164	T4196	T4195	amod	clinical,scoring
R1165	T4198	T4195	prep	of,scoring
R1166	T4199	T4198	pobj	arthritis,of
R1167	T4200	T4201	nummod	18,days
R1168	T4201	T4202	npadvmod	days,after
R1169	T4202	T4197	prep	after,commenced
R117	T585	T582	advcl	using,identified
R1170	T4203	T4202	pobj	immunisation,after
R1171	T4204	T4197	punct	", ",commenced
R1172	T4205	T4197	cc	and,commenced
R1173	T4206	T4207	nsubjpass	animals,monitored
R1174	T4207	T4197	conj	monitored,commenced
R1175	T4208	T4207	auxpass	were,monitored
R1176	T4209	T4210	nummod	three,times
R1177	T4210	T4211	npadvmod	times,weekly
R1178	T4211	T4207	advmod	weekly,monitored
R1179	T4212	T4207	prep	for,monitored
R118	T586	T587	nummod	three,criteria
R1180	T4213	T4212	pobj	signs,for
R1181	T4214	T4213	prep	of,signs
R1182	T4215	T4214	pobj	CIA,of
R1183	T4216	T4207	punct	.,monitored
R1184	T4218	T4219	compound	Arthritis,development
R1185	T4219	T4220	nsubjpass	development,monitored
R1186	T4221	T4220	auxpass	was,monitored
R1187	T4222	T4220	prep	in,monitored
R1188	T4223	T4224	det	all,limbs
R1189	T4224	T4222	pobj	limbs,in
R119	T587	T585	dobj	criteria,using
R1190	T4225	T4224	nummod	four,limbs
R1191	T4226	T4220	advcl	using,monitored
R1192	T4227	T4228	det	a,system
R1193	T4228	T4226	dobj	system,using
R1194	T4229	T4230	nummod	three,score
R1195	T4230	T4228	compound	score,system
R1196	T4231	T4230	punct	-,score
R1197	T4232	T4228	prep	per,system
R1198	T4233	T4232	pobj	limb,per
R1199	T4234	T4235	mark	as,described
R12	T469	T470	amod	small,effect
R120	T588	T584	punct	: ,located
R1200	T4235	T4226	advcl	described,using
R1201	T4236	T4235	advmod	previously,described
R1202	T4237	T4238	punct	[,10
R1203	T4238	T4220	parataxis	10,monitored
R1204	T4239	T4238	punct	],10
R1205	T4240	T4220	punct	.,monitored
R1206	T4242	T4243	nummod	Eight,week
R1207	T4243	T4245	npadvmod	week,old
R1208	T4244	T4243	punct	-,week
R1209	T4245	T4246	amod	old,mice
R121	T589	T584	nsubjpass	they,located
R1210	T4246	T4254	nsubjpass	mice,used
R1211	T4247	T4248	nmod	FVB,N
R1212	T4248	T4246	nmod	N,mice
R1213	T4249	T4248	punct	/,N
R1214	T4250	T4248	cc	and,N
R1215	T4251	T4252	compound	DBA,1J
R1216	T4252	T4248	conj	1J,N
R1217	T4253	T4252	punct	/,1J
R1218	T4255	T4254	auxpass	were,used
R1219	T4256	T4254	prep	for,used
R122	T590	T584	auxpass	are,located
R1220	T4257	T4258	det	the,detection
R1221	T4258	T4256	pobj	detection,for
R1222	T4259	T4258	prep	of,detection
R1223	T4260	T4261	compound	gene,expression
R1224	T4261	T4259	pobj	expression,of
R1225	T4262	T4254	punct	.,used
R1226	T4264	T4265	nsubjpass	They,divided
R1227	T4266	T4265	auxpass	were,divided
R1228	T4267	T4265	prep	into,divided
R1229	T4268	T4269	nummod	four,groups
R123	T591	T584	prep	in,located
R1230	T4269	T4267	pobj	groups,into
R1231	T4270	T4269	amod	experimental,groups
R1232	T4271	T4265	prep	according,divided
R1233	T4272	T4271	prep	to,according
R1234	T4273	T4274	det	the,phases
R1235	T4274	T4272	pobj	phases,to
R1236	T4275	T4274	amod	different,phases
R1237	T4276	T4274	prep	of,phases
R1238	T4277	T4276	pobj	CIA,of
R1239	T4278	T4274	punct	", ",phases
R124	T592	T593	det	a,region
R1240	T4279	T4280	advmod	namely,control
R1241	T4280	T4274	appos	control,phases
R1242	T4281	T4280	amod	naive,control
R1243	T4282	T4280	punct	(,control
R1244	T4283	T4280	appos	NC,control
R1245	T4284	T4280	punct	),control
R1246	T4285	T4280	punct	", ",control
R1247	T4286	T4280	conj	post-immunisation,control
R1248	T4287	T4286	punct	(,post-immunisation
R1249	T4288	T4286	appos	PI,post-immunisation
R125	T593	T591	pobj	region,in
R1250	T4289	T4286	punct	),post-immunisation
R1251	T4290	T4286	punct	", ",post-immunisation
R1252	T4291	T4286	conj	onset,post-immunisation
R1253	T4292	T4291	prep	of,onset
R1254	T4293	T4292	pobj	arthritis,of
R1255	T4294	T4291	punct	(,onset
R1256	T4295	T4291	appos	OA,onset
R1257	T4296	T4291	punct	),onset
R1258	T4297	T4291	cc	and,onset
R1259	T4298	T4299	amod	chronic,arthritis
R126	T594	T593	amod	genomic,region
R1260	T4299	T4291	conj	arthritis,onset
R1261	T4300	T4299	punct	(,arthritis
R1262	T4301	T4299	appos	CA,arthritis
R1263	T4302	T4299	punct	),arthritis
R1264	T4303	T4304	punct	(,Table
R1265	T4304	T4265	parataxis	Table,divided
R1266	T4305	T4304	nummod	1,Table
R1267	T4306	T4304	punct	),Table
R1268	T4307	T4265	punct	.,divided
R1269	T4309	T4310	det	The,group
R127	T595	T593	acl	linked,region
R1270	T4310	T4312	nsubj	group,contained
R1271	T4311	T4310	compound	NC,group
R1272	T4313	T4314	amod	non-immunised,mice
R1273	T4314	T4312	dobj	mice,contained
R1274	T4315	T4316	dep	that,sacrificed
R1275	T4316	T4314	relcl	sacrificed,mice
R1276	T4317	T4316	auxpass	were,sacrificed
R1277	T4318	T4316	prep	at,sacrificed
R1278	T4319	T4320	det	the,age
R1279	T4320	T4318	pobj	age,at
R128	T596	T595	prep	to,linked
R1280	T4321	T4320	prep	of,age
R1281	T4322	T4323	nummod	8,weeks
R1282	T4323	T4321	pobj	weeks,of
R1283	T4324	T4312	punct	.,contained
R1284	T4326	T4327	det	The,mice
R1285	T4327	T4328	nsubjpass	mice,sacrificed
R1286	T4329	T4327	prep	in,mice
R1287	T4330	T4331	det	the,group
R1288	T4331	T4329	pobj	group,in
R1289	T4332	T4331	compound	PI,group
R129	T597	T596	pobj	CIA,to
R1290	T4333	T4328	auxpass	were,sacrificed
R1291	T4334	T4328	prep	on,sacrificed
R1292	T4335	T4334	pobj	day,on
R1293	T4336	T4335	nummod	10,day
R1294	T4337	T4335	prep	after,day
R1295	T4338	T4337	pobj	immunisation,after
R1296	T4339	T4328	punct	.,sacrificed
R1297	T4341	T4342	det	The,mice
R1298	T4342	T4343	nsubjpass	mice,sacrificed
R1299	T4344	T4342	prep	in,mice
R13	T470	T472	nmod	effect,loci
R130	T598	T584	punct	;,located
R1300	T4345	T4346	det	the,group
R1301	T4346	T4344	pobj	group,in
R1302	T4347	T4346	compound	OA,group
R1303	T4348	T4343	auxpass	were,sacrificed
R1304	T4349	T4343	prep	on,sacrificed
R1305	T4350	T4349	pobj	day,on
R1306	T4351	T4350	nummod	35,day
R1307	T4352	T4350	prep	after,day
R1308	T4353	T4352	pobj	immunisation,after
R1309	T4354	T4343	punct	.,sacrificed
R131	T599	T600	nsubjpass	they,expressed
R1310	T4356	T4357	nummod	Three,mice
R1311	T4357	T4362	nsubjpass	mice,sacrificed
R1312	T4358	T4359	nmod	FVB,N
R1313	T4359	T4357	nmod	N,mice
R1314	T4360	T4359	punct	/,N
R1315	T4361	T4357	amod	non-arthritic,mice
R1316	T4363	T4357	cc	and,mice
R1317	T4364	T4365	nummod	three,mice
R1318	T4365	T4357	conj	mice,mice
R1319	T4366	T4365	nmod	DBA,mice
R132	T600	T584	conj	expressed,located
R1320	T4367	T4366	punct	/,DBA
R1321	T4368	T4366	nummod	1,DBA
R1322	T4369	T4370	dep	that,showed
R1323	T4370	T4365	relcl	showed,mice
R1324	T4371	T4370	dobj	signs,showed
R1325	T4372	T4371	prep	of,signs
R1326	T4373	T4372	pobj	arthritis,of
R1327	T4374	T4370	prep	on,showed
R1328	T4375	T4376	nmod	day,33
R1329	T4376	T4374	pobj	33,on
R133	T601	T600	auxpass	are,expressed
R1330	T4377	T4376	cc	or,33
R1331	T4378	T4376	conj	34,33
R1332	T4379	T4376	prep	after,33
R1333	T4380	T4379	pobj	immunisation,after
R1334	T4381	T4362	auxpass	were,sacrificed
R1335	T4382	T4362	prep	on,sacrificed
R1336	T4383	T4382	pobj	day,on
R1337	T4384	T4383	nummod	35,day
R1338	T4385	T4383	prep	after,day
R1339	T4386	T4385	pobj	immunisation,after
R134	T602	T603	npadvmod	disease,specific
R1340	T4387	T4362	punct	.,sacrificed
R1341	T4389	T4390	det	The,mice
R1342	T4390	T4391	nsubjpass	mice,sacrificed
R1343	T4392	T4390	prep	in,mice
R1344	T4393	T4394	det	the,group
R1345	T4394	T4392	pobj	group,in
R1346	T4395	T4394	compound	CA,group
R1347	T4396	T4391	auxpass	were,sacrificed
R1348	T4397	T4391	prep	on,sacrificed
R1349	T4398	T4397	pobj	day,on
R135	T603	T600	advmod	specific,expressed
R1350	T4399	T4398	nummod	95,day
R1351	T4400	T4398	prep	after,day
R1352	T4401	T4400	pobj	immunisation,after
R1353	T4402	T4391	punct	.,sacrificed
R1354	T4404	T4405	nummod	Three,mice
R1355	T4405	T4410	nsubjpass	mice,sacrificed
R1356	T4406	T4405	amod	non-arthritic,mice
R1357	T4407	T4408	compound	FVB,N
R1358	T4408	T4405	compound	N,mice
R1359	T4409	T4408	punct	/,N
R136	T604	T603	punct	-,specific
R1360	T4411	T4405	cc	and,mice
R1361	T4412	T4413	nummod	three,mice
R1362	T4413	T4405	conj	mice,mice
R1363	T4414	T4413	nmod	DBA,mice
R1364	T4415	T4414	punct	/,DBA
R1365	T4416	T4414	nummod	1,DBA
R1366	T4417	T4418	dep	that,developed
R1367	T4418	T4413	relcl	developed,mice
R1368	T4419	T4418	aux	had,developed
R1369	T4420	T4418	dobj	arthritis,developed
R137	T605	T600	advmod	differentially,expressed
R1370	T4421	T4418	prep	for,developed
R1371	T4422	T4423	advmod	at,two
R1372	T4423	T4425	nummod	two,months
R1373	T4424	T4423	advmod	least,two
R1374	T4425	T4421	pobj	months,for
R1375	T4426	T4410	auxpass	were,sacrificed
R1376	T4427	T4410	prep	on,sacrificed
R1377	T4428	T4427	pobj	day,on
R1378	T4429	T4428	nummod	95,day
R1379	T4430	T4428	prep	after,day
R138	T606	T600	prep	during,expressed
R1380	T4431	T4430	pobj	immunisation,after
R1381	T4432	T4410	punct	.,sacrificed
R1382	T4628	T4629	compound	Linkage,analysis
R1383	T4631	T4632	amod	Detailed,information
R1384	T4632	T4633	nsubjpass	information,described
R1385	T4634	T4632	prep	on,information
R1386	T4635	T4634	pobj	genotyping,on
R1387	T4636	T4635	prep	of,genotyping
R1388	T4637	T4638	det	the,screen
R1389	T4638	T4636	pobj	screen,of
R139	T607	T606	pobj	CIA,during
R1390	T4639	T4638	compound	genome,screen
R1391	T4640	T4633	aux	has,described
R1392	T4641	T4633	auxpass	been,described
R1393	T4642	T4633	advmod	previously,described
R1394	T4643	T4644	punct	[,10
R1395	T4644	T4633	parataxis	10,described
R1396	T4645	T4644	punct	],10
R1397	T4646	T4633	punct	.,described
R1398	T4648	T4649	prep	In,genotyped
R1399	T4650	T4648	amod	short,In
R14	T471	T470	punct	-,effect
R140	T608	T600	punct	;,expressed
R1400	T4651	T4649	punct	", ",genotyped
R1401	T4652	T4649	nsubj	we,genotyped
R1402	T4653	T4654	nummod	290,mice
R1403	T4654	T4649	dobj	mice,genotyped
R1404	T4655	T4654	compound	F2,mice
R1405	T4656	T4649	advcl	using,genotyped
R1406	T4657	T4658	nummod	126,markers
R1407	T4658	T4656	dobj	markers,using
R1408	T4659	T4658	amod	informative,markers
R1409	T4660	T4658	compound	microsatellite,markers
R141	T609	T600	cc	and,expressed
R1410	T4661	T4658	acl	covering,markers
R1411	T4662	T4663	det	the,genome
R1412	T4663	T4661	dobj	genome,covering
R1413	T4664	T4661	prep	with,covering
R1414	T4665	T4666	det	an,distance
R1415	T4666	T4664	pobj	distance,with
R1416	T4667	T4666	amod	average,distance
R1417	T4668	T4666	amod	inter-marker,distance
R1418	T4669	T4666	prep	of,distance
R1419	T4670	T4671	nummod	11.5,cM
R142	T610	T611	nsubjpass	they,expressed
R1420	T4671	T4669	pobj	cM,of
R1421	T4672	T4666	prep	for,distance
R1422	T4673	T4674	nummod	290,progeny
R1423	T4674	T4672	pobj	progeny,for
R1424	T4675	T4674	compound	F2,progeny
R1425	T4676	T4649	punct	.,genotyped
R1426	T4678	T4679	det	All,analyses
R1427	T4679	T4681	nsubjpass	analyses,performed
R1428	T4680	T4679	compound	linkage,analyses
R1429	T4682	T4681	auxpass	were,performed
R143	T611	T600	conj	expressed,expressed
R1430	T4683	T4681	prep	with,performed
R1431	T4684	T4685	compound	QTX,software
R1432	T4685	T4683	pobj	software,with
R1433	T4686	T4687	compound	Map,manager
R1434	T4687	T4685	compound	manager,software
R1435	T4688	T4689	punct	[,23
R1436	T4689	T4681	parataxis	23,performed
R1437	T4690	T4689	punct	],23
R1438	T4691	T4681	punct	.,performed
R1439	T4693	T4694	det	The,phenotype
R144	T612	T611	auxpass	are,expressed
R1440	T4694	T4697	nsubjpass	phenotype,taken
R1441	T4695	T4694	amod	main,phenotype
R1442	T4696	T4694	amod	clinical,phenotype
R1443	T4698	T4694	prep	of,phenotype
R1444	T4699	T4698	pobj	CIA,of
R1445	T4700	T4694	punct	", ",phenotype
R1446	T4701	T4702	compound	arthritis,severity
R1447	T4702	T4694	appos	severity,phenotype
R1448	T4703	T4697	punct	", ",taken
R1449	T4704	T4697	auxpass	was,taken
R145	T613	T614	npadvmod	strain,specific
R1450	T4705	T4697	prep	as,taken
R1451	T4706	T4705	pobj	phenotype,as
R1452	T4707	T4697	punct	.,taken
R1453	T4709	T4710	aux	To,detect
R1454	T4710	T4711	advcl	detect,set
R1455	T4712	T4713	det	the,QTL
R1456	T4713	T4710	dobj	QTL,detect
R1457	T4714	T4715	amod	small,effect
R1458	T4715	T4713	compound	effect,QTL
R1459	T4716	T4715	punct	-,effect
R146	T614	T611	advmod	specific,expressed
R1460	T4717	T4711	punct	", ",set
R1461	T4718	T4719	det	the,value
R1462	T4719	T4711	nsubjpass	value,set
R1463	T4720	T4719	compound	threshold,value
R1464	T4721	T4719	prep	of,value
R1465	T4722	T4721	pobj	linkage,of
R1466	T4723	T4711	auxpass	was,set
R1467	T4724	T4711	prep	as,set
R1468	T4725	T4726	nsubj	P,0.05
R1469	T4726	T4724	pcomp	0.05,as
R147	T615	T614	punct	-,specific
R1470	T4727	T4726	punct	=,0.05
R1471	T4728	T4729	punct	(,test
R1472	T4729	T4726	parataxis	test,0.05
R1473	T4730	T4731	compound	Chi,square
R1474	T4731	T4729	compound	square,test
R1475	T4732	T4731	punct	-,square
R1476	T4733	T4729	punct	),test
R1477	T4734	T4711	punct	.,set
R1478	T5000	T5001	compound	Sample,preparation
R1479	T5002	T5001	cc	and,preparation
R148	T616	T611	advmod	differentially,expressed
R1480	T5003	T5004	compound	microarray,hybridisation
R1481	T5004	T5001	conj	hybridisation,preparation
R1482	T5006	T5007	compound	Lymph,nodes
R1483	T5007	T5008	nsubjpass	nodes,used
R1484	T5009	T5007	punct	(,nodes
R1485	T5010	T5007	appos	LNs,nodes
R1486	T5011	T5007	punct	),nodes
R1487	T5012	T5007	acl	draining,nodes
R1488	T5013	T5014	det	the,site
R1489	T5014	T5012	dobj	site,draining
R149	T617	T611	prep	regarding,expressed
R1490	T5015	T5014	compound	immunisation,site
R1491	T5016	T5008	auxpass	were,used
R1492	T5017	T5008	prep	for,used
R1493	T5018	T5019	amod	total,preparation
R1494	T5019	T5017	pobj	preparation,for
R1495	T5020	T5019	compound	RNA,preparation
R1496	T5021	T5008	punct	.,used
R1497	T5023	T5024	det	The,RNA
R1498	T5024	T5026	nsubjpass	RNA,extracted
R1499	T5025	T5024	amod	total,RNA
R15	T472	T468	pobj	loci,of
R150	T618	T619	det	the,strains
R1500	T5027	T5026	auxpass	was,extracted
R1501	T5028	T5026	prep	from,extracted
R1502	T5029	T5030	det	the,homogenates
R1503	T5030	T5028	pobj	homogenates,from
R1504	T5031	T5030	compound	tissue,homogenates
R1505	T5032	T5026	advcl	using,extracted
R1506	T5033	T5034	det	a,kit
R1507	T5034	T5032	dobj	kit,using
R1508	T5035	T5034	amod	commercial,kit
R1509	T5036	T5026	prep	in,extracted
R151	T619	T617	pobj	strains,regarding
R1510	T5037	T5036	pobj	accordance,in
R1511	T5038	T5037	prep	with,accordance
R1512	T5039	T5040	det	the,protocol
R1513	T5040	T5038	pobj	protocol,with
R1514	T5041	T5040	amod	provided,protocol
R1515	T5042	T5043	punct	(,QIGEN
R1516	T5043	T5026	parataxis	QIGEN,extracted
R1517	T5044	T5043	punct	", ",QIGEN
R1518	T5045	T5043	npadvmod	Hilden,QIGEN
R1519	T5046	T5043	punct	", ",QIGEN
R152	T620	T619	nummod	two,strains
R1520	T5047	T5043	npadvmod	Germany,QIGEN
R1521	T5048	T5043	punct	),QIGEN
R1522	T5049	T5026	punct	.,extracted
R1523	T5051	T5052	nsubjpass	Analysis,conducted
R1524	T5053	T5051	prep	of,Analysis
R1525	T5054	T5055	compound	gene,expression
R1526	T5055	T5053	pobj	expression,of
R1527	T5056	T5052	auxpass	was,conducted
R1528	T5057	T5052	advcl	using,conducted
R1529	T5058	T5059	det	a,array
R153	T621	T619	amod	parental,strains
R1530	T5059	T5057	dobj	array,using
R1531	T5060	T5059	compound	U430A,array
R1532	T5061	T5062	punct	(,Affymetrix
R1533	T5062	T5059	parataxis	Affymetrix,array
R1534	T5063	T5062	punct	", ",Affymetrix
R1535	T5064	T5065	compound	Santa,Clara
R1536	T5065	T5062	npadvmod	Clara,Affymetrix
R1537	T5066	T5062	punct	", ",Affymetrix
R1538	T5067	T5062	npadvmod	CA,Affymetrix
R1539	T5068	T5062	punct	", ",Affymetrix
R154	T622	T584	punct	.,located
R1540	T5069	T5062	npadvmod	USA,Affymetrix
R1541	T5070	T5062	punct	),Affymetrix
R1542	T5071	T5059	acl	interrogating,array
R1543	T5072	T5073	amod	more,"22,000"
R1544	T5073	T5075	nummod	"22,000",genes
R1545	T5074	T5073	quantmod	than,"22,000"
R1546	T5075	T5071	dobj	genes,interrogating
R1547	T5076	T5052	punct	.,conducted
R1548	T5078	T5079	compound	RNA,probes
R1549	T5079	T5080	nsubjpass	probes,labelled
R155	T624	T625	nummod	Eight,QTL
R1550	T5081	T5080	auxpass	were,labelled
R1551	T5082	T5080	prep	in,labelled
R1552	T5083	T5082	pobj	accordance,in
R1553	T5084	T5083	prep	with,accordance
R1554	T5085	T5086	det	the,manufacturer
R1555	T5086	T5087	poss	manufacturer,instructions
R1556	T5087	T5084	pobj	instructions,with
R1557	T5088	T5086	case	's,manufacturer
R1558	T5089	T5080	punct	.,labelled
R1559	T5091	T5092	nsubjpass	Samples,hybridised
R156	T625	T629	nsubjpass	QTL,identified
R1560	T5093	T5091	prep	from,Samples
R1561	T5094	T5095	amod	individual,mice
R1562	T5095	T5093	pobj	mice,from
R1563	T5096	T5092	auxpass	were,hybridised
R1564	T5097	T5092	prep	onto,hybridised
R1565	T5098	T5099	amod	individual,arrays
R1566	T5099	T5097	pobj	arrays,onto
R1567	T5100	T5092	punct	.,hybridised
R1568	T5102	T5103	nsubjpass	Hybridisation,done
R1569	T5104	T5102	cc	and,Hybridisation
R157	T626	T627	amod	small,effect
R1570	T5105	T5102	conj	washing,Hybridisation
R1571	T5106	T5102	prep	of,Hybridisation
R1572	T5107	T5108	compound	gene,chips
R1573	T5108	T5106	pobj	chips,of
R1574	T5109	T5103	auxpass	were,done
R1575	T5110	T5111	mark	as,described
R1576	T5111	T5103	advcl	described,done
R1577	T5112	T5111	advmod	previously,described
R1578	T5113	T5114	punct	[,16
R1579	T5114	T5103	parataxis	16,done
R158	T627	T625	compound	effect,QTL
R1580	T5115	T5114	punct	],16
R1581	T5116	T5103	punct	.,done
R1582	T5118	T5119	amod	Fluorescent,signals
R1583	T5119	T5120	nsubjpass	signals,collected
R1584	T5121	T5120	auxpass	were,collected
R1585	T5122	T5120	prep	by,collected
R1586	T5123	T5124	compound	laser,scan
R1587	T5124	T5122	pobj	scan,by
R1588	T5125	T5126	punct	(,Scanner
R1589	T5126	T5124	parataxis	Scanner,scan
R159	T628	T627	punct	-,effect
R1590	T5127	T5128	compound	Hewlett,Packard
R1591	T5128	T5126	compound	Packard,Scanner
R1592	T5129	T5128	punct	-,Packard
R1593	T5130	T5126	compound	Gene,Scanner
R1594	T5131	T5126	punct	),Scanner
R1595	T5132	T5120	punct	.,collected
R1596	T5603	T5604	compound	Microarray,analysis
R1597	T5606	T5607	nsubjpass	Normalisation,done
R1598	T5608	T5606	prep	of,Normalisation
R1599	T5609	T5610	det	the,level
R16	T473	T474	amod	quantitative,trait
R160	T630	T625	acl	controlling,QTL
R1600	T5610	T5608	pobj	level,of
R1601	T5611	T5610	compound	expression,level
R1602	T5612	T5607	auxpass	was,done
R1603	T5613	T5607	advcl	using,done
R1604	T5614	T5615	compound	Affymetrix,MAS
R1605	T5615	T5613	dobj	MAS,using
R1606	T5616	T5615	compound	software,MAS
R1607	T5617	T5615	nummod	5,MAS
R1608	T5618	T5615	punct	", ",MAS
R1609	T5619	T5620	dep	which,based
R161	T631	T632	compound	CIA,severity
R1610	T5620	T5615	relcl	based,MAS
R1611	T5621	T5620	auxpass	is,based
R1612	T5622	T5620	prep	on,based
R1613	T5623	T5624	amod	global,scaling
R1614	T5624	T5622	pobj	scaling,on
R1615	T5625	T5624	prep	of,scaling
R1616	T5626	T5627	amod	total,level
R1617	T5627	T5625	pobj	level,of
R1618	T5628	T5629	compound	gene,expression
R1619	T5629	T5627	compound	expression,level
R162	T632	T630	dobj	severity,controlling
R1620	T5630	T5627	prep	per,level
R1621	T5631	T5630	pobj	microarray,per
R1622	T5632	T5607	punct	.,done
R1623	T5634	T5635	det	The,values
R1624	T5635	T5638	nsubjpass	values,imported
R1625	T5636	T5635	amod	normalised,values
R1626	T5637	T5635	compound	expression,values
R1627	T5639	T5638	auxpass	were,imported
R1628	T5640	T5638	prep	to,imported
R1629	T5641	T5638	cc	and,imported
R163	T633	T629	auxpass	were,identified
R1630	T5642	T5638	conj	analysed,imported
R1631	T5643	T5642	prep	by,analysed
R1632	T5644	T5642	dobj	dCHIP,analysed
R1633	T5645	T5646	punct	[,24
R1634	T5646	T5642	parataxis	24,analysed
R1635	T5647	T5646	punct	],24
R1636	T5648	T5638	punct	.,imported
R1637	T5650	T5651	advmod	Differentially,expressed
R1638	T5651	T5652	amod	expressed,genes
R1639	T5652	T5653	nsubjpass	genes,identified
R164	T634	T629	punct	.,identified
R1640	T5654	T5653	auxpass	were,identified
R1641	T5655	T5653	prep	by,identified
R1642	T5656	T5655	pcomp	defining,by
R1643	T5657	T5658	det	the,criteria
R1644	T5658	T5656	dobj	criteria,defining
R1645	T5659	T5658	amod	appropriate,criteria
R1646	T5660	T5658	compound	filtering,criteria
R1647	T5661	T5656	prep	in,defining
R1648	T5662	T5663	det	the,software
R1649	T5663	T5661	pobj	software,in
R165	T636	T637	prep	Of,expressed
R1650	T5664	T5663	compound	dCHIP,software
R1651	T5665	T5656	prep	as,defining
R1652	T5666	T5665	punct	: ,as
R1653	T5667	T5668	amod	lower,%
R1654	T5668	T5670	compound	%,boundary
R1655	T5669	T5668	nummod	90,%
R1656	T5670	T5672	nsubj	boundary,exceeded
R1657	T5671	T5670	compound	confidence,boundary
R1658	T5672	T5680	ccomp	exceeded,was
R1659	T5673	T5670	prep	of,boundary
R166	T638	T639	nummod	"22,000",genes
R1660	T5674	T5675	compound	fold,change
R1661	T5675	T5673	pobj	change,of
R1662	T5676	T5670	prep	between,boundary
R1663	T5677	T5678	det	the,means
R1664	T5678	T5676	pobj	means,between
R1665	T5679	T5678	compound	group,means
R1666	T5680	T5665	pcomp	was,as
R1667	T5681	T5672	advmod	twofold,exceeded
R1668	T5682	T5680	punct	;,was
R1669	T5683	T5684	det	the,difference
R167	T639	T636	pobj	genes,Of
R1670	T5684	T5686	nsubj	difference,exceeded
R1671	T5685	T5684	amod	absolute,difference
R1672	T5686	T5680	ccomp	exceeded,was
R1673	T5687	T5684	prep	between,difference
R1674	T5688	T5689	det	the,groups
R1675	T5689	T5687	pobj	groups,between
R1676	T5690	T5689	nummod	two,groups
R1677	T5691	T5686	dobj	100,exceeded
R1678	T5692	T5680	punct	;,was
R1679	T5693	T5694	det	the,threshold
R168	T640	T639	amod	screened,genes
R1680	T5694	T5680	nsubj	threshold,was
R1681	T5695	T5696	compound	P,value
R1682	T5696	T5694	compound	value,threshold
R1683	T5697	T5694	prep	of,threshold
R1684	T5698	T5699	det	the,test
R1685	T5699	T5697	pobj	test,of
R1686	T5700	T5699	amod	unpaired,test
R1687	T5701	T5699	compound	t,test
R1688	T5702	T5699	punct	-,test
R1689	T5703	T5680	attr	0.05,was
R169	T641	T637	punct	", ",expressed
R1690	T5704	T5653	punct	.,identified
R1691	T5706	T5707	det	The,rate
R1692	T5707	T5710	nsubjpass	rate,established
R1693	T5708	T5709	amod	false,discovery
R1694	T5709	T5707	compound	discovery,rate
R1695	T5711	T5710	auxpass	was,established
R1696	T5712	T5710	prep	with,established
R1697	T5713	T5714	det	a,test
R1698	T5714	T5712	pobj	test,with
R1699	T5715	T5714	compound	permutation,test
R17	T474	T472	compound	trait,loci
R170	T642	T637	nsubjpass	117,expressed
R1700	T5716	T5714	prep	for,test
R1701	T5717	T5718	det	each,comparison
R1702	T5718	T5716	pobj	comparison,for
R1703	T5719	T5718	amod	pairwise,comparison
R1704	T5720	T5721	aux	to,estimate
R1705	T5721	T5710	advcl	estimate,established
R1706	T5722	T5723	det	the,proportion
R1707	T5723	T5721	dobj	proportion,estimate
R1708	T5724	T5723	prep	of,proportion
R1709	T5725	T5726	amod	false,positive
R171	T643	T637	auxpass	were,expressed
R1710	T5726	T5728	amod	positive,genes
R1711	T5727	T5726	punct	-,positive
R1712	T5728	T5724	pobj	genes,of
R1713	T5729	T5710	punct	.,established
R1714	T5731	T5732	amod	Hierarchical,clustering
R1715	T5732	T5734	nsubjpass	clustering,performed
R1716	T5733	T5732	compound	gene,clustering
R1717	T5735	T5734	auxpass	was,performed
R1718	T5736	T5734	prep	with,performed
R1719	T5737	T5736	pobj	dCHIP,with
R172	T644	T645	preconj	both,specific
R1720	T5738	T5739	aux	to,characterise
R1721	T5739	T5734	advcl	characterise,performed
R1722	T5740	T5741	det	the,patterns
R1723	T5741	T5739	dobj	patterns,characterise
R1724	T5742	T5743	compound	gene,expression
R1725	T5743	T5741	compound	expression,patterns
R1726	T5744	T5741	prep	during,patterns
R1727	T5745	T5744	pobj	CIA,during
R1728	T5746	T5734	punct	.,performed
R1729	T5748	T5749	det	The,algorithm
R173	T645	T637	advmod	specific,expressed
R1730	T5749	T5752	nsubj	algorithm,was
R1731	T5750	T5749	compound	default,algorithm
R1732	T5751	T5749	compound	clustering,algorithm
R1733	T5752	T5755	ccomp	was,defined
R1734	T5753	T5749	prep	of,algorithm
R1735	T5754	T5753	pobj	genes,of
R1736	T5756	T5757	mark	as,follows
R1737	T5757	T5752	advcl	follows,was
R1738	T5758	T5755	punct	: ,defined
R1739	T5759	T5760	det	the,distance
R174	T646	T645	npadvmod	strain,specific
R1740	T5760	T5755	nsubjpass	distance,defined
R1741	T5761	T5760	prep	between,distance
R1742	T5762	T5763	nummod	two,genes
R1743	T5763	T5761	pobj	genes,between
R1744	T5764	T5755	auxpass	is,defined
R1745	T5765	T5755	prep	as,defined
R1746	T5766	T5767	nummod	1,r
R1747	T5767	T5765	pobj	r,as
R1748	T5768	T5767	punct	–,r
R1749	T5769	T5767	punct	", ",r
R175	T647	T645	punct	-,specific
R1750	T5770	T5771	advmod	where,is
R1751	T5771	T5767	relcl	is,r
R1752	T5772	T5771	nsubj	r,is
R1753	T5773	T5774	det	the,coefficient
R1754	T5774	T5771	attr	coefficient,is
R1755	T5775	T5774	compound	Pearson,coefficient
R1756	T5776	T5774	compound	correlation,coefficient
R1757	T5777	T5774	prep	between,coefficient
R1758	T5778	T5779	det	the,values
R1759	T5779	T5777	pobj	values,between
R176	T648	T645	cc	and,specific
R1760	T5780	T5779	amod	standardised,values
R1761	T5781	T5779	compound	expression,values
R1762	T5782	T5779	prep	of,values
R1763	T5783	T5784	det	the,genes
R1764	T5784	T5782	pobj	genes,of
R1765	T5785	T5784	nummod	two,genes
R1766	T5786	T5784	prep	across,genes
R1767	T5787	T5788	det	the,samples
R1768	T5788	T5786	pobj	samples,across
R1769	T5789	T5788	acl	used,samples
R177	T649	T650	npadvmod	disease,specific
R1770	T5790	T5755	punct	.,defined
R1771	T5792	T5793	aux	To,characterise
R1772	T5793	T5794	advcl	characterise,performed
R1773	T5795	T5796	det	the,relationship
R1774	T5796	T5793	dobj	relationship,characterise
R1775	T5797	T5796	amod	functional,relationship
R1776	T5798	T5796	prep	between,relationship
R1777	T5799	T5800	advmod	differentially,genes
R1778	T5800	T5798	pobj	genes,between
R1779	T5801	T5800	amod	expressed,genes
R178	T650	T645	conj	specific,specific
R1780	T5802	T5794	punct	", ",performed
R1781	T5803	T5804	nmod	Gene,Ontology
R1782	T5804	T5805	nmod	Ontology,classification
R1783	T5805	T5794	nsubjpass	classification,performed
R1784	T5806	T5804	punct	(,Ontology
R1785	T5807	T5804	appos	GO,Ontology
R1786	T5808	T5805	punct	),classification
R1787	T5809	T5805	compound	term,classification
R1788	T5810	T5805	acl	incorporated,classification
R1789	T5811	T5810	prep	in,incorporated
R179	T651	T650	punct	-,specific
R1790	T5812	T5813	compound	DNA,Chip
R1791	T5813	T5815	compound	Chip,Analyzer
R1792	T5814	T5813	punct	-,Chip
R1793	T5815	T5811	pobj	Analyzer,in
R1794	T5816	T5794	auxpass	was,performed
R1795	T5817	T5794	punct	.,performed
R1796	T5819	T5820	det	The,level
R1797	T5820	T5822	nsubjpass	level,set
R1798	T5821	T5820	amod	significant,level
R1799	T5823	T5820	prep	for,level
R18	T475	T464	prep	in,identify
R180	T652	T637	advmod	differentially,expressed
R1800	T5824	T5825	det	a,cluster
R1801	T5825	T5823	pobj	cluster,for
R1802	T5826	T5825	compound	function,cluster
R1803	T5827	T5822	auxpass	was,set
R1804	T5828	T5822	prep	at,set
R1805	T5829	T5828	pobj	P,at
R1806	T5830	T5831	punct	<,0.005
R1807	T5831	T5829	amod	0.005,P
R1808	T5832	T5822	punct	", ",set
R1809	T5833	T5822	cc	and,set
R181	T653	T637	prep	during,expressed
R1810	T5834	T5835	det	the,size
R1811	T5835	T5837	nsubj	size,was
R1812	T5836	T5835	amod	minimum,size
R1813	T5837	T5822	conj	was,set
R1814	T5838	T5835	prep	of,size
R1815	T5839	T5840	det	a,cluster
R1816	T5840	T5838	pobj	cluster,of
R1817	T5841	T5842	nummod	three,genes
R1818	T5842	T5837	attr	genes,was
R1819	T5843	T5837	punct	.,was
R182	T654	T653	pobj	CIA,during
R1824	T7078	T7079	amod	Small,effect
R1825	T7079	T7081	compound	effect,QTL
R1826	T7080	T7079	punct	-,effect
R1827	T7082	T7081	prep	of,QTL
R1828	T7083	T7082	pobj	CIA,of
R1829	T7084	T7081	prep	in,QTL
R183	T655	T637	punct	.,expressed
R1830	T7085	T7086	punct	(,DBA
R1831	T7086	T7087	nmod	DBA,progeny
R1832	T7087	T7084	pobj	progeny,in
R1833	T7088	T7086	punct	/,DBA
R1834	T7089	T7086	nummod	1,DBA
R1835	T7090	T7086	punct	×,DBA
R1836	T7091	T7092	compound	FVB,N
R1837	T7092	T7086	appos	N,DBA
R1838	T7093	T7092	punct	/,N
R1839	T7094	T7086	punct	),DBA
R184	T657	T658	prep	Of,located
R1840	T7095	T7087	compound	F2,progeny
R1841	T7097	T7098	prep	In,carried
R1842	T7099	T7100	det	a,study
R1843	T7100	T7097	pobj	study,In
R1844	T7101	T7100	amod	previous,study
R1845	T7102	T7098	punct	", ",carried
R1846	T7103	T7098	nsubj	we,carried
R1847	T7104	T7098	prt	out,carried
R1848	T7105	T7106	det	a,screen
R1849	T7106	T7098	dobj	screen,carried
R185	T659	T660	det	these,genes
R1850	T7107	T7106	compound	genome,screen
R1851	T7108	T7109	aux	to,identify
R1852	T7109	T7098	advcl	identify,carried
R1853	T7110	T7109	dobj	QTL,identify
R1854	T7111	T7110	acl	controlling,QTL
R1855	T7112	T7113	compound	CIA,susceptibility
R1856	T7113	T7111	dobj	susceptibility,controlling
R1857	T7114	T7111	prep	in,controlling
R1858	T7115	T7116	punct	(,DBA
R1859	T7116	T7117	nmod	DBA,progeny
R186	T660	T657	pobj	genes,Of
R1860	T7117	T7114	pobj	progeny,in
R1861	T7118	T7116	punct	/,DBA
R1862	T7119	T7116	nummod	1,DBA
R1863	T7120	T7121	punct	×,N
R1864	T7121	T7116	prep	N,DBA
R1865	T7122	T7121	compound	FVB,N
R1866	T7123	T7121	punct	/,N
R1867	T7124	T7116	punct	),DBA
R1868	T7125	T7117	compound	F2,progeny
R1869	T7126	T7098	punct	.,carried
R187	T661	T660	nummod	117,genes
R1870	T7128	T7129	prep	For,identified
R1871	T7130	T7131	det	the,phenotype
R1872	T7131	T7128	pobj	phenotype,For
R1873	T7132	T7131	prep	of,phenotype
R1874	T7133	T7134	compound	arthritis,severity
R1875	T7134	T7132	pobj	severity,of
R1876	T7135	T7129	punct	", ",identified
R1877	T7136	T7137	advmod	only,QTL
R1878	T7137	T7129	nsubjpass	QTL,identified
R1879	T7138	T7137	nummod	one,QTL
R188	T662	T658	punct	", ",located
R1880	T7139	T7137	punct	", ",QTL
R1881	T7140	T7137	appos	Cia2,QTL
R1882	T7141	T7129	punct	", ",identified
R1883	T7142	T7129	auxpass	was,identified
R1884	T7143	T7129	punct	", ",identified
R1885	T7144	T7129	prep	with,identified
R1886	T7145	T7146	det	a,score
R1887	T7146	T7144	pobj	score,with
R1888	T7147	T7148	advmod	highly,significant
R1889	T7148	T7146	amod	significant,score
R189	T663	T658	nsubjpass	21,located
R1890	T7149	T7146	nmod	logarithm,score
R1891	T7150	T7149	prep	of,logarithm
R1892	T7151	T7152	det	the,odds
R1893	T7152	T7150	pobj	odds,of
R1894	T7153	T7149	punct	(,logarithm
R1895	T7154	T7149	appos	LOD,logarithm
R1896	T7155	T7146	punct	),score
R1897	T7156	T7146	prep	of,score
R1898	T7157	T7156	pobj	12,of
R1899	T7158	T7159	punct	[,10
R19	T476	T477	npadvmod	collagen,induced
R190	T664	T658	auxpass	were,located
R1900	T7159	T7129	parataxis	10,identified
R1901	T7160	T7159	punct	],10
R1902	T7161	T7129	punct	.,identified
R1903	T7163	T7164	advmod	However,contributed
R1904	T7165	T7164	punct	", ",contributed
R1905	T7166	T7164	nsubj	Cia2,contributed
R1906	T7167	T7164	prep	to,contributed
R1907	T7168	T7169	advmod	only,%
R1908	T7169	T7167	pobj	%,to
R1909	T7170	T7169	nummod	16,%
R191	T665	T658	prep	inside,located
R1910	T7171	T7169	prep	of,%
R1911	T7172	T7173	det	the,variations
R1912	T7173	T7171	pobj	variations,of
R1913	T7174	T7173	compound	phenotype,variations
R1914	T7175	T7164	punct	", ",contributed
R1915	T7176	T7164	advcl	indicating,contributed
R1916	T7177	T7178	mark	that,be
R1917	T7178	T7176	ccomp	be,indicating
R1918	T7179	T7178	expl	there,be
R1919	T7180	T7178	aux	should,be
R192	T666	T667	det	the,intervals
R1920	T7181	T7182	det	some,QTL
R1921	T7182	T7178	attr	QTL,be
R1922	T7183	T7184	amod	small,effect
R1923	T7184	T7182	compound	effect,QTL
R1924	T7185	T7184	punct	-,effect
R1925	T7186	T7187	poss	whose,contributions
R1926	T7187	T7188	dep	contributions,were
R1927	T7188	T7182	relcl	were,QTL
R1928	T7189	T7187	prep	to,contributions
R1929	T7190	T7189	pobj	CIA,to
R193	T667	T665	pobj	intervals,inside
R1930	T7191	T7188	neg	not,were
R1931	T7192	T7188	acomp	big,were
R1932	T7193	T7192	advmod	enough,big
R1933	T7194	T7195	aux	to,reach
R1934	T7195	T7192	xcomp	reach,big
R1935	T7196	T7197	det	the,value
R1936	T7197	T7195	dobj	value,reach
R1937	T7198	T7199	amod	significant,threshold
R1938	T7199	T7197	compound	threshold,value
R1939	T7200	T7197	prep	of,value
R194	T668	T667	compound	support,intervals
R1940	T7201	T7200	pobj	linkage,of
R1941	T7202	T7164	punct	.,contributed
R1942	T7204	T7205	aux	To,identify
R1943	T7205	T7206	advcl	identify,reanalyzed
R1944	T7207	T7208	det	these,QTL
R1945	T7208	T7205	dobj	QTL,identify
R1946	T7209	T7208	amod	potential,QTL
R1947	T7210	T7211	amod	small,effect
R1948	T7211	T7208	compound	effect,QTL
R1949	T7212	T7211	punct	-,effect
R195	T669	T667	prep	of,intervals
R1950	T7213	T7206	punct	", ",reanalyzed
R1951	T7214	T7206	nsubj	we,reanalyzed
R1952	T7215	T7216	det	the,data
R1953	T7216	T7206	dobj	data,reanalyzed
R1954	T7217	T7206	advcl	using,reanalyzed
R1955	T7218	T7219	det	a,value
R1956	T7219	T7217	dobj	value,using
R1957	T7220	T7221	amod	lower,threshold
R1958	T7221	T7219	compound	threshold,value
R1959	T7222	T7219	prep	of,value
R196	T670	T671	det	the,QTL
R1960	T7223	T7222	pobj	linkage,of
R1961	T7224	T7225	punct	(,0.05
R1962	T7225	T7219	parataxis	0.05,value
R1963	T7226	T7225	nsubj	P,0.05
R1964	T7227	T7225	punct	=,0.05
R1965	T7228	T7225	punct	),0.05
R1966	T7229	T7206	punct	.,reanalyzed
R1967	T7231	T7232	nsubj	We,reasoned
R1968	T7233	T7234	mark	that,masked
R1969	T7234	T7232	ccomp	masked,reasoned
R197	T671	T669	pobj	QTL,of
R1970	T7235	T7236	mark	since,proven
R1971	T7236	T7234	advcl	proven,masked
R1972	T7237	T7238	det	the,gene
R1973	T7238	T7236	nsubjpass	gene,proven
R1974	T7239	T7238	amod	main,gene
R1975	T7240	T7238	compound	candidate,gene
R1976	T7241	T7238	prep	of,gene
R1977	T7242	T7241	pobj	Cia2,of
R1978	T7243	T7238	punct	", ",gene
R1979	T7244	T7245	compound	complement,C5
R198	T672	T671	nummod	8,QTL
R1980	T7245	T7238	appos	C5,gene
R1981	T7246	T7245	compound	component,C5
R1982	T7247	T7248	punct	(,Hc
R1983	T7248	T7245	parataxis	Hc,C5
R1984	T7249	T7248	punct	),Hc
R1985	T7250	T7236	punct	", ",proven
R1986	T7251	T7236	auxpass	was,proven
R1987	T7252	T7253	aux	to,be
R1988	T7253	T7236	xcomp	be,proven
R1989	T7254	T7253	acomp	essential,be
R199	T673	T674	amod	small,effect
R1990	T7255	T7254	prep	for,essential
R1991	T7256	T7257	compound	CIA,development
R1992	T7257	T7255	pobj	development,for
R1993	T7258	T7236	cc	and,proven
R1994	T7259	T7260	mark	because,is
R1995	T7260	T7236	conj	is,proven
R1996	T7261	T7262	det	the,strain
R1997	T7262	T7260	nsubj	strain,is
R1998	T7263	T7264	compound	FVB,N
R1999	T7264	T7262	compound	N,strain
R2	T459	T456	dobj	approaches,Combining
R20	T477	T479	amod	induced,arthritis
R200	T674	T671	compound	effect,QTL
R2000	T7265	T7264	punct	/,N
R2001	T7266	T7267	npadvmod	C5,deficient
R2002	T7267	T7260	acomp	deficient,is
R2003	T7268	T7269	punct	[,25
R2004	T7269	T7260	parataxis	25,is
R2005	T7270	T7269	nummod	10,25
R2006	T7271	T7269	punct	",",25
R2007	T7272	T7269	punct	],25
R2008	T7273	T7234	punct	", ",masked
R2009	T7274	T7275	det	some,QTL
R201	T675	T674	punct	-,effect
R2010	T7275	T7234	nsubjpass	QTL,masked
R2011	T7276	T7277	amod	small,effect
R2012	T7277	T7275	compound	effect,QTL
R2013	T7278	T7277	punct	-,effect
R2014	T7279	T7234	aux	might,masked
R2015	T7280	T7234	auxpass	be,masked
R2016	T7281	T7234	agent	by,masked
R2017	T7282	T7281	pobj	Cia2,by
R2018	T7283	T7232	punct	.,reasoned
R2019	T7285	T7286	aux	To,exclude
R202	T676	T658	cc	and,located
R2020	T7286	T7287	advcl	exclude,performed
R2021	T7288	T7289	det	the,effect
R2022	T7289	T7286	dobj	effect,exclude
R2023	T7290	T7289	compound	masking,effect
R2024	T7291	T7289	prep	of,effect
R2025	T7292	T7291	pobj	C5,of
R2026	T7293	T7287	punct	", ",performed
R2027	T7294	T7287	nsubj	we,performed
R2028	T7295	T7296	compound	linkage,analysis
R2029	T7296	T7287	dobj	analysis,performed
R203	T677	T678	advmod	thus,considered
R2030	T7297	T7287	prep	with,performed
R2031	T7298	T7299	nummod	3,datasets
R2032	T7299	T7297	pobj	datasets,with
R2033	T7300	T7287	punct	", ",performed
R2034	T7301	T7302	det	the,first
R2035	T7302	T7303	nsubj	first,containing
R2036	T7303	T7287	advcl	containing,performed
R2037	T7304	T7305	det	all,progeny
R2038	T7305	T7303	dobj	progeny,containing
R2039	T7306	T7305	nummod	290,progeny
R204	T678	T658	conj	considered,located
R2040	T7307	T7305	compound	F2,progeny
R2041	T7308	T7303	punct	", ",containing
R2042	T7309	T7310	det	the,second
R2043	T7310	T7311	nsubj	second,progeny
R2044	T7311	T7303	conj	progeny,containing
R2045	T7312	T7311	nummod	77,progeny
R2046	T7313	T7311	nmod	C5+,progeny
R2047	T7314	T7313	punct	/,C5+
R2048	T7315	T7313	punct	+,C5+
R2049	T7316	T7311	compound	F2,progeny
R205	T679	T678	auxpass	were,considered
R2050	T7317	T7311	cc	and,progeny
R2051	T7318	T7319	det	the,third
R2052	T7319	T7320	nsubj	third,progeny
R2053	T7320	T7311	conj	progeny,progeny
R2054	T7321	T7320	nummod	133,progeny
R2055	T7322	T7320	nmod	C5+,progeny
R2056	T7323	T7322	punct	/,C5+
R2057	T7324	T7322	punct	-,C5+
R2058	T7325	T7320	compound	F2,progeny
R2059	T7326	T7287	punct	.,performed
R206	T680	T678	prep	as,considered
R2060	T7328	T7329	nummod	Eight,regions
R2061	T7329	T7331	nsubjpass	regions,linked
R2062	T7330	T7329	amod	genomic,regions
R2063	T7332	T7331	auxpass	were,linked
R2064	T7333	T7331	prep	to,linked
R2065	T7334	T7335	det	the,phenotype
R2066	T7335	T7333	pobj	phenotype,to
R2067	T7336	T7335	prep	of,phenotype
R2068	T7337	T7338	compound	CIA,severity
R2069	T7338	T7336	pobj	severity,of
R207	T681	T682	compound	candidate,genes
R2070	T7339	T7340	punct	(,Table
R2071	T7340	T7331	parataxis	Table,linked
R2072	T7341	T7342	nmod	loci,1
R2073	T7342	T7340	dep	1,Table
R2074	T7343	T7342	prep	to,1
R2075	T7344	T7343	pobj	8,to
R2076	T7345	T7340	punct	", ",Table
R2077	T7346	T7340	nummod	2,Table
R2078	T7347	T7340	punct	),Table
R2079	T7348	T7331	punct	", ",linked
R208	T682	T680	pobj	genes,as
R2080	T7349	T7350	mark	with,varying
R2081	T7350	T7331	advcl	varying,linked
R2082	T7351	T7352	compound	P,values
R2083	T7352	T7350	nsubj	values,varying
R2084	T7353	T7350	prep	between,varying
R2085	T7354	T7353	pobj	0.043,between
R2086	T7355	T7354	cc	and,0.043
R2087	T7356	T7354	conj	0.003,0.043
R2088	T7357	T7331	punct	.,linked
R2089	T7359	T7360	det	These,QTL
R209	T683	T658	punct	.,located
R2090	T7360	T7365	nsubjpass	QTL,located
R2091	T7361	T7360	nummod	eight,QTL
R2092	T7362	T7363	amod	small,effect
R2093	T7363	T7360	compound	effect,QTL
R2094	T7364	T7363	punct	-,effect
R2095	T7366	T7365	auxpass	were,located
R2096	T7367	T7365	prep	on,located
R2097	T7368	T7369	nmod	chromosomes,5
R2098	T7369	T7367	pobj	5,on
R2099	T7370	T7369	punct	", ",5
R21	T478	T477	punct	-,induced
R210	T2422	T2423	nsubjpass	Susceptibility,controlled
R2100	T7371	T7369	conj	6,5
R2101	T7372	T7371	punct	", ",6
R2102	T7373	T7371	conj	7,6
R2103	T7374	T7373	punct	", ",7
R2104	T7375	T7373	conj	10,7
R2105	T7376	T7375	punct	", ",10
R2106	T7377	T7375	conj	11,10
R2107	T7378	T7377	punct	", ",11
R2108	T7379	T7377	conj	16,11
R2109	T7380	T7379	punct	", ",16
R211	T2424	T2422	prep	to,Susceptibility
R2110	T7381	T7379	cc	and,16
R2111	T7382	T7379	conj	17,16
R2112	T7383	T7365	punct	.,located
R2113	T7385	T7386	nummod	Five,loci
R2114	T7386	T7387	nsubjpass	loci,identified
R2115	T7388	T7387	auxpass	were,identified
R2116	T7389	T7387	prep	in,identified
R2117	T7390	T7391	advmod	at,two
R2118	T7391	T7393	nummod	two,datasets
R2119	T7392	T7391	advmod	least,two
R212	T2425	T2426	advmod	most,diseases
R2120	T7393	T7389	pobj	datasets,in
R2121	T7394	T7387	punct	.,identified
R2122	T7396	T7397	prep	Of,had
R2123	T7398	T7399	det	the,loci
R2124	T7399	T7396	pobj	loci,Of
R2125	T7400	T7399	nummod	eight,loci
R2126	T7401	T7397	punct	", ",had
R2127	T7402	T7397	nsubj	five,had
R2128	T7403	T7397	dobj	DBA,had
R2129	T7404	T7403	punct	/,DBA
R213	T2426	T2424	pobj	diseases,to
R2130	T7405	T7403	nummod	1,DBA
R2131	T7406	T7397	prep	as,had
R2132	T7407	T7408	det	the,allele
R2133	T7408	T7406	pobj	allele,as
R2134	T7409	T7408	compound	susceptibility,allele
R2135	T7410	T7397	punct	", ",had
R2136	T7411	T7397	cc	and,had
R2137	T7412	T7413	nsubj	three,had
R2138	T7413	T7397	conj	had,had
R2139	T7414	T7415	compound	FVB,N
R214	T2427	T2426	amod	complex,diseases
R2140	T7415	T7413	dobj	N,had
R2141	T7416	T7415	punct	/,N
R2142	T7417	T7413	prep	as,had
R2143	T7418	T7419	det	the,allele
R2144	T7419	T7417	pobj	allele,as
R2145	T7420	T7419	compound	susceptibility,allele
R2146	T7421	T7397	punct	.,had
R2147	T7423	T7424	nsubj	Lander,suggested
R2148	T7425	T7423	cc	and,Lander
R2149	T7426	T7423	conj	Botstein,Lander
R215	T2428	T2423	auxpass	is,controlled
R2150	T7427	T7428	punct	[,26
R2151	T7428	T7426	parataxis	26,Botstein
R2152	T7429	T7428	punct	],26
R2153	T7430	T7431	det	a,score
R2154	T7431	T7424	dobj	score,suggested
R2155	T7432	T7431	compound	LOD,score
R2156	T7433	T7431	prep	of,score
R2157	T7434	T7435	quantmod	between,2
R2158	T7435	T7433	pobj	2,of
R2159	T7436	T7435	cc	and,2
R216	T2429	T2423	agent	by,controlled
R2160	T7437	T7435	conj	3,2
R2161	T7438	T7439	aux	to,ensure
R2162	T7439	T7424	advcl	ensure,suggested
R2163	T7440	T7441	det	an,rate
R2164	T7441	T7439	dobj	rate,ensure
R2165	T7442	T7441	amod	overall,rate
R2166	T7443	T7444	amod	false,positive
R2167	T7444	T7441	amod	positive,rate
R2168	T7445	T7441	prep	of,rate
R2169	T7446	T7447	nummod	5,%
R217	T2430	T2431	amod	many,genes
R2170	T7447	T7445	pobj	%,of
R2171	T7448	T7424	punct	", ",suggested
R2172	T7449	T7450	dep	which,means
R2173	T7450	T7424	advcl	means,suggested
R2174	T7451	T7452	mark	that,prevent
R2175	T7452	T7450	ccomp	prevent,means
R2176	T7453	T7452	csubj	using,prevent
R2177	T7454	T7455	det	a,value
R2178	T7455	T7453	dobj	value,using
R2179	T7456	T7455	amod	lower,value
R218	T2431	T2429	pobj	genes,by
R2180	T7457	T7455	compound	threshold,value
R2181	T7458	T7452	aux	will,prevent
R2182	T7459	T7460	amod	false,negative
R2183	T7460	T7461	amod	negative,QTL
R2184	T7461	T7452	dobj	QTL,prevent
R2185	T7462	T7452	prep	at,prevent
R2186	T7463	T7464	det	the,expense
R2187	T7464	T7462	pobj	expense,at
R2188	T7465	T7464	prep	of,expense
R2189	T7466	T7465	pcomp	increasing,of
R219	T2432	T2431	punct	", ",genes
R2190	T7467	T7468	amod	false,positive
R2191	T7468	T7469	amod	positive,QTL
R2192	T7469	T7466	dobj	QTL,increasing
R2193	T7470	T7424	punct	.,suggested
R2194	T7472	T7473	advcl	Being,examined
R2195	T7474	T7472	acomp	aware,Being
R2196	T7475	T7474	prep	of,aware
R2197	T7476	T7475	pobj	this,of
R2198	T7477	T7473	punct	", ",examined
R2199	T7478	T7473	nsubj	we,examined
R22	T479	T475	pobj	arthritis,in
R220	T2433	T2434	advmod	each,having
R2200	T7479	T7480	det	these,regions
R2201	T7480	T7473	dobj	regions,examined
R2202	T7481	T7480	amod	genomic,regions
R2203	T7482	T7483	aux	to,search
R2204	T7483	T7473	advcl	search,examined
R2205	T7484	T7485	mark	whether,linked
R2206	T7485	T7483	ccomp	linked,search
R2207	T7486	T7485	nsubjpass	they,linked
R2208	T7487	T7486	punct	", ",they
R2209	T7488	T7486	cc	or,they
R221	T2434	T2431	acl	having,genes
R2210	T7489	T7490	poss	their,regions
R2211	T7490	T7486	conj	regions,they
R2212	T7491	T7490	amod	syntenic,regions
R2213	T7492	T7490	amod	genomic,regions
R2214	T7493	T7490	prep	on,regions
R2215	T7494	T7495	det	the,genome
R2216	T7495	T7493	pobj	genome,on
R2217	T7496	T7495	amod	human,genome
R2218	T7497	T7485	punct	", ",linked
R2219	T7498	T7485	aux	have,linked
R222	T2435	T2436	det	a,effect
R2220	T7499	T7485	auxpass	been,linked
R2221	T7500	T7485	advmod	previously,linked
R2222	T7501	T7485	prep	to,linked
R2223	T7502	T7501	pobj	arthritis,to
R2224	T7503	T7473	punct	.,examined
R2225	T7505	T7506	nummod	Four,QTL
R2226	T7506	T7510	nsubj	QTL,overlapped
R2227	T7507	T7508	amod	small,effect
R2228	T7508	T7506	compound	effect,QTL
R2229	T7509	T7508	punct	-,effect
R223	T2436	T2434	dobj	effect,having
R2230	T7511	T7510	prep	with,overlapped
R2231	T7512	T7513	compound	arthritis,QTL
R2232	T7513	T7511	pobj	QTL,with
R2233	T7514	T7510	prep	on,overlapped
R2234	T7515	T7516	det	the,genome
R2235	T7516	T7514	pobj	genome,on
R2236	T7517	T7516	compound	mouse,genome
R2237	T7518	T7516	acl	identified,genome
R2238	T7519	T7518	advmod	previously,identified
R2239	T7520	T7510	punct	.,overlapped
R224	T2437	T2436	amod	small,effect
R2240	T7522	T7523	nmod	Locus,1
R2241	T7523	T7524	nsubj	1,overlap
R2242	T7525	T7523	cc	and,1
R2243	T7526	T7523	conj	2,1
R2244	T7527	T7524	prep	with,overlap
R2245	T7528	T7527	pobj	Cia13,with
R2246	T7529	T7528	cc	and,Cia13
R2247	T7530	T7528	conj	Cia14,Cia13
R2248	T7531	T7528	punct	", ",Cia13
R2249	T7532	T7533	dep	which,control
R225	T2438	T2436	prep	on,effect
R2250	T7533	T7528	relcl	control,Cia13
R2251	T7534	T7533	dobj	severity,control
R2252	T7535	T7534	prep	of,severity
R2253	T7536	T7535	pobj	CIA,of
R2254	T7537	T7533	prep	in,control
R2255	T7538	T7539	punct	(,DBA
R2256	T7539	T7540	nmod	DBA,progeny
R2257	T7540	T7537	pobj	progeny,in
R2258	T7541	T7539	punct	/,DBA
R2259	T7542	T7539	nummod	1,DBA
R226	T2439	T2440	det	the,disease
R2260	T7543	T7539	punct	×,DBA
R2261	T7544	T7545	compound	BALB,C
R2262	T7545	T7539	appos	C,DBA
R2263	T7546	T7545	punct	/,C
R2264	T7547	T7539	punct	),DBA
R2265	T7548	T7540	compound	F2,progeny
R2266	T7549	T7550	punct	[,27
R2267	T7550	T7524	parataxis	27,overlap
R2268	T7551	T7550	punct	],27
R2269	T7552	T7524	punct	.,overlap
R227	T2440	T2438	pobj	disease,on
R2270	T7554	T7555	nsubj	Locus,overlaps
R2271	T7556	T7554	nummod	5,Locus
R2272	T7557	T7554	acl	located,Locus
R2273	T7558	T7557	prep	on,located
R2274	T7559	T7558	pobj	chromosome,on
R2275	T7560	T7559	nummod	10,chromosome
R2276	T7561	T7555	prep	with,overlaps
R2277	T7562	T7561	pobj	Cia8,with
R2278	T7563	T7562	punct	", ",Cia8
R2279	T7564	T7565	dep	which,identified
R228	T2441	T2423	punct	.,controlled
R2280	T7565	T7562	relcl	identified,Cia8
R2281	T7566	T7565	auxpass	was,identified
R2282	T7567	T7565	prep	in,identified
R2283	T7568	T7569	punct	(,DBA
R2284	T7569	T7570	nmod	DBA,progeny
R2285	T7570	T7567	pobj	progeny,in
R2286	T7571	T7569	punct	/,DBA
R2287	T7572	T7569	nummod	1,DBA
R2288	T7573	T7569	punct	×,DBA
R2289	T7574	T7569	appos	B10.Q,DBA
R229	T2443	T2444	nummod	One,example
R2290	T7575	T7570	punct	),progeny
R2291	T7576	T7570	compound	F2,progeny
R2292	T7577	T7578	punct	[,28
R2293	T7578	T7555	parataxis	28,overlaps
R2294	T7579	T7578	punct	],28
R2295	T7580	T7555	punct	.,overlaps
R2296	T7582	T7583	nsubj	Locus,overlaps
R2297	T7584	T7582	nummod	6,Locus
R2298	T7585	T7583	prep	with,overlaps
R2299	T7586	T7585	pobj	Pgia7,with
R23	T482	T483	amod	Quantitative,traits
R230	T2444	T2445	nsubj	example,is
R2300	T7587	T7586	punct	", ",Pgia7
R2301	T7588	T7589	dep	which,controls
R2302	T7589	T7586	relcl	controls,Pgia7
R2303	T7590	T7589	dobj	susceptibility,controls
R2304	T7591	T7590	prep	to,susceptibility
R2305	T7592	T7593	npadvmod	proteoglycan,induced
R2306	T7593	T7595	amod	induced,arthritis
R2307	T7594	T7593	punct	-,induced
R2308	T7595	T7591	pobj	arthritis,to
R2309	T7596	T7595	punct	(,arthritis
R231	T2446	T2447	amod	rheumatoid,arthritis
R2310	T7597	T7595	appos	PGIA,arthritis
R2311	T7598	T7589	punct	),controls
R2312	T7599	T7589	cc	and,controls
R2313	T7600	T7601	auxpass	was,identified
R2314	T7601	T7589	conj	identified,controls
R2315	T7602	T7601	prep	in,identified
R2316	T7603	T7604	punct	(,C
R2317	T7604	T7607	nmod	C,progeny
R2318	T7605	T7604	nmod	BALB,C
R2319	T7606	T7604	punct	/,C
R232	T2447	T2445	attr	arthritis,is
R2320	T7607	T7602	pobj	progeny,in
R2321	T7608	T7604	punct	×,C
R2322	T7609	T7604	appos	DBA,C
R2323	T7610	T7609	punct	/,DBA
R2324	T7611	T7609	nummod	2,DBA
R2325	T7612	T7604	punct	),C
R2326	T7613	T7607	compound	F2,progeny
R2327	T7614	T7615	punct	[,29
R2328	T7615	T7583	parataxis	29,overlaps
R2329	T7616	T7615	punct	],29
R233	T2448	T2447	punct	(,arthritis
R2330	T7617	T7583	punct	.,overlaps
R2331	T7619	T7620	det	The,regions
R2332	T7620	T7623	nsubjpass	regions,reported
R2333	T7621	T7620	amod	syntenic,regions
R2334	T7622	T7620	amod	genomic,regions
R2335	T7624	T7620	prep	of,regions
R2336	T7625	T7626	nummod	five,QTL
R2337	T7626	T7624	pobj	QTL,of
R2338	T7627	T7628	amod	small,effect
R2339	T7628	T7626	compound	effect,QTL
R234	T2449	T2447	appos	RA,arthritis
R2340	T7629	T7628	punct	-,effect
R2341	T7630	T7626	prep	on,QTL
R2342	T7631	T7632	det	the,genome
R2343	T7632	T7630	pobj	genome,on
R2344	T7633	T7632	amod	human,genome
R2345	T7634	T7623	aux	have,reported
R2346	T7635	T7623	auxpass	been,reported
R2347	T7636	T7637	aux	to,linked
R2348	T7637	T7623	xcomp	linked,reported
R2349	T7638	T7637	auxpass	be,linked
R235	T2450	T2447	punct	),arthritis
R2350	T7639	T7637	prep	to,linked
R2351	T7640	T7639	pobj	RA,to
R2352	T7641	T7623	punct	.,reported
R2353	T7643	T7644	nsubj	These,are
R2354	T7645	T7646	amod	genomic,regions
R2355	T7646	T7644	attr	regions,are
R2356	T7647	T7646	appos	22q11,regions
R2357	T7648	T7647	cc	and,22q11
R2358	T7649	T7650	compound	12p13,q24
R2359	T7650	T7647	conj	q24,22q11
R236	T2451	T2447	punct	", ",arthritis
R2360	T7651	T7650	punct	-,q24
R2361	T7652	T7646	prep	on,regions
R2362	T7653	T7654	nmod	chromosome,22
R2363	T7654	T7652	pobj	22,on
R2364	T7655	T7654	cc	and,22
R2365	T7656	T7654	conj	12,22
R2366	T7657	T7658	punct	(,counterparts
R2367	T7658	T7646	parataxis	counterparts,regions
R2368	T7659	T7658	det	the,counterparts
R2369	T7660	T7658	prep	of,counterparts
R237	T2452	T2453	det	a,disease
R2370	T7661	T7660	pobj	locus,of
R2371	T7662	T7661	nummod	2,locus
R2372	T7663	T7658	punct	),counterparts
R2373	T7664	T7646	punct	", ",regions
R2374	T7665	T7666	compound	12p13,pter
R2375	T7666	T7646	conj	pter,regions
R2376	T7667	T7666	punct	-,pter
R2377	T7668	T7666	prep	on,pter
R2378	T7669	T7668	pobj	chromosome,on
R2379	T7670	T7669	nummod	12,chromosome
R238	T2453	T2447	appos	disease,arthritis
R2380	T7671	T7672	punct	(,counterpart
R2381	T7672	T7666	parataxis	counterpart,pter
R2382	T7673	T7672	det	the,counterpart
R2383	T7674	T7672	prep	of,counterpart
R2384	T7675	T7674	pobj	locus,of
R2385	T7676	T7675	nummod	3,locus
R2386	T7677	T7672	punct	),counterpart
R2387	T7678	T7666	punct	", ",pter
R2388	T7679	T7680	compound	21q22,qter
R2389	T7680	T7666	conj	qter,pter
R239	T2454	T2453	amod	common,disease
R2390	T7681	T7680	punct	-,qter
R2391	T7682	T7680	cc	and,qter
R2392	T7683	T7680	conj	10q22,qter
R2393	T7684	T7683	punct	-,10q22
R2394	T7685	T7683	nummod	23,10q22
R2395	T7686	T7680	prep	on,qter
R2396	T7687	T7688	nmod	chromosome,21
R2397	T7688	T7686	pobj	21,on
R2398	T7689	T7688	cc	and,21
R2399	T7690	T7688	conj	10,21
R24	T483	T484	nsubjpass	traits,controlled
R240	T2455	T2453	nmod	complex,disease
R2400	T7691	T7692	punct	(,counterparts
R2401	T7692	T7680	parataxis	counterparts,qter
R2402	T7693	T7692	det	the,counterparts
R2403	T7694	T7692	prep	of,counterparts
R2404	T7695	T7694	pobj	locus,of
R2405	T7696	T7695	nummod	5,locus
R2406	T7697	T7692	punct	),counterparts
R2407	T7698	T7680	punct	", ",qter
R2408	T7699	T7680	conj	17q21,qter
R2409	T7700	T7699	punct	-,17q21
R241	T2456	T2453	amod	multifactorial,disease
R2410	T7701	T7699	nummod	25,17q21
R2411	T7702	T7699	prep	on,17q21
R2412	T7703	T7702	pobj	chromosome,on
R2413	T7704	T7703	nummod	17,chromosome
R2414	T7705	T7706	punct	(,counterpart
R2415	T7706	T7699	parataxis	counterpart,17q21
R2416	T7707	T7706	det	the,counterpart
R2417	T7708	T7706	prep	of,counterpart
R2418	T7709	T7708	pobj	locus,of
R2419	T7710	T7709	nummod	6,locus
R242	T2457	T2453	amod	autoimmune,disease
R2420	T7711	T7706	punct	),counterpart
R2421	T7712	T7699	cc	and,17q21
R2422	T7713	T7714	compound	3q29,qter
R2423	T7714	T7699	conj	qter,17q21
R2424	T7715	T7714	punct	-,qter
R2425	T7716	T7714	prep	on,qter
R2426	T7717	T7716	pobj	chromosome,on
R2427	T7718	T7717	nummod	3,chromosome
R2428	T7719	T7720	punct	(,counterpart
R2429	T7720	T7714	parataxis	counterpart,qter
R243	T2458	T2445	punct	.,is
R2430	T7721	T7720	det	the,counterpart
R2431	T7722	T7720	prep	of,counterpart
R2432	T7723	T7722	pobj	locus,of
R2433	T7724	T7723	nummod	7,locus
R2434	T7725	T7720	punct	),counterpart
R2435	T7726	T7727	punct	[,4
R2436	T7727	T7644	parataxis	4,are
R2437	T7728	T7727	nummod	2,4
R2438	T7729	T7727	punct	",",4
R2439	T7730	T7727	punct	],4
R244	T2460	T2461	amod	Several,studies
R2440	T7731	T7644	punct	.,are
R2441	T8314	T8315	npadvmod	Strain,specific
R2442	T8315	T8317	amod	specific,genes
R2443	T8316	T8315	punct	-,specific
R2444	T8318	T8319	advmod	differentially,expressed
R2445	T8319	T8317	amod	expressed,genes
R2446	T8321	T8322	nsubj	We,detected
R2447	T8323	T8324	det	the,profiles
R2448	T8324	T8322	dobj	profiles,detected
R2449	T8325	T8326	compound	gene,expression
R245	T2461	T2462	nsubjpass	studies,carried
R2450	T8326	T8324	compound	expression,profiles
R2451	T8327	T8322	advcl	using,detected
R2452	T8328	T8329	nummod	three,mice
R2453	T8329	T8327	dobj	mice,using
R2454	T8330	T8329	prep	per,mice
R2455	T8331	T8330	pobj	group,per
R2456	T8332	T8329	punct	", ",mice
R2457	T8333	T8334	dep	which,is
R2458	T8334	T8329	relcl	is,mice
R2459	T8335	T8336	det	a,number
R246	T2463	T2462	aux	have,carried
R2460	T8336	T8334	attr	number,is
R2461	T8337	T8336	amod	small,number
R2462	T8338	T8322	punct	.,detected
R2463	T8340	T8341	advcl	Being,determined
R2464	T8342	T8340	acomp	aware,Being
R2465	T8343	T8342	prep	of,aware
R2466	T8344	T8345	det	the,importance
R2467	T8345	T8343	pobj	importance,of
R2468	T8346	T8345	prep	of,importance
R2469	T8347	T8348	compound	data,reproducibility
R247	T2464	T2462	auxpass	been,carried
R2470	T8348	T8346	pobj	reproducibility,of
R2471	T8349	T8341	punct	", ",determined
R2472	T8350	T8341	nsubj	we,determined
R2473	T8351	T8352	det	the,coefficient
R2474	T8352	T8341	dobj	coefficient,determined
R2475	T8353	T8352	prep	of,coefficient
R2476	T8354	T8353	pobj	variation,of
R2477	T8355	T8352	punct	(,coefficient
R2478	T8356	T8352	appos	CV,coefficient
R2479	T8357	T8341	punct	),determined
R248	T2465	T2462	prt	out,carried
R2480	T8358	T8359	aux	to,measure
R2481	T8359	T8341	advcl	measure,determined
R2482	T8360	T8361	compound	data,variability
R2483	T8361	T8359	dobj	variability,measure
R2484	T8362	T8341	punct	.,determined
R2485	T8364	T8365	det	The,CV
R2486	T8365	T8366	nsubjpass	CV,calculated
R2487	T8367	T8365	prep	for,CV
R2488	T8368	T8369	det	each,gene
R2489	T8369	T8367	pobj	gene,for
R249	T2466	T2467	aux	to,detect
R2490	T8370	T8369	prep	on,gene
R2491	T8371	T8372	det	the,chip
R2492	T8372	T8370	pobj	chip,on
R2493	T8373	T8365	cc	and,CV
R2494	T8374	T8375	det	the,CV
R2495	T8375	T8365	conj	CV,CV
R2496	T8376	T8375	amod	mean,CV
R2497	T8377	T8375	prep	for,CV
R2498	T8378	T8379	det	the,probe
R2499	T8379	T8377	pobj	probe,for
R25	T485	T486	amod	such,as
R250	T2467	T2462	advcl	detect,carried
R2500	T8380	T8379	amod	entire,probe
R2501	T8381	T8379	amod	set,probe
R2502	T8382	T8366	auxpass	were,calculated
R2503	T8383	T8366	punct	.,calculated
R2504	T8385	T8386	det	The,CV
R2505	T8386	T8388	nsubj	CV,ranged
R2506	T8387	T8386	amod	mean,CV
R2507	T8389	T8388	prep	between,ranged
R2508	T8390	T8391	nummod	18.4,%
R2509	T8391	T8389	pobj	%,between
R251	T2468	T2469	det	the,basis
R2510	T8392	T8391	cc	and,%
R2511	T8393	T8394	nummod	25.8,%
R2512	T8394	T8391	conj	%,%
R2513	T8395	T8388	prep	for,ranged
R2514	T8396	T8397	det	all,groups
R2515	T8397	T8395	pobj	groups,for
R2516	T8398	T8397	amod	experimental,groups
R2517	T8399	T8388	punct	", ",ranged
R2518	T8400	T8388	cc	and,ranged
R2519	T8401	T8402	det	this,CV
R252	T2469	T2467	dobj	basis,detect
R2520	T8402	T8405	nsubj	CV,indicated
R2521	T8403	T8404	advmod	relatively,low
R2522	T8404	T8402	amod	low,CV
R2523	T8405	T8388	conj	indicated,ranged
R2524	T8406	T8407	mark	that,used
R2525	T8407	T8405	ccomp	used,indicated
R2526	T8408	T8409	det	these,data
R2527	T8409	T8407	nsubjpass	data,used
R2528	T8410	T8407	aux	could,used
R2529	T8411	T8407	auxpass	be,used
R253	T2470	T2469	amod	genetic,basis
R2530	T8412	T8407	prep	for,used
R2531	T8413	T8414	amod	further,analysis
R2532	T8414	T8412	pobj	analysis,for
R2533	T8415	T8416	punct	(,Table
R2534	T8416	T8405	parataxis	Table,indicated
R2535	T8417	T8416	nummod	1,Table
R2536	T8418	T8416	punct	),Table
R2537	T8419	T8405	punct	.,indicated
R2538	T8421	T8422	aux	To,search
R2539	T8422	T8423	advcl	search,performed
R254	T2471	T2469	prep	of,basis
R2540	T8424	T8422	prep	for,search
R2541	T8425	T8426	npadvmod	strain,specific
R2542	T8426	T8428	amod	specific,genes
R2543	T8427	T8426	punct	-,specific
R2544	T8428	T8424	pobj	genes,for
R2545	T8429	T8430	advmod	differentially,expressed
R2546	T8430	T8428	amod	expressed,genes
R2547	T8431	T8423	punct	", ",performed
R2548	T8432	T8423	nsubj	we,performed
R2549	T8433	T8423	dobj	comparisons,performed
R255	T2472	T2471	pobj	RA,of
R2550	T8434	T8433	prep	of,comparisons
R2551	T8435	T8436	compound	gene,expression
R2552	T8436	T8434	pobj	expression,of
R2553	T8437	T8433	prep	between,comparisons
R2554	T8438	T8439	det	the,strains
R2555	T8439	T8437	pobj	strains,between
R2556	T8440	T8439	nmod	DBA,strains
R2557	T8441	T8440	punct	/,DBA
R2558	T8442	T8440	nummod	1,DBA
R2559	T8443	T8440	cc	and,DBA
R256	T2473	T2462	punct	", ",carried
R2560	T8444	T8445	compound	FVB,N
R2561	T8445	T8440	conj	N,DBA
R2562	T8446	T8445	punct	/,N
R2563	T8447	T8423	prep	at,performed
R2564	T8448	T8449	det	all,phases
R2565	T8449	T8447	pobj	phases,at
R2566	T8450	T8449	nummod	four,phases
R2567	T8451	T8449	prep	of,phases
R2568	T8452	T8451	pobj	CIA,of
R2569	T8453	T8449	punct	", ",phases
R257	T2474	T2462	cc	and,carried
R2570	T8454	T8449	prep	including,phases
R2571	T8455	T8454	pobj	NC,including
R2572	T8456	T8455	punct	", ",NC
R2573	T8457	T8455	conj	PI,NC
R2574	T8458	T8457	punct	", ",PI
R2575	T8459	T8457	conj	OA,PI
R2576	T8460	T8459	cc	and,OA
R2577	T8461	T8459	conj	CA,OA
R2578	T8462	T8423	punct	.,performed
R2579	T8464	T8465	prep	For,expressed
R258	T2475	T2476	amod	more,30
R2580	T8466	T8467	det	the,mice
R2581	T8467	T8464	pobj	mice,For
R2582	T8468	T8467	amod	naive,mice
R2583	T8469	T8467	prep	without,mice
R2584	T8470	T8469	pobj	immunisation,without
R2585	T8471	T8465	punct	", ",expressed
R2586	T8472	T8473	nummod	361,genes
R2587	T8473	T8465	nsubjpass	genes,expressed
R2588	T8474	T8465	auxpass	were,expressed
R2589	T8475	T8465	advmod	differentially,expressed
R259	T2476	T2478	nummod	30,regions
R2590	T8476	T8465	prep	between,expressed
R2591	T8477	T8478	det	the,strains
R2592	T8478	T8476	pobj	strains,between
R2593	T8479	T8478	nummod	two,strains
R2594	T8480	T8465	punct	.,expressed
R2595	T8482	T8483	prep	On,expressed
R2596	T8484	T8482	pobj	day,On
R2597	T8485	T8484	nummod	10,day
R2598	T8486	T8484	prep	after,day
R2599	T8487	T8486	pobj	immunisation,after
R26	T486	T483	prep	as,traits
R260	T2477	T2476	quantmod	than,30
R2600	T8488	T8484	punct	", ",day
R2601	T8489	T8490	advmod	when,show
R2602	T8490	T8484	relcl	show,day
R2603	T8491	T8492	det	both,strains
R2604	T8492	T8490	nsubj	strains,show
R2605	T8493	T8490	aux	did,show
R2606	T8494	T8490	neg	not,show
R2607	T8495	T8496	det	any,sign
R2608	T8496	T8490	dobj	sign,show
R2609	T8497	T8496	prep	of,sign
R261	T2478	T2480	nsubj	regions,shown
R2610	T8498	T8499	det	the,disease
R2611	T8499	T8497	pobj	disease,of
R2612	T8500	T8483	punct	", ",expressed
R2613	T8501	T8502	nummod	141,genes
R2614	T8502	T8483	nsubjpass	genes,expressed
R2615	T8503	T8483	auxpass	were,expressed
R2616	T8504	T8483	advmod	differentially,expressed
R2617	T8505	T8483	punct	.,expressed
R2618	T8507	T8508	mark	After,developed
R2619	T8508	T8513	advcl	developed,identified
R262	T2479	T2478	amod	genomic,regions
R2620	T8509	T8510	nmod	DBA,mice
R2621	T8510	T8508	nsubj	mice,developed
R2622	T8511	T8509	punct	/,DBA
R2623	T8512	T8509	nummod	1,DBA
R2624	T8514	T8508	dobj	CIA,developed
R2625	T8515	T8513	punct	", ",identified
R2626	T8516	T8517	nummod	184,genes
R2627	T8517	T8513	nsubjpass	genes,identified
R2628	T8518	T8516	cc	and,184
R2629	T8519	T8516	conj	85,184
R263	T2480	T2462	conj	shown,carried
R2630	T8520	T8521	advmod	differentially,expressed
R2631	T8521	T8517	amod	expressed,genes
R2632	T8522	T8513	auxpass	were,identified
R2633	T8523	T8513	prep	between,identified
R2634	T8524	T8525	det	these,strains
R2635	T8525	T8523	pobj	strains,between
R2636	T8526	T8525	nummod	two,strains
R2637	T8527	T8513	prep	at,identified
R2638	T8528	T8529	det	the,phases
R2639	T8529	T8527	pobj	phases,at
R264	T2481	T2480	aux	have,shown
R2640	T8530	T8529	nmod	onset,phases
R2641	T8531	T8530	cc	and,onset
R2642	T8532	T8530	conj	chronic,onset
R2643	T8533	T8513	punct	", ",identified
R2644	T8534	T8513	advmod	respectively,identified
R2645	T8535	T8513	punct	.,identified
R2646	T8537	T8538	advmod	When,merged
R2647	T8538	T8551	advcl	merged,identified
R2648	T8539	T8540	det	the,lists
R2649	T8540	T8538	nsubjpass	lists,merged
R265	T2482	T2480	dobj	evidence,shown
R2650	T8541	T8540	prep	of,lists
R2651	T8542	T8543	det	the,genes
R2652	T8543	T8541	pobj	genes,of
R2653	T8544	T8545	advmod	differentially,expressed
R2654	T8545	T8543	amod	expressed,genes
R2655	T8546	T8540	prep	at,lists
R2656	T8547	T8548	det	the,phases
R2657	T8548	T8546	pobj	phases,at
R2658	T8549	T8548	nummod	four,phases
R2659	T8550	T8538	auxpass	were,merged
R266	T2483	T2482	prep	of,evidence
R2660	T8552	T8538	cc	and,merged
R2661	T8553	T8554	amod	overlapping,genes
R2662	T8554	T8555	nsubjpass	genes,excluded
R2663	T8555	T8538	conj	excluded,merged
R2664	T8556	T8555	auxpass	were,excluded
R2665	T8557	T8551	punct	", ",identified
R2666	T8558	T8559	nummod	509,genes
R2667	T8559	T8551	nsubjpass	genes,identified
R2668	T8560	T8551	auxpass	were,identified
R2669	T8561	T8562	punct	(,file
R267	T2484	T2483	pobj	linkage,of
R2670	T8562	T8551	parataxis	file,identified
R2671	T8563	T8562	amod	Additional,file
R2672	T8564	T8562	nummod	1,file
R2673	T8565	T8562	punct	),file
R2674	T8566	T8551	punct	.,identified
R2675	T8568	T8569	compound	Twenty,one
R2676	T8569	T8571	nummod	one,genes
R2677	T8570	T8569	punct	-,one
R2678	T8571	T8572	nsubj	genes,showed
R2679	T8573	T8572	advmod	consistently,showed
R268	T2485	T2484	prep	to,linkage
R2680	T8574	T8575	amod	differential,expression
R2681	T8575	T8572	dobj	expression,showed
R2682	T8576	T8572	prep	between,showed
R2683	T8577	T8578	det	the,strains
R2684	T8578	T8576	pobj	strains,between
R2685	T8579	T8578	nummod	two,strains
R2686	T8580	T8572	prep	at,showed
R2687	T8581	T8582	det	all,phases
R2688	T8582	T8580	pobj	phases,at
R2689	T8583	T8572	punct	.,showed
R269	T2486	T2487	det	the,disease
R2690	T8585	T8586	prep	Besides,expressed
R2691	T8587	T8588	det	these,genes
R2692	T8588	T8585	pobj	genes,Besides
R2693	T8589	T8588	nummod	21,genes
R2694	T8590	T8586	punct	", ",expressed
R2695	T8591	T8592	advmod	only,genes
R2696	T8592	T8586	nsubjpass	genes,expressed
R2697	T8593	T8592	nummod	3,genes
R2698	T8594	T8592	amod	additional,genes
R2699	T8595	T8586	auxpass	were,expressed
R27	T487	T488	amod	complex,diseases
R270	T2487	T2485	pobj	disease,to
R2700	T8596	T8597	npadvmod	strain,specific
R2701	T8597	T8586	advmod	specific,expressed
R2702	T8598	T8597	punct	-,specific
R2703	T8599	T8586	advmod	differentially,expressed
R2704	T8600	T8586	prep	during,expressed
R2705	T8601	T8602	det	the,phases
R2706	T8602	T8600	pobj	phases,during
R2707	T8603	T8602	nummod	3,phases
R2708	T8604	T8602	prep	after,phases
R2709	T8605	T8606	compound	CIA,induction
R271	T2488	T2480	punct	.,shown
R2710	T8606	T8604	pobj	induction,after
R2711	T8607	T8608	punct	(,Figure
R2712	T8608	T8586	parataxis	Figure,expressed
R2713	T8609	T8608	dep	PI,Figure
R2714	T8610	T8609	punct	", ",PI
R2715	T8611	T8609	conj	OA,PI
R2716	T8612	T8611	cc	and,OA
R2717	T8613	T8611	conj	CA,OA
R2718	T8614	T8608	punct	;,Figure
R2719	T8615	T8608	nummod	1,Figure
R272	T2490	T2491	nsubj	Most,reach
R2720	T8616	T8608	punct	),Figure
R2721	T8617	T8586	punct	.,expressed
R2724	T9552	T9553	npadvmod	Disease,specific
R2725	T9553	T9555	amod	specific,genes
R2726	T9554	T9553	punct	-,specific
R2727	T9556	T9557	advmod	differentially,expressed
R2728	T9557	T9555	amod	expressed,genes
R2729	T9559	T9560	aux	To,identify
R273	T2492	T2490	prep	of,Most
R2730	T9560	T9561	advcl	identify,detected
R2731	T9562	T9563	det	the,genes
R2732	T9563	T9560	dobj	genes,identify
R2733	T9564	T9565	npadvmod	disease,specific
R2734	T9565	T9563	amod	specific,genes
R2735	T9566	T9565	punct	-,specific
R2736	T9567	T9568	advmod	differentially,expressed
R2737	T9568	T9563	amod	expressed,genes
R2738	T9569	T9560	prep	in,identify
R2739	T9570	T9569	pobj	CIA,in
R274	T2493	T2494	det	these,regions
R2740	T9571	T9561	punct	", ",detected
R2741	T9572	T9561	nsubj	we,detected
R2742	T9573	T9574	det	the,genes
R2743	T9574	T9561	dobj	genes,detected
R2744	T9575	T9576	dep	that,expressed
R2745	T9576	T9574	relcl	expressed,genes
R2746	T9577	T9576	auxpass	were,expressed
R2747	T9578	T9576	advmod	differentially,expressed
R2748	T9579	T9576	prep	in,expressed
R2749	T9580	T9579	pobj	LNs,in
R275	T2494	T2492	pobj	regions,of
R2750	T9581	T9576	prep	during,expressed
R2751	T9582	T9581	pobj	CIA,during
R2752	T9583	T9576	prep	in,expressed
R2753	T9584	T9585	det	the,strain
R2754	T9585	T9583	pobj	strain,in
R2755	T9586	T9585	amod	susceptible,strain
R2756	T9587	T9561	punct	.,detected
R2757	T9589	T9590	nummod	Three,conditions
R2758	T9590	T9592	nsubjpass	conditions,compared
R2759	T9591	T9590	amod	experimental,conditions
R276	T2495	T2494	amod	genomic,regions
R2760	T9593	T9590	punct	", ",conditions
R2761	T9594	T9590	appos	PI,conditions
R2762	T9595	T9594	punct	", ",PI
R2763	T9596	T9594	conj	OA,PI
R2764	T9597	T9596	cc	and,OA
R2765	T9598	T9596	conj	CA,OA
R2766	T9599	T9592	punct	", ",compared
R2767	T9600	T9592	auxpass	were,compared
R2768	T9601	T9592	prep	with,compared
R2769	T9602	T9603	det	the,group
R277	T2496	T2491	aux	did,reach
R2770	T9603	T9601	pobj	group,with
R2771	T9604	T9603	compound	NC,group
R2772	T9605	T9592	punct	.,compared
R2773	T9607	T9608	prep	On,upregulated
R2774	T9609	T9607	pobj	day,On
R2775	T9610	T9609	nummod	10,day
R2776	T9611	T9609	prep	after,day
R2777	T9612	T9611	pobj	immunisation,after
R2778	T9613	T9608	punct	", ",upregulated
R2779	T9614	T9615	nummod	102,genes
R278	T2497	T2491	neg	not,reach
R2780	T9615	T9616	nsubjpass	genes,expressed
R2781	T9616	T9608	ccomp	expressed,upregulated
R2782	T9617	T9616	auxpass	were,expressed
R2783	T9618	T9616	advmod	differentially,expressed
R2784	T9619	T9608	punct	–,upregulated
R2785	T9620	T9608	nsubjpass	most,upregulated
R2786	T9621	T9620	prep	of,most
R2787	T9622	T9621	pobj	them,of
R2788	T9623	T9608	auxpass	were,upregulated
R2789	T9624	T9625	punct	(,102
R279	T2498	T2499	det	a,value
R2790	T9625	T9608	parataxis	102,upregulated
R2791	T9626	T9625	quantmod	78,102
R2792	T9627	T9625	quantmod	out,102
R2793	T9628	T9625	quantmod	of,102
R2794	T9629	T9625	punct	),102
R2795	T9630	T9608	punct	–,upregulated
R2796	T9631	T9632	mark	while,expressed
R2797	T9632	T9608	advcl	expressed,upregulated
R2798	T9633	T9632	prep	at,expressed
R2799	T9634	T9635	det	the,phase
R28	T488	T486	pobj	diseases,as
R280	T2499	T2491	dobj	value,reach
R2800	T9635	T9633	pobj	phase,at
R2801	T9636	T9635	compound	onset,phase
R2802	T9637	T9635	prep	of,phase
R2803	T9638	T9639	det	the,disease
R2804	T9639	T9637	pobj	disease,of
R2805	T9640	T9632	punct	", ",expressed
R2806	T9641	T9642	advmod	only,genes
R2807	T9642	T9632	nsubjpass	genes,expressed
R2808	T9643	T9642	nummod	26,genes
R2809	T9644	T9632	auxpass	were,expressed
R281	T2500	T2501	npadvmod	genome,wide
R2810	T9645	T9632	advmod	differentially,expressed
R2811	T9646	T9608	punct	.,upregulated
R2812	T9648	T9649	prep	At,identified
R2813	T9650	T9651	det	the,phase
R2814	T9651	T9648	pobj	phase,At
R2815	T9652	T9651	amod	chronic,phase
R2816	T9653	T9651	prep	of,phase
R2817	T9654	T9655	det	the,disease
R2818	T9655	T9653	pobj	disease,of
R2819	T9656	T9649	punct	", ",identified
R282	T2501	T2499	amod	wide,value
R2820	T9657	T9658	nummod	184,genes
R2821	T9658	T9649	nsubjpass	genes,identified
R2822	T9659	T9660	advmod	differentially,expressed
R2823	T9660	T9658	amod	expressed,genes
R2824	T9661	T9649	auxpass	were,identified
R2825	T9662	T9649	punct	", ",identified
R2826	T9663	T9649	prep	with,identified
R2827	T9664	T9665	nummod	156,genes
R2828	T9665	T9663	pobj	genes,with
R2829	T9666	T9665	amod	downregulated,genes
R283	T2502	T2501	punct	-,wide
R2830	T9667	T9649	punct	.,identified
R2831	T9669	T9670	advmod	Only,gene
R2832	T9670	T9672	nsubjpass	gene,expressed
R2833	T9671	T9670	nummod	one,gene
R2834	T9673	T9672	auxpass	was,expressed
R2835	T9674	T9672	advmod	differentially,expressed
R2836	T9675	T9672	prep	at,expressed
R2837	T9676	T9677	det	all,phases
R2838	T9677	T9675	pobj	phases,at
R2839	T9678	T9677	nummod	three,phases
R284	T2503	T2499	amod	significant,value
R2840	T9679	T9677	prep	of,phases
R2841	T9680	T9679	pobj	CIA,of
R2842	T9681	T9672	punct	.,expressed
R2843	T9683	T9684	prep	Besides,shared
R2844	T9685	T9686	det	this,gene
R2845	T9686	T9683	pobj	gene,Besides
R2846	T9687	T9684	punct	", ",shared
R2847	T9688	T9689	nummod	five,genes
R2848	T9689	T9684	nsubjpass	genes,shared
R2849	T9690	T9688	punct	", ",five
R285	T2504	T2499	compound	threshold,value
R2850	T9691	T9688	conj	one,five
R2851	T9692	T9691	cc	and,one
R2852	T9693	T9691	conj	six,one
R2853	T9694	T9695	advmod	differentially,expressed
R2854	T9695	T9689	amod	expressed,genes
R2855	T9696	T9684	auxpass	were,shared
R2856	T9697	T9684	agent	by,shared
R2857	T9698	T9697	pobj	PI,by
R2858	T9699	T9698	prep	with,PI
R2859	T9700	T9699	pobj	OA,with
R286	T2505	T2499	prep	of,value
R2860	T9701	T9698	punct	", ",PI
R2861	T9702	T9698	conj	PI,PI
R2862	T9703	T9702	prep	with,PI
R2863	T9704	T9703	pobj	CA,with
R2864	T9705	T9702	cc	and,PI
R2865	T9706	T9702	conj	OA,PI
R2866	T9707	T9706	prep	with,OA
R2867	T9708	T9707	pobj	CA,with
R2868	T9709	T9684	punct	", ",shared
R2869	T9710	T9684	advmod	respectively,shared
R287	T2506	T2505	pobj	linkage,of
R2870	T9711	T9712	punct	(,2a
R2871	T9712	T9684	parataxis	2a,shared
R2872	T9713	T9712	compound	Figure,2a
R2873	T9714	T9712	punct	),2a
R2874	T9715	T9684	punct	.,shared
R2875	T9717	T9718	advcl	Taken,regulated
R2876	T9719	T9717	advmod	together,Taken
R2877	T9720	T9718	punct	", ",regulated
R2878	T9721	T9722	nummod	310,genes
R2879	T9722	T9718	nsubjpass	genes,regulated
R288	T2507	T2499	punct	", ",value
R2880	T9723	T9724	npadvmod	disease,specific
R2881	T9724	T9722	amod	specific,genes
R2882	T9725	T9724	punct	-,specific
R2883	T9726	T9727	advmod	differentially,expressed
R2884	T9727	T9722	amod	expressed,genes
R2885	T9728	T9718	auxpass	were,regulated
R2886	T9729	T9718	advmod	differentially,regulated
R2887	T9730	T9718	prep	during,regulated
R2888	T9731	T9730	pobj	CIA,during
R2889	T9732	T9718	prep	in,regulated
R289	T2508	T2499	prep	with,value
R2890	T9733	T9734	nmod	DBA,mice
R2891	T9734	T9732	pobj	mice,in
R2892	T9735	T9733	punct	/,DBA
R2893	T9736	T9733	nummod	1,DBA
R2894	T9737	T9738	punct	(,file
R2895	T9738	T9718	parataxis	file,regulated
R2896	T9739	T9738	amod	Additional,file
R2897	T9740	T9738	nummod	2,file
R2898	T9741	T9738	punct	),file
R2899	T9742	T9718	punct	.,regulated
R29	T489	T484	auxpass	are,controlled
R290	T2509	T2510	compound	P,values
R2900	T9744	T9745	aux	To,characterise
R2901	T9745	T9747	advcl	characterise,performed
R2902	T9746	T9745	advmod	further,characterise
R2903	T9748	T9749	det	the,pattern
R2904	T9749	T9745	dobj	pattern,characterise
R2905	T9750	T9751	compound	gene,expression
R2906	T9751	T9749	compound	expression,pattern
R2907	T9752	T9745	prep	during,characterise
R2908	T9753	T9752	pobj	CIA,during
R2909	T9754	T9747	punct	", ",performed
R291	T2510	T2508	pobj	values,with
R2910	T9755	T9747	nsubj	we,performed
R2911	T9756	T9757	amod	hierarchical,analysis
R2912	T9757	T9747	dobj	analysis,performed
R2913	T9758	T9757	compound	cluster,analysis
R2914	T9759	T9747	prep	for,performed
R2915	T9760	T9761	det	these,genes
R2916	T9761	T9759	pobj	genes,for
R2917	T9762	T9761	nummod	310,genes
R2918	T9763	T9747	punct	.,performed
R2919	T9765	T9766	nummod	Six,clusters
R292	T2511	T2510	prep	between,values
R2920	T9766	T9768	nsubjpass	clusters,identified
R2921	T9767	T9766	compound	gene,clusters
R2922	T9769	T9768	auxpass	were,identified
R2923	T9770	T9771	punct	(,I
R2924	T9771	T9768	parataxis	I,identified
R2925	T9772	T9771	nmod	clusters,I
R2926	T9773	T9771	prep	to,I
R2927	T9774	T9773	pobj	VI,to
R2928	T9775	T9771	punct	", ",I
R2929	T9776	T9777	compound	Figure,2b
R293	T2512	T2511	pobj	0.05,between
R2930	T9777	T9771	appos	2b,I
R2931	T9778	T9771	punct	),I
R2932	T9779	T9768	punct	", ",identified
R2933	T9780	T9768	npadvmod	each,identified
R2934	T9781	T9780	prep	with,each
R2935	T9782	T9783	det	a,pattern
R2936	T9783	T9781	pobj	pattern,with
R2937	T9784	T9783	amod	distinct,pattern
R2938	T9785	T9786	compound	gene,expression
R2939	T9786	T9783	compound	expression,pattern
R294	T2513	T2512	cc	and,0.05
R2940	T9787	T9768	prep	during,identified
R2941	T9788	T9787	pobj	CIA,during
R2942	T9789	T9768	punct	.,identified
R2943	T9791	T9792	nsubj	Cluster,contains
R2944	T9793	T9791	nummod	I,Cluster
R2945	T9794	T9795	nummod	16,genes
R2946	T9795	T9792	dobj	genes,contains
R2947	T9796	T9795	punct	", ",genes
R2948	T9797	T9795	acl	representing,genes
R2949	T9798	T9797	dobj	genes,representing
R295	T2514	T2512	conj	0.001,0.05
R2950	T9799	T9800	dep	that,upregulated
R2951	T9800	T9798	relcl	upregulated,genes
R2952	T9801	T9800	auxpass	were,upregulated
R2953	T9802	T9800	prep	after,upregulated
R2954	T9803	T9802	pobj	induction,after
R2955	T9804	T9803	prep	of,induction
R2956	T9805	T9804	pobj	CIA,of
R2957	T9806	T9792	punct	.,contains
R2958	T9808	T9809	det	The,expression
R2959	T9809	T9810	nsubj	expression,reached
R296	T2515	T2516	punct	[,1
R2960	T9811	T9809	prep	of,expression
R2961	T9812	T9813	det	these,genes
R2962	T9813	T9811	pobj	genes,of
R2963	T9814	T9815	det	a,peak
R2964	T9815	T9810	dobj	peak,reached
R2965	T9816	T9810	prep	at,reached
R2966	T9817	T9818	det	the,phase
R2967	T9818	T9816	pobj	phase,at
R2968	T9819	T9818	compound	onset,phase
R2969	T9820	T9818	prep	of,phase
R297	T2516	T2491	parataxis	1,reach
R2970	T9821	T9822	det	the,disease
R2971	T9822	T9820	pobj	disease,of
R2972	T9823	T9810	cc	and,reached
R2973	T9824	T9825	amod	functional,results
R2974	T9825	T9827	nsubj	results,revealed
R2975	T9826	T9825	compound	clustering,results
R2976	T9827	T9810	conj	revealed,reached
R2977	T9828	T9829	mark	that,related
R2978	T9829	T9827	ccomp	related,revealed
R2979	T9830	T9829	nsubjpass	they,related
R298	T2517	T2518	punct	-,5
R2980	T9831	T9829	auxpass	are,related
R2981	T9832	T9829	prep	to,related
R2982	T9833	T9834	det	the,response
R2983	T9834	T9832	pobj	response,to
R2984	T9835	T9834	amod	immune,response
R2985	T9836	T9827	punct	.,revealed
R2986	T9838	T9839	nsubj	Cluster,contains
R2987	T9840	T9838	nummod	II,Cluster
R2988	T9841	T9842	nummod	12,genes
R2989	T9842	T9839	dobj	genes,contains
R299	T2518	T2516	prep	5,1
R2990	T9843	T9844	poss	whose,expression
R2991	T9844	T9845	dep	expression,upregulated
R2992	T9845	T9842	relcl	upregulated,genes
R2993	T9846	T9845	auxpass	was,upregulated
R2994	T9847	T9845	advmod	gradually,upregulated
R2995	T9848	T9845	cc	and,upregulated
R2996	T9849	T9845	conj	reached,upregulated
R2997	T9850	T9851	det	a,peak
R2998	T9851	T9849	dobj	peak,reached
R2999	T9852	T9849	prep	at,reached
R3	T460	T459	nmod	genome,approaches
R30	T490	T484	agent	by,controlled
R300	T2519	T2516	punct	],1
R3000	T9853	T9854	det	the,phase
R3001	T9854	T9852	pobj	phase,at
R3002	T9855	T9854	amod	chronic,phase
R3003	T9856	T9854	prep	of,phase
R3004	T9857	T9856	pobj	CIA,of
R3005	T9858	T9839	punct	.,contains
R3006	T9860	T9861	det	These,genes
R3007	T9861	T9862	nsubjpass	genes,related
R3008	T9863	T9862	auxpass	are,related
R3009	T9864	T9862	advmod	mainly,related
R301	T2520	T2491	punct	.,reach
R3010	T9865	T9862	prep	to,related
R3011	T9866	T9867	det	the,response
R3012	T9867	T9865	pobj	response,to
R3013	T9868	T9867	amod	immune,response
R3014	T9869	T9867	punct	", ",response
R3015	T9870	T9871	compound	organelle,membrane
R3016	T9871	T9867	conj	membrane,response
R3017	T9872	T9871	cc	and,membrane
R3018	T9873	T9874	amod	extracellular,region
R3019	T9874	T9871	conj	region,membrane
R302	T2522	T2523	advmod	Thus,have
R3020	T9875	T9874	cc	and,region
R3021	T9876	T9874	conj	space,region
R3022	T9877	T9862	punct	.,related
R3023	T9879	T9880	nsubj	Cluster,contains
R3024	T9881	T9879	nummod	III,Cluster
R3025	T9882	T9883	nummod	78,genes
R3026	T9883	T9880	dobj	genes,contains
R3027	T9884	T9885	dep	that,upregulated
R3028	T9885	T9883	relcl	upregulated,genes
R3029	T9886	T9885	auxpass	were,upregulated
R303	T2524	T2523	punct	", ",have
R3030	T9887	T9885	advmod	only,upregulated
R3031	T9888	T9885	prep	at,upregulated
R3032	T9889	T9890	det	the,phase
R3033	T9890	T9888	pobj	phase,at
R3034	T9891	T9890	compound	PI,phase
R3035	T9892	T9880	punct	.,contains
R3036	T9894	T9895	det	These,genes
R3037	T9895	T9896	nsubjpass	genes,related
R3038	T9897	T9896	auxpass	are,related
R3039	T9898	T9896	prep	to,related
R304	T2525	T2526	det	these,loci
R3040	T9899	T9900	det	the,junction
R3041	T9900	T9898	pobj	junction,to
R3042	T9901	T9900	amod	intercellular,junction
R3043	T9902	T9896	punct	.,related
R3044	T9904	T9905	amod	More,half
R3045	T9905	T9907	nsubj	half,belong
R3046	T9906	T9905	quantmod	than,half
R3047	T9908	T9905	prep	of,half
R3048	T9909	T9910	det	the,genes
R3049	T9910	T9908	pobj	genes,of
R305	T2526	T2523	nsubj	loci,have
R3050	T9911	T9912	punct	(,310
R3051	T9912	T9905	parataxis	310,half
R3052	T9913	T9912	quantmod	156,310
R3053	T9914	T9912	quantmod	of,310
R3054	T9915	T9912	punct	),310
R3055	T9916	T9907	prep	to,belong
R3056	T9917	T9916	pobj	cluster,to
R3057	T9918	T9917	nummod	IV,cluster
R3058	T9919	T9907	cc	and,belong
R3059	T9920	T9907	conj	represent,belong
R306	T2527	T2523	advmod	only,have
R3060	T9921	T9920	dobj	genes,represent
R3061	T9922	T9923	advmod	specifically,downregultaed
R3062	T9923	T9921	acl	downregultaed,genes
R3063	T9924	T9923	prep	at,downregultaed
R3064	T9925	T9926	det	the,phase
R3065	T9926	T9924	pobj	phase,at
R3066	T9927	T9926	amod	chronic,phase
R3067	T9928	T9907	punct	.,belong
R3068	T9930	T9931	det	These,genes
R3069	T9931	T9932	nsubjpass	genes,related
R307	T2528	T2529	det	a,effect
R3070	T9933	T9932	auxpass	are,related
R3071	T9934	T9932	advmod	functionally,related
R3072	T9935	T9932	prep	to,related
R3073	T9936	T9937	compound	lymphocyte,proliferation
R3074	T9937	T9935	pobj	proliferation,to
R3075	T9938	T9937	punct	", ",proliferation
R3076	T9939	T9940	compound	T,cell
R3077	T9940	T9941	compound	cell,activation
R3078	T9941	T9937	appos	activation,proliferation
R3079	T9942	T9937	punct	", ",proliferation
R308	T2529	T2523	dobj	effect,have
R3080	T9943	T9944	compound	protein,binding
R3081	T9944	T9937	appos	binding,proliferation
R3082	T9945	T9946	advmod	as,as
R3083	T9946	T9937	cc	as,proliferation
R3084	T9947	T9946	advmod	well,as
R3085	T9948	T9949	det	the,pathway
R3086	T9949	T9937	conj	pathway,proliferation
R3087	T9950	T9949	compound	notch,pathway
R3088	T9951	T9949	compound	signal,pathway
R3089	T9952	T9932	punct	.,related
R309	T2530	T2529	amod	small,effect
R3090	T9954	T9955	nsubj	Cluster,contains
R3091	T9956	T9954	nummod	V,Cluster
R3092	T9957	T9958	nummod	eight,genes
R3093	T9958	T9955	dobj	genes,contains
R3094	T9959	T9958	acl	downregulated,genes
R3095	T9960	T9959	prep	at,downregulated
R3096	T9961	T9962	det	the,phase
R3097	T9962	T9960	pobj	phase,at
R3098	T9963	T9962	compound	PI,phase
R3099	T9964	T9955	punct	.,contains
R31	T491	T492	amod	many,genes
R310	T2531	T2529	prep	on,effect
R3100	T9966	T9967	nsubj	Cluster,contains
R3101	T9968	T9966	nummod	VI,Cluster
R3102	T9969	T9970	nummod	18,genes
R3103	T9970	T9967	dobj	genes,contains
R3104	T9971	T9970	acl	downregulated,genes
R3105	T9972	T9971	prep	at,downregulated
R3106	T9973	T9974	det	the,phase
R3107	T9974	T9972	pobj	phase,at
R3108	T9975	T9974	compound	OA,phase
R3109	T9976	T9967	punct	.,contains
R311	T2532	T2531	pobj	RA,on
R3110	T9978	T9979	det	The,classification
R3111	T9979	T9982	nsubj	classification,showed
R3112	T9980	T9979	compound	GO,classification
R3113	T9981	T9979	compound	term,classification
R3114	T9983	T9984	det	no,cluster
R3115	T9984	T9982	dobj	cluster,showed
R3116	T9985	T9984	amod	functional,cluster
R3117	T9986	T9987	dep	that,enriched
R3118	T9987	T9984	relcl	enriched,cluster
R3119	T9988	T9987	auxpass	was,enriched
R312	T2533	T2523	punct	.,have
R3120	T9989	T9987	advmod	significantly,enriched
R3121	T9990	T9987	prep	in,enriched
R3122	T9991	T9992	det	these,clusters
R3123	T9992	T9990	pobj	clusters,in
R3124	T9993	T9992	nummod	two,clusters
R3125	T9994	T9992	compound	gene,clusters
R3126	T9995	T9982	punct	.,showed
R3127	T10781	T10782	compound	Candidate,genes
R3128	T10783	T10782	prep	for,genes
R3129	T10784	T10785	det	the,QTL
R313	T2535	T2536	amod	Small,contributions
R3130	T10785	T10783	pobj	QTL,for
R3131	T10786	T10787	amod	small,effect
R3132	T10787	T10785	compound	effect,QTL
R3133	T10788	T10787	punct	-,effect
R3134	T10789	T10785	prep	of,QTL
R3135	T10790	T10789	pobj	CIA,of
R3136	T10792	T10793	aux	To,identify
R3137	T10793	T10794	advcl	identify,compared
R3138	T10794	T10807	ccomp	compared,shared
R3139	T10795	T10796	compound	candidate,genes
R314	T2536	T2538	nsubjpass	contributions,seen
R3140	T10796	T10793	dobj	genes,identify
R3141	T10797	T10796	compound	susceptibility,genes
R3142	T10798	T10796	prep	for,genes
R3143	T10799	T10800	det	the,QTL
R3144	T10800	T10798	pobj	QTL,for
R3145	T10801	T10800	nmod	CIA,QTL
R3146	T10802	T10803	amod	small,effect
R3147	T10803	T10800	compound	effect,QTL
R3148	T10804	T10803	punct	-,effect
R3149	T10805	T10794	punct	", ",compared
R315	T2537	T2536	amod	genetic,contributions
R3150	T10806	T10794	nsubj	we,compared
R3151	T10808	T10809	det	the,list
R3152	T10809	T10794	dobj	list,compared
R3153	T10810	T10809	prep	of,list
R3154	T10811	T10812	npadvmod	strain,specific
R3155	T10812	T10814	amod	specific,genes
R3156	T10813	T10812	punct	-,specific
R3157	T10814	T10810	pobj	genes,of
R3158	T10815	T10816	advmod	differentially,expressed
R3159	T10816	T10814	amod	expressed,genes
R316	T2539	T2538	aux	could,seen
R3160	T10817	T10794	prep	with,compared
R3161	T10818	T10819	det	the,list
R3162	T10819	T10817	pobj	list,with
R3163	T10820	T10819	prep	of,list
R3164	T10821	T10822	npadvmod	disease,specific
R3165	T10822	T10824	amod	specific,genes
R3166	T10823	T10822	punct	-,specific
R3167	T10824	T10820	pobj	genes,of
R3168	T10825	T10826	advmod	differentially,expressed
R3169	T10826	T10824	amod	expressed,genes
R317	T2540	T2538	advmod	also,seen
R3170	T10827	T10807	punct	;,shared
R3171	T10828	T10829	nummod	117,genes
R3172	T10829	T10807	nsubjpass	genes,shared
R3173	T10830	T10807	auxpass	were,shared
R3174	T10831	T10807	agent	by,shared
R3175	T10832	T10833	det	both,lists
R3176	T10833	T10831	pobj	lists,by
R3177	T10834	T10835	punct	(,file
R3178	T10835	T10807	parataxis	file,shared
R3179	T10836	T10835	amod	Additional,file
R318	T2541	T2538	auxpass	be,seen
R3180	T10837	T10835	nummod	3,file
R3181	T10838	T10835	punct	),file
R3182	T10839	T10807	punct	.,shared
R3183	T10841	T10842	nsubj	Figure,visualises
R3184	T10843	T10841	nummod	3,Figure
R3185	T10844	T10842	dobj	positions,visualises
R3186	T10845	T10844	prep	of,positions
R3187	T10846	T10847	det	the,genes
R3188	T10847	T10845	pobj	genes,of
R3189	T10848	T10847	nummod	117,genes
R319	T2542	T2538	prep	from,seen
R3190	T10849	T10847	acl	retrieved,genes
R3191	T10850	T10849	prep	from,retrieved
R3192	T10851	T10850	pobj	Ensembl,from
R3193	T10852	T10853	punct	[,30
R3194	T10853	T10849	parataxis	30,retrieved
R3195	T10854	T10853	punct	],30
R3196	T10855	T10842	prep	in,visualises
R3197	T10856	T10855	pobj	relation,in
R3198	T10857	T10856	prep	to,relation
R3199	T10858	T10859	det	the,QTL
R32	T492	T490	pobj	genes,by
R320	T2543	T2544	det	the,genes
R3200	T10859	T10857	pobj	QTL,to
R3201	T10860	T10859	nummod	8,QTL
R3202	T10861	T10862	amod	small,effect
R3203	T10862	T10859	compound	effect,QTL
R3204	T10863	T10862	punct	-,effect
R3205	T10864	T10842	punct	.,visualises
R3206	T10866	T10867	det	The,loci
R3207	T10867	T10869	nsubjpass	loci,located
R3208	T10868	T10867	nummod	eight,loci
R3209	T10870	T10869	auxpass	were,located
R321	T2544	T2542	pobj	genes,from
R3210	T10871	T10869	prep	on,located
R3211	T10872	T10873	nummod	7,chromosomes
R3212	T10873	T10871	pobj	chromosomes,on
R3213	T10874	T10873	punct	", ",chromosomes
R3214	T10875	T10873	appos	5,chromosomes
R3215	T10876	T10875	punct	", ",5
R3216	T10877	T10875	conj	6,5
R3217	T10878	T10877	punct	", ",6
R3218	T10879	T10877	conj	7,6
R3219	T10880	T10879	punct	", ",7
R322	T2545	T2544	compound	susceptibility,genes
R3220	T10881	T10879	conj	10,7
R3221	T10882	T10881	punct	", ",10
R3222	T10883	T10881	conj	11,10
R3223	T10884	T10883	punct	", ",11
R3224	T10885	T10883	conj	16,11
R3225	T10886	T10885	cc	and,16
R3226	T10887	T10885	conj	17,16
R3227	T10888	T10869	punct	.,located
R3228	T10890	T10891	mark	Since,are
R3229	T10891	T10900	advcl	are,used
R323	T2546	T2544	prep	of,genes
R3230	T10892	T10893	det	the,intervals
R3231	T10893	T10891	nsubj	intervals,are
R3232	T10894	T10893	compound	confidence,intervals
R3233	T10895	T10893	prep	of,intervals
R3234	T10896	T10895	pobj	QTL,of
R3235	T10897	T10893	prep	in,intervals
R3236	T10898	T10899	compound	F2,progeny
R3237	T10899	T10897	pobj	progeny,in
R3238	T10901	T10902	quantmod	around,20
R3239	T10902	T10903	nummod	20,cM
R324	T2547	T2546	pobj	RA,of
R3240	T10903	T10891	attr	cM,are
R3241	T10904	T10905	punct	[,26
R3242	T10905	T10891	parataxis	26,are
R3243	T10906	T10905	punct	],26
R3244	T10907	T10900	punct	", ",used
R3245	T10908	T10900	nsubj	we,used
R3246	T10909	T10910	nummod	40,Mb
R3247	T10910	T10900	dobj	Mb,used
R3248	T10911	T10900	prep	as,used
R3249	T10912	T10913	det	the,intervals
R325	T2548	T2544	acl	identified,genes
R3250	T10913	T10911	pobj	intervals,as
R3251	T10914	T10913	compound	confidence,intervals
R3252	T10915	T10913	prep	for,intervals
R3253	T10916	T10917	det	all,loci
R3254	T10917	T10915	pobj	loci,for
R3255	T10918	T10900	punct	.,used
R3256	T10920	T10921	compound	Twenty,one
R3257	T10921	T10923	nummod	one,genes
R3258	T10922	T10921	punct	-,one
R3259	T10923	T10924	nsubjpass	genes,located
R326	T2549	T2550	advmod	so,far
R3260	T10925	T10924	auxpass	were,located
R3261	T10926	T10924	prep	in,located
R3262	T10927	T10928	det	the,intervals
R3263	T10928	T10926	pobj	intervals,in
R3264	T10929	T10928	compound	confidence,intervals
R3265	T10930	T10928	prep	of,intervals
R3266	T10931	T10932	quantmod	six,eight
R3267	T10932	T10935	nummod	eight,QTL
R3268	T10933	T10932	quantmod	of,eight
R3269	T10934	T10932	quantmod	the,eight
R327	T2550	T2548	advmod	far,identified
R3270	T10935	T10930	pobj	QTL,of
R3271	T10936	T10924	punct	.,located
R3272	T10938	T10939	nsubj	We,located
R3273	T10940	T10941	nummod	5,genes
R3274	T10941	T10939	dobj	genes,located
R3275	T10942	T10940	punct	", ",5
R3276	T10943	T10940	conj	4,5
R3277	T10944	T10943	punct	", ",4
R3278	T10945	T10943	conj	2,4
R3279	T10946	T10945	punct	", ",2
R328	T2551	T2544	punct	", ",genes
R3280	T10947	T10945	conj	1,2
R3281	T10948	T10947	punct	", ",1
R3282	T10949	T10947	conj	3,1
R3283	T10950	T10949	cc	and,3
R3284	T10951	T10949	conj	6,3
R3285	T10952	T10941	amod	potential,genes
R3286	T10953	T10941	compound	candidate,genes
R3287	T10954	T10939	prep	within,located
R3288	T10955	T10956	det	the,intervals
R3289	T10956	T10954	pobj	intervals,within
R329	T2552	T2544	prep	including,genes
R3290	T10957	T10956	compound	confidence,intervals
R3291	T10958	T10956	prep	of,intervals
R3292	T10959	T10960	nmod	loci,1
R3293	T10960	T10958	pobj	1,of
R3294	T10961	T10960	punct	", ",1
R3295	T10962	T10960	conj	2,1
R3296	T10963	T10962	punct	", ",2
R3297	T10964	T10962	conj	3,2
R3298	T10965	T10964	punct	", ",3
R3299	T10966	T10964	conj	5,3
R33	T493	T494	amod	small,effect
R330	T2553	T2554	compound	HLA,DR4
R3300	T10967	T10966	punct	", ",5
R3301	T10968	T10966	conj	6,5
R3302	T10969	T10968	cc	and,6
R3303	T10970	T10968	conj	8,6
R3304	T10971	T10939	punct	", ",located
R3305	T10972	T10939	advmod	respectively,located
R3306	T10973	T10939	punct	", ",located
R3307	T10974	T10975	mark	while,identified
R3308	T10975	T10939	advcl	identified,located
R3309	T10976	T10977	det	no,gene
R331	T2554	T2552	pobj	DR4,including
R3310	T10977	T10975	nsubjpass	gene,identified
R3311	T10978	T10977	compound	candidate,gene
R3312	T10979	T10975	auxpass	was,identified
R3313	T10980	T10975	prep	for,identified
R3314	T10981	T10982	nmod	loci,4
R3315	T10982	T10980	pobj	4,for
R3316	T10983	T10982	cc	and,4
R3317	T10984	T10982	conj	7,4
R3318	T10985	T10939	punct	.,located
R3319	T10987	T10988	nsubj	Table,summarises
R332	T2555	T2554	punct	-,DR4
R3320	T10989	T10987	nummod	3,Table
R3321	T10990	T10991	det	the,genes
R3322	T10991	T10988	dobj	genes,summarises
R3323	T10992	T10991	nummod	21,genes
R3324	T10993	T10991	compound	candidate,genes
R3325	T10994	T10991	acl	identified,genes
R3326	T10995	T10994	prep	in,identified
R3327	T10996	T10997	det	this,study
R3328	T10997	T10995	pobj	study,in
R3329	T10998	T10988	punct	.,summarises
R333	T2556	T2554	punct	", ",DR4
R3330	T11000	T11001	nummod	Two,genes
R3331	T11001	T11002	nsubjpass	genes,upregulated
R3332	T11003	T11001	punct	", ",genes
R3333	T11004	T11001	appos	hspa1a,genes
R3334	T11005	T11004	cc	and,hspa1a
R3335	T11006	T11004	conj	Oas1a,hspa1a
R3336	T11007	T11002	punct	", ",upregulated
R3337	T11008	T11002	auxpass	were,upregulated
R3338	T11009	T11002	prep	at,upregulated
R3339	T11010	T11011	det	the,phase
R334	T2557	T2554	conj	PADI4,DR4
R3340	T11011	T11009	pobj	phase,at
R3341	T11012	T11011	compound	OA,phase
R3342	T11013	T11011	prep	of,phase
R3343	T11014	T11013	pobj	CIA,of
R3344	T11015	T11002	cc	and,upregulated
R3345	T11016	T11017	nsubjpass	Oas1a,upregulated
R3346	T11017	T11002	conj	upregulated,upregulated
R3347	T11018	T11017	auxpass	was,upregulated
R3348	T11019	T11017	advmod	also,upregulated
R3349	T11020	T11017	prep	at,upregulated
R335	T2558	T2557	punct	", ",PADI4
R3350	T11021	T11022	det	the,phase
R3351	T11022	T11020	pobj	phase,at
R3352	T11023	T11022	compound	PI,phase
R3353	T11024	T11017	punct	.,upregulated
R3354	T11026	T11027	prep	Except,downregulated
R3355	T11028	T11026	prep	for,Except
R3356	T11029	T11030	det	these,genes
R3357	T11030	T11028	pobj	genes,for
R3358	T11031	T11030	nummod	two,genes
R3359	T11032	T11027	punct	", ",downregulated
R336	T2559	T2557	conj	PTPN22,PADI4
R3360	T11033	T11034	det	all,genes
R3361	T11034	T11027	nsubjpass	genes,downregulated
R3362	T11035	T11034	amod	other,genes
R3363	T11036	T11034	nummod	19,genes
R3364	T11037	T11027	auxpass	were,downregulated
R3365	T11038	T11027	prep	at,downregulated
R3366	T11039	T11040	det	the,phase
R3367	T11040	T11038	pobj	phase,at
R3368	T11041	T11040	amod	chronic,phase
R3369	T11042	T11040	prep	of,phase
R337	T2560	T2559	cc	and,PTPN22
R3370	T11043	T11042	pobj	CIA,of
R3371	T11044	T11027	punct	.,downregulated
R3372	T11046	T11047	det	All,genes
R3373	T11047	T11048	nsubj	genes,showed
R3374	T11049	T11047	punct	", ",genes
R3375	T11050	T11047	prep	except,genes
R3376	T11051	T11050	pobj	hspa1a,except
R3377	T11052	T11048	punct	", ",showed
R3378	T11053	T11054	compound	expression,differences
R3379	T11054	T11048	dobj	differences,showed
R338	T2561	T2559	conj	FCRL3,PTPN22
R3380	T11055	T11054	prep	between,differences
R3381	T11056	T11057	det	the,strains
R3382	T11057	T11055	pobj	strains,between
R3383	T11058	T11057	nummod	two,strains
R3384	T11059	T11048	prep	at,showed
R3385	T11060	T11061	det	the,phase
R3386	T11061	T11059	pobj	phase,at
R3387	T11062	T11061	compound	NC,phase
R3388	T11063	T11048	punct	.,showed
R3389	T11065	T11066	nummod	Five,genes
R339	T2562	T2563	punct	[,6
R3390	T11066	T11067	nsubjpass	genes,expressed
R3391	T11068	T11067	auxpass	were,expressed
R3392	T11069	T11067	advmod	differentially,expressed
R3393	T11070	T11067	prep	at,expressed
R3394	T11071	T11072	det	all,phases
R3395	T11072	T11070	pobj	phases,at
R3396	T11073	T11072	prep	of,phases
R3397	T11074	T11073	pobj	CIA,of
R3398	T11075	T11067	punct	", ",expressed
R3399	T11076	T11067	prep	including,expressed
R34	T494	T492	compound	effect,genes
R340	T2563	T2538	parataxis	6,seen
R3400	T11077	T11078	compound	H2,Q10
R3401	T11078	T11076	pobj	Q10,including
R3402	T11079	T11078	punct	-,Q10
R3403	T11080	T11078	punct	", ",Q10
R3404	T11081	T11078	conj	Mapk14,Q10
R3405	T11082	T11081	punct	", ",Mapk14
R3406	T11083	T11081	conj	Pscd1,Mapk14
R3407	T11084	T11083	punct	", ",Pscd1
R3408	T11085	T11083	conj	Kpnb1,Pscd1
R3409	T11086	T11085	cc	and,Kpnb1
R341	T2564	T2565	punct	-,9
R3410	T11087	T11085	conj	Wdr1,Kpnb1
R3411	T11088	T11067	punct	.,expressed
R3412	T11090	T11091	prep	Among,had
R3413	T11092	T11093	det	these,genes
R3414	T11093	T11090	pobj	genes,Among
R3415	T11094	T11093	nummod	five,genes
R3416	T11095	T11091	punct	", ",had
R3417	T11096	T11097	compound	H2,Q10
R3418	T11097	T11091	nsubj	Q10,had
R3419	T11098	T11097	punct	-,Q10
R342	T2565	T2563	prep	9,6
R3420	T11099	T11100	det	a,expression
R3421	T11100	T11091	dobj	expression,had
R3422	T11101	T11102	advmod	consistently,higher
R3423	T11102	T11100	amod	higher,expression
R3424	T11103	T11091	prep	in,had
R3425	T11104	T11105	det	the,DBA
R3426	T11105	T11103	pobj	DBA,in
R3427	T11106	T11105	punct	/,DBA
R3428	T11107	T11105	nummod	1,DBA
R3429	T11108	T11091	prep	than,had
R343	T2566	T2563	punct	],6
R3430	T11109	T11110	det	the,strain
R3431	T11110	T11108	pobj	strain,than
R3432	T11111	T11112	compound	FVB,N
R3433	T11112	T11110	compound	N,strain
R3434	T11113	T11112	punct	/,N
R3435	T11114	T11091	prep	in,had
R3436	T11115	T11116	det	all,phases
R3437	T11116	T11114	pobj	phases,in
R3438	T11117	T11116	compound	CIA,phases
R3439	T11118	T11091	punct	", ",had
R344	T2567	T2538	punct	.,seen
R3440	T11119	T11120	mark	while,had
R3441	T11120	T11091	advcl	had,had
R3442	T11121	T11122	det	the,genes
R3443	T11122	T11120	nsubj	genes,had
R3444	T11123	T11122	amod	other,genes
R3445	T11124	T11122	nummod	four,genes
R3446	T11125	T11126	det	a,expression
R3447	T11126	T11120	dobj	expression,had
R3448	T11127	T11126	amod	higher,expression
R3449	T11128	T11120	prep	in,had
R345	T2569	T2570	prep	Except,have
R3450	T11129	T11130	det	the,strain
R3451	T11130	T11128	pobj	strain,in
R3452	T11131	T11130	nmod	DBA,strain
R3453	T11132	T11131	punct	/,DBA
R3454	T11133	T11131	nummod	1,DBA
R3455	T11134	T11120	prep	at,had
R3456	T11135	T11136	det	the,stages
R3457	T11136	T11134	pobj	stages,at
R3458	T11137	T11136	amod	early,stages
R3459	T11138	T11120	punct	", ",had
R346	T2571	T2569	prep	for,Except
R3460	T11139	T11120	prep	including,had
R3461	T11140	T11139	pobj	NC,including
R3462	T11141	T11140	punct	", ",NC
R3463	T11142	T11140	conj	PI,NC
R3464	T11143	T11142	cc	and,PI
R3465	T11144	T11142	conj	OA,PI
R3466	T11145	T11120	punct	", ",had
R3467	T11146	T11120	cc	but,had
R3468	T11147	T11148	det	a,expression
R3469	T11148	T11120	conj	expression,had
R347	T2572	T2573	compound	HLA,DR4
R3470	T11149	T11148	amod	lower,expression
R3471	T11150	T11148	prep	at,expression
R3472	T11151	T11152	det	the,phase
R3473	T11152	T11150	pobj	phase,at
R3474	T11153	T11152	amod	chronic,phase
R3475	T11154	T11091	punct	.,had
R3476	T11156	T11157	compound	GO,analysis
R3477	T11157	T11160	nsubj	analysis,revealed
R3478	T11158	T11157	compound	term,analysis
R3479	T11159	T11157	compound	classification,analysis
R348	T2573	T2571	pobj	DR4,for
R3480	T11161	T11162	mark	that,enriched
R3481	T11162	T11160	ccomp	enriched,revealed
R3482	T11163	T11164	det	the,cluster
R3483	T11164	T11162	nsubjpass	cluster,enriched
R3484	T11165	T11164	amod	functional,cluster
R3485	T11166	T11164	prep	of,cluster
R3486	T11167	T11168	compound	protein,cascade
R3487	T11168	T11166	pobj	cascade,of
R3488	T11169	T11168	compound	kinase,cascade
R3489	T11170	T11162	auxpass	was,enriched
R349	T2574	T2573	punct	-,DR4
R3490	T11171	T11162	advmod	significantly,enriched
R3491	T11172	T11162	prep	in,enriched
R3492	T11173	T11174	det	the,genes
R3493	T11174	T11172	pobj	genes,in
R3494	T11175	T11174	nummod	21,genes
R3495	T11176	T11174	compound	candidate,genes
R3496	T11177	T11160	punct	.,revealed
R3497	T11179	T11180	det	This,cluster
R3498	T11180	T11182	nsubj	cluster,contained
R3499	T11181	T11180	amod	functional,cluster
R35	T495	T494	punct	-,effect
R350	T2575	T2573	punct	", ",DR4
R3500	T11183	T11184	nummod	four,genes
R3501	T11184	T11182	dobj	genes,contained
R3502	T11185	T11184	punct	", ",genes
R3503	T11186	T11184	prep	including,genes
R3504	T11187	T11186	pobj	Mapk14,including
R3505	T11188	T11187	punct	", ",Mapk14
R3506	T11189	T11187	conj	Mapk8ip3,Mapk14
R3507	T11190	T11189	punct	", ",Mapk8ip3
R3508	T11191	T11189	conj	Stat5a,Mapk8ip3
R3509	T11192	T11191	cc	and,Stat5a
R351	T2576	T2577	dep	which,associated
R3510	T11193	T11191	conj	Gna12,Stat5a
R3511	T11194	T11182	punct	.,contained
R352	T2577	T2573	relcl	associated,DR4
R3525	T13481	T13482	prep	In,attempted
R3526	T13483	T13484	det	this,study
R3527	T13484	T13481	pobj	study,In
R3528	T13485	T13482	punct	", ",attempted
R3529	T13486	T13482	nsubj	we,attempted
R353	T2578	T2577	auxpass	is,associated
R3530	T13487	T13482	prep	for,attempted
R3531	T13488	T13489	det	the,time
R3532	T13489	T13487	pobj	time,for
R3533	T13490	T13489	amod	first,time
R3534	T13491	T13492	aux	to,identify
R3535	T13492	T13482	xcomp	identify,attempted
R3536	T13493	T13494	amod	small,effect
R3537	T13494	T13496	compound	effect,QTL
R3538	T13495	T13494	punct	-,effect
R3539	T13496	T13492	dobj	QTL,identify
R354	T2579	T2577	advmod	strongly,associated
R3540	T13497	T13492	prep	in,identify
R3541	T13498	T13499	det	an,progeny
R3542	T13499	T13497	pobj	progeny,in
R3543	T13500	T13499	compound	F2,progeny
R3544	T13501	T13482	punct	.,attempted
R3545	T13503	T13504	amod	Small,effect
R3546	T13504	T13506	compound	effect,QTL
R3547	T13505	T13504	punct	-,effect
R3548	T13506	T13507	nsubjpass	QTL,defined
R3549	T13508	T13507	auxpass	are,defined
R355	T2580	T2577	prep	with,associated
R3550	T13509	T13507	prep	as,defined
R3551	T13510	T13509	pobj	those,as
R3552	T13511	T13510	acl	reaching,those
R3553	T13512	T13513	det	the,value
R3554	T13513	T13511	dobj	value,reaching
R3555	T13514	T13513	compound	threshold,value
R3556	T13515	T13513	prep	of,value
R3557	T13516	T13517	nsubj	P,0.05
R3558	T13517	T13515	pcomp	0.05,of
R3559	T13518	T13517	punct	=,0.05
R356	T2581	T2580	pobj	RA,with
R3560	T13519	T13507	cc	but,defined
R3561	T13520	T13521	nsubj	that,reach
R3562	T13521	T13507	conj	reach,defined
R3563	T13522	T13521	aux	did,reach
R3564	T13523	T13521	neg	not,reach
R3565	T13524	T13525	det	the,value
R3566	T13525	T13521	dobj	value,reach
R3567	T13526	T13527	amod	significant,threshold
R3568	T13527	T13525	compound	threshold,value
R3569	T13528	T13525	acl	suggested,value
R357	T2582	T2570	punct	", ",have
R3570	T13529	T13528	agent	by,suggested
R3571	T13530	T13529	pobj	Lander,by
R3572	T13531	T13530	cc	and,Lander
R3573	T13532	T13530	conj	Botstein,Lander
R3574	T13533	T13534	punct	[,26
R3575	T13534	T13528	parataxis	26,suggested
R3576	T13535	T13534	punct	],26
R3577	T13536	T13521	punct	.,reach
R3578	T13538	T13539	mark	Although,significant
R3579	T13539	T13541	advcl	significant,is
R358	T2583	T2584	predet	all,genes
R3580	T13540	T13539	neg	not,significant
R3581	T13542	T13541	punct	", ",is
R3582	T13543	T13541	expl	there,is
R3583	T13544	T13541	attr	evidence,is
R3584	T13545	T13546	mark	that,contain
R3585	T13546	T13544	acl	contain,evidence
R3586	T13547	T13546	nsubj	most,contain
R3587	T13548	T13547	prep	of,most
R3588	T13549	T13550	det	the,QTL
R3589	T13550	T13548	pobj	QTL,of
R359	T2584	T2570	nsubj	genes,have
R3590	T13551	T13550	nummod	eight,QTL
R3591	T13552	T13553	amod	small,effect
R3592	T13553	T13550	compound	effect,QTL
R3593	T13554	T13553	punct	-,effect
R3594	T13555	T13546	advmod	likely,contain
R3595	T13556	T13557	compound	susceptibility,genes
R3596	T13557	T13546	dobj	genes,contain
R3597	T13558	T13557	prep	for,genes
R3598	T13559	T13558	pobj	CIA,for
R3599	T13560	T13541	punct	.,is
R36	T496	T497	dep	that,are
R360	T2585	T2584	det	the,genes
R3600	T13562	T13563	advmod	First,performed
R3601	T13564	T13563	punct	", ",performed
R3602	T13565	T13563	nsubj	we,performed
R3603	T13566	T13567	det	the,analysis
R3604	T13567	T13563	dobj	analysis,performed
R3605	T13568	T13567	compound	linkage,analysis
R3606	T13569	T13563	prep	in,performed
R3607	T13570	T13571	nummod	three,datasets
R3608	T13571	T13569	pobj	datasets,in
R3609	T13572	T13571	punct	", ",datasets
R361	T2586	T2584	amod	other,genes
R3610	T13573	T13571	prep	including,datasets
R3611	T13574	T13575	det	all,progeny
R3612	T13575	T13573	pobj	progeny,including
R3613	T13576	T13575	nummod	290,progeny
R3614	T13577	T13575	compound	F,progeny
R3615	T13578	T13575	punct	", ",progeny
R3616	T13579	T13580	nummod	76,progeny
R3617	T13580	T13575	conj	progeny,progeny
R3618	T13581	T13580	nmod	C5+,progeny
R3619	T13582	T13581	punct	/,C5+
R362	T2587	T2584	compound	susceptibility,genes
R3620	T13583	T13581	punct	+,C5+
R3621	T13584	T13580	compound	F2,progeny
R3622	T13585	T13580	cc	and,progeny
R3623	T13586	T13587	nummod	133,progeny
R3624	T13587	T13580	conj	progeny,progeny
R3625	T13588	T13587	nmod	C5+,progeny
R3626	T13589	T13588	punct	/,C5+
R3627	T13590	T13588	punct	-,C5+
R3628	T13591	T13587	compound	F2,progeny
R3629	T13592	T13563	punct	.,performed
R363	T2588	T2589	advmod	only,effect
R3630	T13594	T13595	quantmod	Five,eight
R3631	T13595	T13598	nummod	eight,QTL
R3632	T13596	T13595	quantmod	of,eight
R3633	T13597	T13595	quantmod	the,eight
R3634	T13598	T13602	nsubjpass	QTL,identified
R3635	T13599	T13600	amod	small,effect
R3636	T13600	T13598	compound	effect,QTL
R3637	T13601	T13600	punct	-,effect
R3638	T13603	T13602	auxpass	were,identified
R3639	T13604	T13602	prep	in,identified
R364	T2589	T2570	dobj	effect,have
R3640	T13605	T13606	advmod	at,two
R3641	T13606	T13608	nummod	two,datasets
R3642	T13607	T13606	advmod	least,two
R3643	T13608	T13604	pobj	datasets,in
R3644	T13609	T13602	punct	", ",identified
R3645	T13610	T13602	advcl	suggesting,identified
R3646	T13611	T13612	mark	that,are
R3647	T13612	T13610	ccomp	are,suggesting
R3648	T13613	T13614	det	these,QTL
R3649	T13614	T13612	nsubj	QTL,are
R365	T2590	T2589	det	a,effect
R3650	T13615	T13612	acomp	reproducible,are
R3651	T13616	T13602	punct	.,identified
R3652	T13618	T13619	advmod	Second,overlap
R3653	T13620	T13619	punct	", ",overlap
R3654	T13621	T13622	amod	many,QTL
R3655	T13622	T13619	nsubj	QTL,overlap
R3656	T13623	T13622	acl	identified,QTL
R3657	T13624	T13623	prep	in,identified
R3658	T13625	T13626	det	the,study
R3659	T13626	T13624	pobj	study,in
R366	T2591	T2589	amod	small,effect
R3660	T13627	T13626	amod	present,study
R3661	T13628	T13619	prep	with,overlap
R3662	T13629	T13630	compound	arthritis,QTL
R3663	T13630	T13628	pobj	QTL,with
R3664	T13631	T13632	advmod	previously,identified
R3665	T13632	T13630	acl	identified,QTL
R3666	T13633	T13630	punct	", ",QTL
R3667	T13634	T13630	prep	including,QTL
R3668	T13635	T13636	nmod	loci,1
R3669	T13636	T13634	pobj	1,including
R367	T2592	T2589	prep	on,effect
R3670	T13637	T13636	punct	", ",1
R3671	T13638	T13636	conj	2,1
R3672	T13639	T13638	punct	", ",2
R3673	T13640	T13638	conj	5,2
R3674	T13641	T13640	cc	and,5
R3675	T13642	T13640	conj	6,5
R3676	T13643	T13619	punct	.,overlap
R3677	T13645	T13646	prep	In,revealed
R3678	T13647	T13645	pobj	addition,In
R3679	T13648	T13646	punct	", ",revealed
R368	T2593	T2594	det	the,disease
R3680	T13649	T13650	amod	syntenic,analysis
R3681	T13650	T13646	nsubj	analysis,revealed
R3682	T13651	T13652	mark	that,linked
R3683	T13652	T13646	ccomp	linked,revealed
R3684	T13653	T13654	det	the,regions
R3685	T13654	T13652	nsubjpass	regions,linked
R3686	T13655	T13654	nmod	counterpart,regions
R3687	T13656	T13654	amod	genomic,regions
R3688	T13657	T13654	prep	on,regions
R3689	T13658	T13659	det	the,genome
R369	T2660	T2657	punct	", ",QTL
R3690	T13659	T13657	pobj	genome,on
R3691	T13660	T13659	amod	human,genome
R3692	T13661	T13659	prep	of,genome
R3693	T13662	T13661	pobj	many,of
R3694	T13663	T13662	prep	of,many
R3695	T13664	T13665	det	these,QTL
R3696	T13665	T13663	pobj	QTL,of
R3697	T13666	T13665	nummod	eight,QTL
R3698	T13667	T13652	auxpass	are,linked
R3699	T13668	T13652	prep	to,linked
R37	T497	T492	relcl	are,genes
R370	T2594	T2592	pobj	disease,on
R3700	T13669	T13668	pobj	RA,to
R3701	T13670	T13646	punct	.,revealed
R3702	T13672	T13673	prep	For,are
R3703	T13674	T13675	quantmod	five,eight
R3704	T13675	T13678	nummod	eight,QTL
R3705	T13676	T13675	quantmod	of,eight
R3706	T13677	T13675	quantmod	the,eight
R3707	T13678	T13672	pobj	QTL,For
R3708	T13679	T13680	amod	small,effect
R3709	T13680	T13678	compound	effect,QTL
R371	T2661	T2657	appos	Cia2,QTL
R3710	T13681	T13680	punct	-,effect
R3711	T13682	T13683	det	the,alleles
R3712	T13683	T13673	nsubj	alleles,are
R3713	T13684	T13683	nmod	DBA,alleles
R3714	T13685	T13684	punct	/,DBA
R3715	T13686	T13684	nummod	1,DBA
R3716	T13687	T13688	det	the,alleles
R3717	T13688	T13673	attr	alleles,are
R3718	T13689	T13690	npadvmod	arthritis,enhancing
R3719	T13690	T13688	amod	enhancing,alleles
R372	T2595	T2570	punct	.,have
R3720	T13691	T13690	punct	-,enhancing
R3721	T13692	T13673	punct	", ",are
R3722	T13693	T13694	mark	while,are
R3723	T13694	T13673	advcl	are,are
R3724	T13695	T13696	det	the,alleles
R3725	T13696	T13694	nsubj	alleles,are
R3726	T13697	T13696	compound	FVBN,alleles
R3727	T13698	T13699	det	the,alleles
R3728	T13699	T13694	attr	alleles,are
R3729	T13700	T13701	npadvmod	arthritis,enhancing
R373	T2662	T2659	punct	", ",identified
R3730	T13701	T13699	amod	enhancing,alleles
R3731	T13702	T13701	punct	-,enhancing
R3732	T13703	T13694	prep	in,are
R3733	T13704	T13705	det	the,QTL
R3734	T13705	T13703	pobj	QTL,in
R3735	T13706	T13705	amod	other,QTL
R3736	T13707	T13705	nummod	three,QTL
R3737	T13708	T13694	punct	", ",are
R3738	T13709	T13694	advcl	indicating,are
R3739	T13710	T13711	mark	that,come
R374	T2663	T2659	auxpass	was,identified
R3740	T13711	T13709	ccomp	come,indicating
R3741	T13712	T13713	det	some,genes
R3742	T13713	T13711	nsubj	genes,come
R3743	T13714	T13713	compound	susceptibility,genes
R3744	T13715	T13711	aux	could,come
R3745	T13716	T13711	prep	from,come
R3746	T13717	T13718	det	the,strain
R3747	T13718	T13716	pobj	strain,from
R3748	T13719	T13718	amod	resistant,strain
R3749	T13720	T13673	punct	.,are
R375	T2597	T2598	prep	In,observed
R3750	T13722	T13723	advmod	Interestingly,overlap
R3751	T13724	T13723	punct	", ",overlap
R3752	T13725	T13726	nmod	loci,2
R3753	T13726	T13723	nsubj	2,overlap
R3754	T13727	T13726	cc	and,2
R3755	T13728	T13726	conj	7,2
R3756	T13729	T13723	advmod	partially,overlap
R3757	T13730	T13723	prep	with,overlap
R3758	T13731	T13732	nummod	two,QTL
R3759	T13732	T13730	pobj	QTL,with
R376	T2664	T2659	prep	for,identified
R3760	T13733	T13734	npadvmod	arthritis,related
R3761	T13734	T13732	amod	related,QTL
R3762	T13735	T13734	punct	-,related
R3763	T13736	T13732	acl	identified,QTL
R3764	T13737	T13736	agent	by,identified
R3765	T13738	T13737	pobj	us,by
R3766	T13739	T13736	prep	in,identified
R3767	T13740	T13741	det	the,progeny
R3768	T13741	T13739	pobj	progeny,in
R3769	T13742	T13741	amod	same,progeny
R377	T2665	T2666	det	the,phenotype
R3770	T13743	T13741	compound	F2,progeny
R3771	T13744	T13745	punct	[,10
R3772	T13745	T13723	parataxis	10,overlap
R3773	T13746	T13745	punct	],10
R3774	T13747	T13723	punct	.,overlap
R3775	T13749	T13750	nsubjpass	Locus,located
R3776	T13751	T13749	nummod	2,Locus
R3777	T13752	T13750	auxpass	was,located
R3778	T13753	T13750	prep	at,located
R3779	T13754	T13755	det	the,region
R378	T2666	T2664	pobj	phenotype,for
R3780	T13755	T13753	pobj	region,at
R3781	T13756	T13755	amod	same,region
R3782	T13757	T13755	amod	genomic,region
R3783	T13758	T13755	prep	as,region
R3784	T13759	T13758	pobj	Cia27,as
R3785	T13760	T13759	punct	", ",Cia27
R3786	T13761	T13762	det	a,QTL
R3787	T13762	T13759	appos	QTL,Cia27
R3788	T13763	T13762	acl	controlling,QTL
R3789	T13764	T13765	compound	IgG2a,levels
R379	T2599	T2600	det	the,model
R3790	T13765	T13763	dobj	levels,controlling
R3791	T13766	T13765	compound	antibody,levels
R3792	T13767	T13765	prep	to,levels
R3793	T13768	T13767	pobj	collagen,to
R3794	T13769	T13768	nummod	II,collagen
R3795	T13770	T13750	punct	.,located
R3796	T13772	T13773	advmod	Recently,refined
R3797	T13774	T13773	punct	", ",refined
R3798	T13775	T13773	nsubj	we,refined
R3799	T13776	T13773	aux	have,refined
R38	T498	T497	acomp	difficult,are
R380	T2667	T2666	prep	of,phenotype
R3800	T13777	T13778	det	this,QTL
R3801	T13778	T13773	dobj	QTL,refined
R3802	T13779	T13773	prep	into,refined
R3803	T13780	T13781	det	a,region
R3804	T13781	T13779	pobj	region,into
R3805	T13782	T13783	nummod	4.1,Mb
R3806	T13783	T13781	nmod	Mb,region
R3807	T13784	T13781	amod	genomic,region
R3808	T13785	T13773	cc	and,refined
R3809	T13786	T13773	conj	showed,refined
R381	T2668	T2669	compound	CIA,severity
R3810	T13787	T13788	mark	that,regulates
R3811	T13788	T13786	ccomp	regulates,showed
R3812	T13789	T13790	det	a,gene
R3813	T13790	T13788	nsubj	gene,regulates
R3814	T13791	T13790	prep	within,gene
R3815	T13792	T13793	det	this,region
R3816	T13793	T13791	pobj	region,within
R3817	T13794	T13795	compound	CIA,severity
R3818	T13795	T13788	dobj	severity,regulates
R3819	T13796	T13788	prep	by,regulates
R382	T2669	T2667	pobj	severity,of
R3820	T13797	T13796	pcomp	controlling,by
R3821	T13798	T13799	det	the,levels
R3822	T13799	T13797	dobj	levels,controlling
R3823	T13800	T13799	compound	IgG2a,levels
R3824	T13801	T13799	compound	antibody,levels
R3825	T13802	T13799	prep	to,levels
R3826	T13803	T13802	pobj	collagen,to
R3827	T13804	T13803	nummod	II,collagen
R3828	T13805	T13806	punct	[,31
R3829	T13806	T13786	parataxis	31,showed
R383	T2670	T2659	punct	", ",identified
R3830	T13807	T13806	punct	],31
R3831	T13808	T13773	punct	.,refined
R3832	T13810	T13811	nsubj	Locus,overlaps
R3833	T13812	T13810	nummod	7,Locus
R3834	T13813	T13810	prep	on,Locus
R3835	T13814	T13813	pobj	chromosome,on
R3836	T13815	T13814	nummod	16,chromosome
R3837	T13816	T13811	prep	with,overlaps
R3838	T13817	T13816	pobj	Lp1,with
R3839	T13818	T13817	punct	", ",Lp1
R384	T2600	T2597	pobj	model,In
R3840	T13819	T13820	dep	which,controls
R3841	T13820	T13817	relcl	controls,Lp1
R3842	T13821	T13822	compound	lymphocyte,proliferation
R3843	T13822	T13820	dobj	proliferation,controls
R3844	T13823	T13811	punct	.,overlaps
R3845	T13825	T13826	advmod	Furthermore,controls
R3846	T13827	T13826	punct	", ",controls
R3847	T13828	T13826	prep	according,controls
R3848	T13829	T13828	prep	to,according
R3849	T13830	T13831	poss	our,data
R385	T2671	T2659	cc	but,identified
R3850	T13831	T13829	pobj	data,to
R3851	T13832	T13831	amod	unpublished,data
R3852	T13833	T13826	punct	", ",controls
R3853	T13834	T13826	nsubj	loci,controls
R3854	T13835	T13834	nummod	8,loci
R3855	T13836	T13834	prep	on,loci
R3856	T13837	T13836	pobj	chromosome,on
R3857	T13838	T13837	nummod	17,chromosome
R3858	T13839	T13840	compound	lymphocyte,adherence
R3859	T13840	T13826	dobj	adherence,controls
R386	T2672	T2673	det	this,QTL
R3860	T13841	T13826	prep	during,controls
R3861	T13842	T13841	pobj	development,during
R3862	T13843	T13842	prep	of,development
R3863	T13844	T13843	pobj	CIA,of
R3864	T13845	T13826	punct	.,controls
R3865	T13847	T13848	advmod	Therefore,affect
R3866	T13849	T13848	punct	", ",affect
R3867	T13850	T13851	det	the,gene
R3868	T13851	T13848	nsubj	gene,affect
R3869	T13852	T13851	prep	within,gene
R387	T2673	T2674	nsubj	QTL,contributes
R3870	T13853	T13854	det	the,QTL
R3871	T13854	T13852	pobj	QTL,within
R3872	T13855	T13856	amod	small,effect
R3873	T13856	T13854	compound	effect,QTL
R3874	T13857	T13856	punct	-,effect
R3875	T13858	T13848	aux	could,affect
R3876	T13859	T13860	compound	CIA,severity
R3877	T13860	T13848	dobj	severity,affect
R3878	T13861	T13848	prep	through,affect
R3879	T13862	T13861	pcomp	controlling,through
R388	T2674	T2659	conj	contributes,identified
R3880	T13863	T13864	npadvmod	arthritis,related
R3881	T13864	T13866	amod	related,phenotypes
R3882	T13865	T13864	punct	-,related
R3883	T13866	T13862	dobj	phenotypes,controlling
R3884	T13867	T13848	punct	.,affect
R3885	T13869	T13870	amod	Several,studies
R3886	T13870	T13871	nsubjpass	studies,carried
R3887	T13872	T13871	aux	have,carried
R3888	T13873	T13871	auxpass	been,carried
R3889	T13874	T13871	prt	out,carried
R389	T2601	T2600	compound	mouse,model
R3890	T13875	T13876	aux	to,detect
R3891	T13876	T13871	advcl	detect,carried
R3892	T13877	T13878	compound	gene,expression
R3893	T13878	T13876	dobj	expression,detect
R3894	T13879	T13876	prep	during,detect
R3895	T13880	T13879	pobj	CIA,during
R3896	T13881	T13871	punct	", ",carried
R3897	T13882	T13883	dep	all,used
R3898	T13883	T13871	ccomp	used,carried
R3899	T13884	T13882	prep	of,all
R39	T499	T500	aux	to,identify
R390	T2675	T2674	prep	to,contributes
R3900	T13885	T13884	pobj	which,of
R3901	T13886	T13883	dobj	joints,used
R3902	T13887	T13883	prep	as,used
R3903	T13888	T13889	det	the,tissue
R3904	T13889	T13887	pobj	tissue,as
R3905	T13890	T13889	compound	target,tissue
R3906	T13891	T13892	punct	[,22
R3907	T13892	T13871	parataxis	22,carried
R3908	T13893	T13892	nummod	15,22
R3909	T13894	T13892	punct	",",22
R391	T2676	T2677	advmod	only,16
R3910	T13895	T13892	nummod	16,22
R3911	T13896	T13892	punct	",",22
R3912	T13897	T13892	nummod	21,22
R3913	T13898	T13892	punct	",",22
R3914	T13899	T13892	punct	],22
R3915	T13900	T13871	punct	.,carried
R3916	T13902	T13903	det	This,study
R3917	T13903	T13904	nsubj	study,detected
R3918	T13905	T13904	punct	", ",detected
R3919	T13906	T13904	prep	for,detected
R392	T2602	T2600	prep	of,model
R3920	T13907	T13908	det	the,time
R3921	T13908	T13906	pobj	time,for
R3922	T13909	T13908	amod	first,time
R3923	T13910	T13904	punct	", ",detected
R3924	T13911	T13912	compound	gene,expression
R3925	T13912	T13904	dobj	expression,detected
R3926	T13913	T13904	prep	in,detected
R3927	T13914	T13913	pobj	LNs,in
R3928	T13915	T13904	prep	during,detected
R3929	T13916	T13915	pobj	CIA,during
R393	T2677	T2678	nummod	16,%
R3930	T13917	T13904	punct	.,detected
R3931	T13919	T13920	nsubj	We,present
R3932	T13921	T13922	det	an,study
R3933	T13922	T13920	dobj	study,present
R3934	T13923	T13922	amod	extensive,study
R3935	T13924	T13922	prep	of,study
R3936	T13925	T13926	compound	gene,patterns
R3937	T13926	T13924	pobj	patterns,of
R3938	T13927	T13926	compound	expression,patterns
R3939	T13928	T13922	prep	in,study
R394	T2678	T2675	pobj	%,to
R3940	T13929	T13928	pobj	LNs,in
R3941	T13930	T13929	prep	of,LNs
R3942	T13931	T13932	preconj	both,strains
R3943	T13932	T13930	pobj	strains,of
R3944	T13933	T13934	advmod	genetically,susceptible
R3945	T13934	T13932	amod	susceptible,strains
R3946	T13935	T13934	cc	and,susceptible
R3947	T13936	T13934	conj	resistant,susceptible
R3948	T13937	T13922	prep	at,study
R3949	T13938	T13939	nummod	four,phases
R395	T2679	T2678	prep	of,%
R3950	T13939	T13937	pobj	phases,at
R3951	T13940	T13939	amod	different,phases
R3952	T13941	T13939	prep	of,phases
R3953	T13942	T13941	pobj	CIA,of
R3954	T13943	T13920	punct	.,present
R3955	T13945	T13946	prep	In,were
R3956	T13947	T13948	det	both,strains
R3957	T13948	T13945	pobj	strains,In
R3958	T13949	T13946	punct	", ",were
R3959	T13950	T13951	advmod	differentially,regulated
R396	T2603	T2602	pobj	RA,of
R3960	T13951	T13952	amod	regulated,genes
R3961	T13952	T13946	nsubj	genes,were
R3962	T13953	T13954	advmod	highly,concentrated
R3963	T13954	T13946	acomp	concentrated,were
R3964	T13955	T13946	prep	at,were
R3965	T13956	T13957	det	the,phases
R3966	T13957	T13955	pobj	phases,at
R3967	T13958	T13957	nmod	PI,phases
R3968	T13959	T13958	cc	and,PI
R3969	T13960	T13958	conj	CA,PI
R397	T2680	T2681	det	the,variations
R3970	T13961	T13946	punct	", ",were
R3971	T13962	T13946	cc	and,were
R3972	T13963	T13964	advmod	only,number
R3973	T13964	T13967	nsubjpass	number,expressed
R3974	T13965	T13964	det	a,number
R3975	T13966	T13964	amod	small,number
R3976	T13967	T13946	conj	expressed,were
R3977	T13968	T13964	prep	of,number
R3978	T13969	T13968	pobj	genes,of
R3979	T13970	T13967	auxpass	were,expressed
R398	T2681	T2679	pobj	variations,of
R3980	T13971	T13967	advmod	differentially,expressed
R3981	T13972	T13967	prep	in,expressed
R3982	T13973	T13974	nummod	two,phases
R3983	T13974	T13972	pobj	phases,in
R3984	T13975	T13973	cc	or,two
R3985	T13976	T13973	conj	three,two
R3986	T13977	T13967	punct	.,expressed
R3987	T13979	T13980	nsubj	This,indicates
R3988	T13981	T13982	mark	that,were
R3989	T13982	T13980	ccomp	were,indicates
R399	T2682	T2681	compound	phenotype,variations
R3990	T13983	T13984	amod	biological,responses
R3991	T13984	T13982	nsubj	responses,were
R3992	T13985	T13984	prep	in,responses
R3993	T13986	T13985	pobj	LNs,in
R3994	T13987	T13982	acomp	stronger,were
R3995	T13988	T13987	prep	in,stronger
R3996	T13989	T13990	det	the,phases
R3997	T13990	T13988	pobj	phases,in
R3998	T13991	T13990	nmod	PI,phases
R3999	T13992	T13991	cc	and,PI
R4	T461	T460	cc	and,genome
R40	T500	T498	advcl	identify,difficult
R400	T2604	T2598	punct	", ",observed
R4000	T13993	T13991	conj	CA,PI
R4001	T13994	T13987	prep	than,stronger
R4002	T13995	T13994	prep	in,than
R4003	T13996	T13997	det	the,phase
R4004	T13997	T13995	pobj	phase,in
R4005	T13998	T13997	compound	OA,phase
R4006	T13999	T13982	punct	", ",were
R4007	T14000	T13982	cc	and,were
R4008	T14001	T14002	det	the,responses
R4009	T14002	T14003	nsubj	responses,were
R401	T2683	T2681	prep	for,variations
R4010	T14003	T13982	conj	were,were
R4011	T14004	T14002	prep	at,responses
R4012	T14005	T14006	amod	different,phases
R4013	T14006	T14004	pobj	phases,at
R4014	T14007	T14003	acomp	different,were
R4015	T14008	T13980	punct	.,indicates
R4016	T14010	T14011	advmod	When,comparing
R4017	T14011	T14012	advcl	comparing,found
R4018	T14013	T14014	det	the,susceptible
R4019	T14014	T14011	dative	susceptible,comparing
R402	T2684	T2685	compound	CIA,susceptibility
R4020	T14015	T14011	prep	to,comparing
R4021	T14016	T14017	det	the,resistant
R4022	T14017	T14015	pobj	resistant,to
R4023	T14018	T14011	dobj	strain,comparing
R4024	T14019	T14012	punct	", ",found
R4025	T14020	T14021	det	the,difference
R4026	T14021	T14012	nsubjpass	difference,found
R4027	T14022	T14021	amod	biggest,difference
R4028	T14023	T14012	auxpass	was,found
R4029	T14024	T14012	prep	in,found
R403	T2685	T2683	pobj	susceptibility,for
R4030	T14025	T14026	nummod	one,cluster
R4031	T14026	T14024	pobj	cluster,in
R4032	T14027	T14026	prep	of,cluster
R4033	T14028	T14027	pobj	genes,of
R4034	T14029	T14026	punct	(,cluster
R4035	T14030	T14026	appos	cluster,cluster
R4036	T14031	T14030	nummod	IV,cluster
R4037	T14032	T14033	punct	", ",Figure
R4038	T14033	T14012	parataxis	Figure,found
R4039	T14034	T14033	nummod	2,Figure
R404	T2605	T2606	amod	small,contributions
R4040	T14035	T14033	punct	),Figure
R4041	T14036	T14012	punct	.,found
R4042	T14038	T14039	det	These,genes
R4043	T14039	T14040	nsubj	genes,had
R4044	T14041	T14042	det	a,expression
R4045	T14042	T14040	dobj	expression,had
R4046	T14043	T14042	amod	higher,expression
R4047	T14044	T14042	prep	in,expression
R4048	T14045	T14044	pobj	DBA,in
R4049	T14046	T14045	punct	/,DBA
R405	T2686	T2674	prep	in,contributes
R4050	T14047	T14045	nummod	1,DBA
R4051	T14048	T14042	prep	than,expression
R4052	T14049	T14048	prep	in,than
R4053	T14050	T14051	compound	FVB,N
R4054	T14051	T14049	pobj	N,in
R4055	T14052	T14051	punct	/,N
R4056	T14053	T14040	prep	at,had
R4057	T14054	T14055	det	the,phases
R4058	T14055	T14053	pobj	phases,at
R4059	T14056	T14055	amod	early,phases
R406	T2687	T2688	compound	F2,progeny
R4060	T14057	T14055	prep	of,phases
R4061	T14058	T14057	pobj	CIA,of
R4062	T14059	T14060	punct	(,NC
R4063	T14060	T14055	parataxis	NC,phases
R4064	T14061	T14060	punct	", ",NC
R4065	T14062	T14060	conj	PI,NC
R4066	T14063	T14062	cc	and,PI
R4067	T14064	T14062	conj	OA,PI
R4068	T14065	T14060	punct	),NC
R4069	T14066	T14040	cc	and,had
R407	T2606	T2598	nsubjpass	contributions,observed
R4070	T14067	T14068	det	the,pattern
R4071	T14068	T14040	conj	pattern,had
R4072	T14069	T14068	amod	opposite,pattern
R4073	T14070	T14068	compound	expression,pattern
R4074	T14071	T14068	prep	in,pattern
R4075	T14072	T14073	det	the,phase
R4076	T14073	T14071	pobj	phase,in
R4077	T14074	T14073	compound	CA,phase
R4078	T14075	T14040	punct	.,had
R4079	T14077	T14078	compound	GO,classification
R408	T2688	T2686	pobj	progeny,in
R4080	T14078	T14080	nsubj	classification,revealed
R4081	T14079	T14078	compound	term,classification
R4082	T14081	T14082	mark	that,related
R4083	T14082	T14080	ccomp	related,revealed
R4084	T14083	T14084	det	these,genes
R4085	T14084	T14082	nsubjpass	genes,related
R4086	T14085	T14082	auxpass	were,related
R4087	T14086	T14082	prep	to,related
R4088	T14087	T14088	compound	lymphocyte,proliferation
R4089	T14088	T14086	pobj	proliferation,to
R409	T2607	T2606	amod	genetic,contributions
R4090	T14089	T14088	cc	and,proliferation
R4091	T14090	T14088	conj	activation,proliferation
R4092	T14091	T14082	punct	", ",related
R4093	T14092	T14082	advcl	suggesting,related
R4094	T14093	T14094	mark	that,are
R4095	T14094	T14092	ccomp	are,suggesting
R4096	T14095	T14094	nsubj	lymphocytes,are
R4097	T14096	T14095	prep	in,lymphocytes
R4098	T14097	T14098	det	the,strain
R4099	T14098	T14096	pobj	strain,in
R41	T501	T484	punct	.,controlled
R410	T2608	T2598	auxpass	are,observed
R4100	T14099	T14098	nmod	DBA,strain
R4101	T14100	T14099	punct	/,DBA
R4102	T14123	T14115	advcl	existed,is
R4103	T14101	T14099	nummod	1,DBA
R4104	T14124	T14125	det	the,difference
R4105	T14102	T14103	advmod	more,activated
R4106	T14125	T14123	nsubj	difference,existed
R4107	T14126	T14125	compound	expression,difference
R4108	T14127	T14125	prep	between,difference
R4109	T14103	T14094	acomp	activated,are
R411	T2689	T2690	punct	[,10
R4110	T14128	T14129	det	the,strains
R4111	T14129	T14127	pobj	strains,between
R4112	T14104	T14103	prep	than,activated
R4113	T14130	T14129	nummod	two,strains
R4114	T14131	T14123	prep	in,existed
R4115	T14132	T14131	pobj	mice,in
R4116	T14105	T14104	pobj	those,than
R4117	T14133	T14132	prep	without,mice
R4118	T14134	T14133	pobj	immunisation,without
R4119	T14135	T14115	punct	.,is
R412	T2609	T2610	advmod	also,often
R4120	T14106	T14105	prep	in,those
R4121	T14137	T14138	advmod	Additionally,upregulated
R4122	T14107	T14108	det	the,strain
R4123	T14139	T14138	punct	", ",upregulated
R4124	T14108	T14106	pobj	strain,in
R4125	T14140	T14141	det	some,genes
R4126	T14141	T14138	nsubjpass	genes,upregulated
R4127	T14142	T14141	acl	related,genes
R4128	T14109	T14110	compound	FVB,N
R4129	T14143	T14142	prep	to,related
R413	T2690	T2674	parataxis	10,contributes
R4130	T14144	T14145	det	the,response
R4131	T14110	T14108	compound	N,strain
R4132	T14145	T14143	pobj	response,to
R4133	T14146	T14145	amod	immune,response
R4134	T14147	T14138	auxpass	were,upregulated
R4135	T14148	T14138	prep	in,upregulated
R4136	T14149	T14150	det	the,strain
R4137	T14150	T14148	pobj	strain,in
R4138	T14111	T14110	punct	/,N
R4139	T14151	T14150	nmod	DBA,strain
R414	T2691	T2690	punct	],10
R4140	T14152	T14151	punct	/,DBA
R4141	T14153	T14151	nummod	1,DBA
R4142	T14112	T14080	punct	.,revealed
R4143	T14154	T14148	cc	but,in
R4144	T14155	T14154	neg	not,but
R4145	T14156	T14148	conj	in,in
R4146	T14157	T14158	det	the,strain
R4147	T14114	T14115	advmod	However,is
R4148	T14158	T14156	pobj	strain,in
R4149	T14159	T14160	compound	FVB,N
R415	T2692	T2674	punct	.,contributes
R4150	T14160	T14158	compound	N,strain
R4151	T14161	T14160	punct	/,N
R4152	T14116	T14115	punct	", ",is
R4153	T14162	T14138	prep	during,upregulated
R4154	T14163	T14162	pobj	CIA,during
R4155	T14164	T14138	punct	.,upregulated
R4156	T14166	T14167	det	These,differences
R4157	T14117	T14118	det	this,difference
R4158	T14167	T14168	nsubj	differences,explain
R4159	T14169	T14168	aux	could,explain
R416	T2610	T2598	advmod	often,observed
R4160	T14118	T14115	nsubj	difference,is
R4161	T14170	T14171	advmod	why,occurred
R4162	T14119	T14115	neg	not,is
R4163	T14120	T14121	npadvmod	CIA,specific
R4164	T14171	T14168	ccomp	occurred,explain
R4165	T14172	T14173	det	a,response
R4166	T14121	T14115	acomp	specific,is
R4167	T14173	T14171	nsubj	response,occurred
R4168	T14174	T14173	amod	higher,response
R4169	T14175	T14173	compound	antibody,response
R417	T2694	T2695	nsubj	This,suggests
R4170	T14122	T14123	mark	because,existed
R4171	T14176	T14173	prep	to,response
R4172	T14177	T14176	pobj	collagen,to
R4173	T14178	T14177	nummod	II,collagen
R4174	T14179	T14171	prep	in,occurred
R4175	T14229	T14228	prep	to,according
R4176	T14180	T14181	det	the,strain
R4177	T14181	T14179	pobj	strain,in
R4178	T14182	T14181	nmod	DBA,strain
R4179	T14183	T14182	punct	/,DBA
R418	T2696	T2697	mark	that,be
R4180	T14230	T14231	poss	their,patterns
R4181	T14184	T14182	nummod	1,DBA
R4182	T14185	T14171	prep	compared,occurred
R4183	T14231	T14229	pobj	patterns,to
R4184	T14186	T14185	prep	to,compared
R4185	T14187	T14188	det	the,strain
R4186	T14188	T14186	pobj	strain,to
R4187	T14189	T14190	compound	FVB,N
R4188	T14190	T14188	compound	N,strain
R4189	T14232	T14233	compound	gene,expression
R419	T2697	T2695	ccomp	be,suggests
R4190	T14191	T14190	punct	/,N
R4191	T14192	T14168	punct	", ",explain
R4192	T14193	T14168	cc	and,explain
R4193	T14194	T14195	aux	might,explain
R4194	T14233	T14231	compound	expression,patterns
R4195	T14195	T14168	conj	explain,explain
R4196	T14234	T14213	prep	during,identified
R4197	T14196	T14195	advmod	partially,explain
R4198	T14197	T14198	det	the,difference
R4199	T14198	T14195	dobj	difference,explain
R42	T503	T504	advmod	Here,present
R420	T2698	T2697	expl	there,be
R4200	T14199	T14198	prep	of,difference
R4201	T14235	T14234	pobj	CIA,during
R4202	T14200	T14201	det	the,susceptibility
R4203	T14201	T14199	pobj	susceptibility,of
R4204	T14202	T14201	prep	to,susceptibility
R4205	T14203	T14202	pobj	CIA,to
R4206	T14236	T14235	cc	and,CIA
R4207	T14204	T14198	prep	between,difference
R4208	T14205	T14206	det	both,strains
R4209	T14206	T14204	pobj	strains,between
R421	T2611	T2598	punct	.,observed
R4210	T14237	T14238	poss	their,locations
R4211	T14207	T14168	punct	.,explain
R4212	T14209	T14210	compound	Twenty,one
R4213	T14238	T14235	conj	locations,CIA
R4214	T14210	T14212	nummod	one,genes
R4215	T14211	T14210	punct	-,one
R4216	T14212	T14213	nsubjpass	genes,identified
R4217	T14239	T14238	amod	genomic,locations
R4218	T14214	T14213	auxpass	were,identified
R4219	T14215	T14213	prep	as,identified
R422	T2699	T2697	aux	must,be
R4220	T14216	T14217	amod	potential,genes
R4221	T14240	T14213	punct	.,identified
R4222	T14217	T14215	pobj	genes,as
R4223	T14218	T14217	compound	candidate,genes
R4224	T14219	T14213	prep	for,identified
R4225	T14242	T14243	det	No,genes
R4226	T14220	T14221	quantmod	six,eight
R4227	T14221	T14224	nummod	eight,QTL
R4228	T14222	T14221	quantmod	of,eight
R4229	T14223	T14221	quantmod	the,eight
R423	T2700	T2701	amod	other,genes
R4230	T14243	T14245	nsubjpass	genes,located
R4231	T14224	T14219	pobj	QTL,for
R4232	T14225	T14226	amod	small,effect
R4233	T14226	T14224	compound	effect,QTL
R4234	T14244	T14243	compound	candidate,genes
R4235	T14227	T14226	punct	-,effect
R4236	T14228	T14213	prep	according,identified
R4237	T14246	T14245	auxpass	were,located
R4238	T14247	T14245	prep	in,located
R4239	T14248	T14249	nmod	QTL,4
R424	T2613	T2614	prep	For,carried
R4240	T14336	T14337	advmod	Moreover,attenuate
R4241	T14249	T14247	pobj	4,in
R4242	T14338	T14337	punct	", ",attenuate
R4243	T14339	T14337	nsubj	inhibitors,attenuate
R4244	T14340	T14339	prep	of,inhibitors
R4245	T14341	T14342	compound	p38,MAPK
R4246	T14250	T14249	cc	and,4
R4247	T14342	T14340	pobj	MAPK,of
R4248	T14343	T14337	aux	could,attenuate
R4249	T14344	T14337	dobj	CIA,attenuate
R425	T2701	T2697	attr	genes,be
R4250	T14251	T14249	conj	7,4
R4251	T14345	T14337	prep	in,attenuate
R4252	T14252	T14245	punct	", ",located
R4253	T14346	T14345	pobj	rats,in
R4254	T14347	T14348	punct	[,33
R4255	T14348	T14337	parataxis	33,attenuate
R4256	T14349	T14348	punct	],33
R4257	T14253	T14245	advcl	suggesting,located
R4258	T14254	T14255	mark	that,affect
R4259	T14350	T14337	punct	", ",attenuate
R426	T2702	T2701	compound	susceptibility,genes
R4260	T14351	T14337	cc	and,attenuate
R4261	T14352	T14353	compound	p38,MAPK
R4262	T14255	T14253	ccomp	affect,suggesting
R4263	T14353	T14354	nsubj	MAPK,becoming
R4264	T14354	T14337	conj	becoming,attenuate
R4265	T14355	T14354	aux	is,becoming
R4266	T14356	T14357	det	a,target
R4267	T14256	T14257	compound	QTG,polymorphisms
R4268	T14357	T14354	attr	target,becoming
R4269	T14358	T14357	amod	potential,target
R427	T2703	T2704	poss	whose,contributions
R4270	T14359	T14357	amod	therapeutic,target
R4271	T14257	T14255	nsubj	polymorphisms,affect
R4272	T14360	T14354	prep	in,becoming
R4273	T14361	T14360	pobj	RA,in
R4274	T14362	T14363	punct	[,32
R4275	T14363	T14354	parataxis	32,becoming
R4276	T14258	T14257	prep	of,polymorphisms
R4277	T14364	T14363	punct	],32
R4278	T14365	T14337	punct	.,attenuate
R4279	T14367	T14368	nsubj	Stat5a,is
R428	T2704	T2705	dep	contributions,were
R4280	T14259	T14260	det	the,genes
R4281	T14369	T14367	punct	", ",Stat5a
R4282	T14370	T14371	det	a,gene
R4283	T14260	T14258	pobj	genes,of
R4284	T14371	T14367	appos	gene,Stat5a
R4285	T14372	T14371	compound	candidate,gene
R4286	T14373	T14371	prep	for,gene
R4287	T14374	T14373	pobj	loci,for
R4288	T14261	T14260	compound	susceptibility,genes
R4289	T14375	T14374	nummod	6,loci
R429	T2705	T2701	relcl	were,genes
R4290	T14376	T14368	punct	", ",is
R4291	T14377	T14378	det	an,molecule
R4292	T14378	T14368	attr	molecule,is
R4293	T14379	T14378	amod	essential,molecule
R4294	T14380	T14378	prep	for,molecule
R4295	T14381	T14382	compound	lymphoid,development
R4296	T14262	T14257	prep	inside,polymorphisms
R4297	T14382	T14380	pobj	development,for
R4298	T14383	T14382	cc	and,development
R4299	T14384	T14382	conj	differentiation,development
R43	T505	T504	nsubj	we,present
R430	T2615	T2613	pobj	example,For
R4300	T14385	T14386	punct	[,34
R4301	T14263	T14264	det	these,QTL
R4302	T14386	T14368	parataxis	34,is
R4303	T14387	T14386	punct	],34
R4304	T14388	T14368	punct	.,is
R4305	T14264	T14262	pobj	QTL,inside
R4306	T14390	T14391	npadvmod	Stat5a,deficient
R4307	T14391	T14393	amod	deficient,mice
R4308	T14265	T14264	nummod	two,QTL
R4309	T14392	T14391	punct	-,deficient
R431	T2706	T2705	neg	not,were
R4310	T14393	T14394	nsubjpass	mice,reported
R4311	T14266	T14255	aux	might,affect
R4312	T14395	T14394	auxpass	were,reported
R4313	T14396	T14397	aux	to,lose
R4314	T14397	T14394	xcomp	lose,reported
R4315	T14267	T14255	neg	not,affect
R4316	T14398	T14397	dobj	tolerance,lose
R4317	T14399	T14397	punct	", ",lose
R4318	T14400	T14397	advcl	resulting,lose
R4319	T14401	T14400	prep	in,resulting
R432	T2707	T2705	acomp	big,were
R4320	T14268	T14269	det	the,phenotype
R4321	T14402	T14403	det	the,development
R4322	T14403	T14401	pobj	development,in
R4323	T14404	T14403	prep	of,development
R4324	T14269	T14255	dobj	phenotype,affect
R4325	T14405	T14406	amod	autoimmune,diseases
R4326	T14406	T14404	pobj	diseases,of
R4327	T14270	T14255	prep	by,affect
R4328	T14407	T14394	punct	.,reported
R4329	T14409	T14410	nsubjpass	Stat5a,suggested
R433	T2708	T2707	advmod	enough,big
R4330	T14271	T14270	pcomp	regulating,by
R4331	T14411	T14410	auxpass	is,suggested
R4332	T14412	T14413	aux	to,contribute
R4333	T14272	T14273	compound	gene,expression
R4334	T14413	T14410	xcomp	contribute,suggested
R4335	T14414	T14413	prep	to,contribute
R4336	T14415	T14414	pobj	tolerance,to
R4337	T14273	T14271	dobj	expression,regulating
R4338	T14416	T14413	prep	through,contribute
R4339	T14417	T14416	pobj	maintenance,through
R434	T2616	T2614	punct	", ",carried
R4340	T14418	T14417	prep	of,maintenance
R4341	T14419	T14420	det	the,population
R4342	T14420	T14418	pobj	population,of
R4343	T14421	T14420	nmod	CD4+CD25+,population
R4344	T14422	T14420	amod	regulatory,population
R4345	T14274	T14245	punct	.,located
R4346	T14423	T14424	compound	T,cell
R4347	T14424	T14420	compound	cell,population
R4348	T14425	T14426	punct	[,35
R4349	T14426	T14410	parataxis	35,suggested
R435	T2709	T2710	aux	to,reach
R4350	T14276	T14277	quantmod	Two,21
R4351	T14427	T14426	punct	],35
R4352	T14428	T14410	punct	.,suggested
R4353	T14430	T14431	advmod	Therefore,presented
R4354	T14277	T14280	nummod	21,genes
R4355	T14432	T14431	punct	", ",presented
R4356	T14278	T14277	quantmod	of,21
R4357	T14433	T14431	nsubj	we,presented
R4358	T14434	T14431	aux	have,presented
R4359	T14435	T14436	det	a,strategy
R436	T2710	T2707	xcomp	reach,big
R4360	T14436	T14431	dobj	strategy,presented
R4361	T14279	T14277	quantmod	the,21
R4362	T14437	T14438	aux	to,identify
R4363	T14438	T14436	advcl	identify,strategy
R4364	T14280	T14282	nsubjpass	genes,reported
R4365	T14439	T14440	amod	small,effect
R4366	T14281	T14280	compound	candidate,genes
R4367	T14440	T14442	compound	effect,QTL
R4368	T14283	T14282	auxpass	were,reported
R4369	T14284	T14285	aux	to,involved
R437	T2711	T2712	det	the,value
R4370	T14441	T14440	punct	-,effect
R4371	T14285	T14282	xcomp	involved,reported
R4372	T14442	T14438	dobj	QTL,identify
R4373	T14443	T14438	cc	and,identify
R4374	T14444	T14438	conj	search,identify
R4375	T14286	T14285	auxpass	be,involved
R4376	T14445	T14444	prep	for,search
R4377	T14446	T14447	amod	potential,genes
R4378	T14287	T14285	prep	in,involved
R4379	T14447	T14445	pobj	genes,for
R438	T2617	T2614	prep	in,carried
R4380	T14448	T14447	compound	candidate,genes
R4381	T14449	T14444	prep	within,search
R4382	T14450	T14449	pobj	them,within
R4383	T14288	T14287	pobj	arthritis,in
R4384	T14451	T14431	punct	.,presented
R4385	T14289	T14282	punct	.,reported
R4386	T14453	T14454	advmod	However,is
R4387	T14455	T14454	punct	", ",is
R4388	T14291	T14292	nsubj	Mapk14,regulates
R4389	T14456	T14454	nsubj	it,is
R439	T2712	T2710	dobj	value,reach
R4390	T14457	T14454	acomp	noteworthy,is
R4391	T14458	T14459	mark	that,lead
R4392	T14459	T14454	ccomp	lead,is
R4393	T14460	T14461	det	the,threshold
R4394	T14461	T14459	nsubj	threshold,lead
R4395	T14462	T14461	amod	low,threshold
R4396	T14293	T14291	punct	", ",Mapk14
R4397	T14463	T14461	amod	statistical,threshold
R4398	T14464	T14461	cc	and,threshold
R4399	T14465	T14466	amod	small,number
R44	T506	T507	det	a,strategy
R440	T2713	T2712	amod	stringent,value
R4400	T14466	T14461	conj	number,threshold
R4401	T14294	T14295	det	a,gene
R4402	T14467	T14466	prep	of,number
R4403	T14468	T14467	pobj	animals,of
R4404	T14469	T14466	prep	per,number
R4405	T14295	T14291	nmod	gene,Mapk14
R4406	T14470	T14469	pobj	group,per
R4407	T14471	T14459	aux	could,lead
R4408	T14472	T14459	prep	to,lead
R4409	T14296	T14295	nmod	candidate,gene
R441	T2714	T2712	compound	significance,value
R4410	T14473	T14474	det	some,results
R4411	T14474	T14472	pobj	results,to
R4412	T14475	T14476	amod	false,positive
R4413	T14297	T14295	prep	for,gene
R4414	T14476	T14474	amod	positive,results
R4415	T14477	T14454	punct	.,is
R4416	T14298	T14297	pobj	locus,for
R4417	T14479	T14480	prep	On,be
R4418	T14481	T14482	det	the,level
R4419	T14299	T14298	nummod	8,locus
R442	T2715	T2712	compound	threshold,value
R4420	T14482	T14479	pobj	level,On
R4421	T14483	T14482	compound	genome,level
R4422	T14484	T14480	punct	", ",be
R4423	T14300	T14295	cc	and,gene
R4424	T14485	T14480	nsubj	some,be
R4425	T14486	T14485	prep	of,some
R4426	T14487	T14488	det	the,QTL
R4427	T14488	T14486	pobj	QTL,of
R4428	T14301	T14302	advmod	also,called
R4429	T14489	T14488	nummod	eight,QTL
R443	T2618	T2619	det	a,study
R4430	T14490	T14491	amod	small,effect
R4431	T14491	T14488	compound	effect,QTL
R4432	T14302	T14295	conj	called,gene
R4433	T14492	T14491	punct	-,effect
R4434	T14493	T14488	acl	identified,QTL
R4435	T14494	T14493	advcl	using,identified
R4436	T14495	T14496	det	a,value
R4437	T14303	T14304	nmod	p38,kinase
R4438	T14496	T14494	dobj	value,using
R4439	T14497	T14498	advmod	very,low
R444	T2716	T2712	prep	of,value
R4440	T14498	T14496	amod	low,value
R4441	T14304	T14309	nmod	kinase,alpha
R4442	T14499	T14496	compound	threshold,value
R4443	T14500	T14501	punct	(,0.05
R4444	T14501	T14496	parataxis	0.05,value
R4445	T14502	T14501	nsubj	P,0.05
R4446	T14503	T14501	punct	<,0.05
R4447	T14504	T14501	punct	),0.05
R4448	T14305	T14306	npadvmod	mitogen,activated
R4449	T14505	T14480	aux	could,be
R445	T2717	T2718	compound	linkage,analysis
R4450	T14506	T14507	amod	false,positives
R4451	T14507	T14480	attr	positives,be
R4452	T14306	T14304	amod	activated,kinase
R4453	T14508	T14480	punct	.,be
R4454	T14510	T14511	prep	For,identified
R4455	T14307	T14306	punct	-,activated
R4456	T14512	T14510	pobj	example,For
R4457	T14513	T14511	punct	", ",identified
R4458	T14308	T14304	nmod	protein,kinase
R4459	T14514	T14511	nsubjpass	locus,identified
R446	T2619	T2617	pobj	study,in
R4460	T14515	T14514	nummod	4,locus
R4461	T14309	T14302	oprd	alpha,called
R4462	T14310	T14304	punct	(,kinase
R4463	T14516	T14511	auxpass	was,identified
R4464	T14311	T14304	appos	MAPK,kinase
R4465	T14517	T14511	prep	with,identified
R4466	T14518	T14519	det	a,value
R4467	T14519	T14517	pobj	value,with
R4468	T14312	T14309	punct	),alpha
R4469	T14520	T14519	amod	low,value
R447	T2718	T2716	pobj	analysis,of
R4470	T14521	T14519	compound	P,value
R4471	T14522	T14511	cc	and,identified
R4472	T14313	T14292	punct	", ",regulates
R4473	T14523	T14524	aux	does,overlap
R4474	T14524	T14511	conj	overlap,identified
R4475	T14525	T14524	neg	not,overlap
R4476	T14314	T14315	det	the,production
R4477	T14315	T14292	dobj	production,regulates
R4478	T14526	T14524	prep	with,overlap
R4479	T14527	T14528	det	any,QTL
R448	T2719	T2695	punct	.,suggests
R4480	T14316	T14315	prep	of,production
R4481	T14528	T14526	pobj	QTL,with
R4482	T14529	T14530	advmod	previously,identified
R4483	T14530	T14528	amod	identified,QTL
R4484	T14317	T14318	npadvmod	arthritis,essential
R4485	T14531	T14528	compound	arthritis,QTL
R4486	T14532	T14511	punct	.,identified
R4487	T14318	T14320	amod	essential,cytokines
R4488	T14534	T14535	prep	On,result
R4489	T14536	T14537	det	the,level
R449	T2620	T2619	amod	previous,study
R4490	T14319	T14318	punct	-,essential
R4491	T14537	T14534	pobj	level,On
R4492	T14538	T14537	compound	transcriptome,level
R4493	T14539	T14535	punct	", ",result
R4494	T14320	T14316	pobj	cytokines,of
R4495	T14540	T14541	det	the,number
R4496	T14541	T14535	nsubj	number,result
R4497	T14542	T14541	amod	small,number
R4498	T14543	T14541	prep	of,number
R4499	T14544	T14543	pobj	animals,of
R45	T507	T504	dobj	strategy,present
R450	T2721	T2722	nummod	One,aim
R4500	T14545	T14541	prep	per,number
R4501	T14546	T14545	pobj	group,per
R4502	T14321	T14320	punct	", ",cytokines
R4503	T14322	T14323	amod	such,as
R4504	T14323	T14320	prep	as,cytokines
R4505	T14547	T14541	cc	and,number
R4506	T14548	T14549	det	the,threshold
R4507	T14549	T14541	conj	threshold,number
R4508	T14324	T14325	compound	tumour,factor
R4509	T14550	T14549	amod	low,threshold
R451	T2722	T2723	nsubj	aim,is
R4510	T14551	T14549	acl	used,threshold
R4511	T14552	T14553	aux	to,detect
R4512	T14325	T14323	pobj	factor,as
R4513	T14553	T14551	advcl	detect,used
R4514	T14554	T14555	compound	gene,expression
R4515	T14555	T14553	dobj	expression,detect
R4516	T14326	T14325	compound	necrosis,factor
R4517	T14556	T14535	aux	could,result
R4518	T14557	T14535	advmod	also,result
R4519	T14327	T14325	cc	and,factor
R452	T2621	T2614	punct	", ",carried
R4520	T14558	T14535	prep	in,result
R4521	T14559	T14560	amod	false,positives
R4522	T14560	T14558	pobj	positives,in
R4523	T14561	T14535	prep	in,result
R4524	T14328	T14325	conj	interleukin,factor
R4525	T14562	T14563	det	the,genes
R4526	T14563	T14561	pobj	genes,in
R4527	T14329	T14328	punct	-,interleukin
R4528	T14564	T14565	advmod	differentially,expressed
R4529	T14565	T14563	amod	expressed,genes
R453	T2724	T2722	prep	of,aim
R4530	T14566	T14535	punct	.,result
R4531	T14330	T14328	nummod	1,interleukin
R4532	T14568	T14569	advmod	Furthermore,result
R4533	T14331	T14332	punct	[,32
R4534	T14570	T14569	punct	", ",result
R4535	T14571	T14572	det	the,expression
R4536	T14572	T14569	nsubj	expression,result
R4537	T14332	T14292	parataxis	32,regulates
R4538	T14573	T14572	amod	differential,expression
R4539	T14574	T14572	prep	of,expression
R454	T2725	T2724	pcomp	using,of
R4540	T14575	T14576	det	a,gene
R4541	T14576	T14574	pobj	gene,of
R4542	T14333	T14332	punct	],32
R4543	T14577	T14569	aux	could,result
R4544	T14578	T14579	preconj	not,from
R4545	T14579	T14569	prep	from,result
R4546	T14334	T14292	punct	.,regulates
R4547	T14580	T14578	advmod	only,not
R4548	T14581	T14582	compound	allele,difference
R4549	T14582	T14579	pobj	difference,from
R455	T2622	T2614	nsubj	we,carried
R4550	T14583	T14582	prep	between,difference
R4551	T14584	T14585	nummod	two,strains
R4552	T14585	T14583	pobj	strains,between
R4553	T14586	T14579	punct	", ",from
R4554	T14587	T14579	cc	but,from
R4555	T14588	T14587	advmod	also,but
R4556	T14589	T14579	conj	from,from
R4557	T14590	T14591	amod	other,factors
R4558	T14591	T14589	pobj	factors,from
R4559	T14592	T14569	punct	.,result
R456	T2726	T2727	compound	animal,models
R4560	T14594	T14595	advmod	Therefore,confirmed
R4561	T14596	T14595	punct	", ",confirmed
R4562	T14597	T14598	poss	our,findings
R4563	T14598	T14595	nsubjpass	findings,confirmed
R4564	T14599	T14595	aux	should,confirmed
R4565	T14600	T14595	auxpass	be,confirmed
R4566	T14601	T14595	prep	in,confirmed
R4567	T14602	T14603	amod	future,studies
R4568	T14603	T14601	pobj	studies,in
R4569	T14604	T14595	punct	.,confirmed
R457	T2727	T2725	dobj	models,using
R4570	T14922	T14923	nsubj	We,present
R4571	T14924	T14925	det	a,strategy
R4572	T14925	T14923	dobj	strategy,present
R4573	T14926	T14927	aux	to,search
R4574	T14927	T14925	advcl	search,strategy
R4575	T14928	T14929	compound	candidate,genes
R4576	T14929	T14927	dobj	genes,search
R4577	T14930	T14927	prep	for,search
R4578	T14931	T14932	amod	small,effect
R4579	T14932	T14934	compound	effect,QTL
R458	T2728	T2725	prep	for,using
R4580	T14933	T14932	punct	-,effect
R4581	T14934	T14930	pobj	QTL,for
R4582	T14935	T14923	punct	.,present
R4583	T14937	T14938	prep	With,identified
R4584	T14939	T14940	det	this,strategy
R4585	T14940	T14937	pobj	strategy,With
R4586	T14941	T14938	punct	", ",identified
R4587	T14942	T14938	nsubj	we,identified
R4588	T14943	T14944	nummod	21,genes
R4589	T14944	T14938	dobj	genes,identified
R459	T2623	T2614	prt	out,carried
R4590	T14945	T14944	compound	candidate,genes
R4591	T14946	T14944	prep	for,genes
R4592	T14947	T14948	nummod	8,susceptibility
R4593	T14948	T14946	pobj	susceptibility,for
R4594	T14949	T14950	amod	small,effect
R4595	T14950	T14948	nmod	effect,susceptibility
R4596	T14951	T14950	punct	-,effect
R4597	T14952	T14953	npadvmod	QTL,regulating
R4598	T14953	T14948	amod	regulating,susceptibility
R4599	T14954	T14948	compound	CIA,susceptibility
R46	T508	T507	amod	novel,strategy
R460	T2729	T2730	amod	complex,diseases
R4600	T14955	T14938	punct	.,identified
R4601	T14957	T14958	poss	Our,studies
R4602	T14958	T14960	nsubjpass	studies,carried
R4603	T14959	T14958	amod	future,studies
R4604	T14961	T14960	aux	will,carried
R4605	T14962	T14960	auxpass	be,carried
R4606	T14963	T14960	prt	out,carried
R4607	T14964	T14960	advcl	using,carried
R4608	T14965	T14966	nummod	two,approaches
R4609	T14966	T14964	dobj	approaches,using
R461	T2730	T2728	pobj	diseases,for
R4610	T14967	T14960	punct	.,carried
R4611	T14969	T14970	det	The,first
R4612	T14970	T14971	nsubj	first,generating
R4613	T14972	T14971	aux	is,generating
R4614	T14973	T14974	amod	congenic,animals
R4615	T14974	T14971	dobj	animals,generating
R4616	T14975	T14971	prep	for,generating
R4617	T14976	T14977	amod	promising,QTL
R4618	T14977	T14975	pobj	QTL,for
R4619	T14978	T14979	amod	small,effect
R462	T2624	T2625	det	a,screen
R4620	T14979	T14977	compound	effect,QTL
R4621	T14980	T14979	punct	-,effect
R4622	T14981	T14982	dep	that,have
R4623	T14982	T14977	relcl	have,QTL
R4624	T14983	T14984	advmod	relatively,high
R4625	T14984	T14985	amod	high,values
R4626	T14985	T14982	dobj	values,have
R4627	T14986	T14985	compound	P,values
R4628	T14987	T14982	cc	and,have
R4629	T14988	T14982	conj	overlap,have
R463	T2731	T2732	aux	to,detect
R4630	T14989	T14988	prep	with,overlap
R4631	T14990	T14991	advmod	previously,identified
R4632	T14991	T14993	amod	identified,QTL
R4633	T14992	T14991	punct	-,identified
R4634	T14993	T14989	pobj	QTL,with
R4635	T14994	T14993	compound	arthritis,QTL
R4636	T14995	T14971	punct	.,generating
R4637	T14997	T14998	det	The,approach
R4638	T14998	T15000	nsubj	approach,is
R4639	T14999	T14998	amod	second,approach
R464	T2732	T2723	xcomp	detect,is
R4640	T15001	T15000	xcomp	investigating,is
R4641	T15002	T15003	compound	candidate,genes
R4642	T15003	T15001	dobj	genes,investigating
R4643	T15004	T15001	advcl	using,investigating
R4644	T15005	T15006	preconj	both,mouse
R4645	T15006	T15007	nmod	mouse,studies
R4646	T15007	T15004	dobj	studies,using
R4647	T15008	T15006	cc	and,mouse
R4648	T15009	T15006	conj	human,mouse
R4649	T15010	T15000	punct	.,is
R465	T2625	T2614	dobj	screen,carried
R4650	T15012	T15013	compound	Candidate,genes
R4651	T15013	T15014	nsubjpass	genes,selected
R4652	T15015	T15014	aux	will,selected
R4653	T15016	T15014	auxpass	be,selected
R4654	T15017	T15014	prep	according,selected
R4655	T15018	T15017	prep	to,according
R4656	T15019	T15020	poss	their,function
R4657	T15020	T15018	pobj	function,to
R4658	T15021	T15020	cc	and,function
R4659	T15022	T15020	conj	polymorphism,function
R466	T2733	T2734	det	the,basis
R4660	T15023	T15022	prep	between,polymorphism
R4661	T15024	T15025	det	the,strains
R4662	T15025	T15023	pobj	strains,between
R4663	T15026	T15025	nummod	two,strains
R4664	T15027	T15014	punct	.,selected
R4665	T15029	T15030	advmod	Thereafter,generate
R4666	T15031	T15030	punct	", ",generate
R4667	T15032	T15030	nsubj	we,generate
R4668	T15033	T15030	aux	will,generate
R4669	T15034	T15035	amod	knock,mice
R467	T2734	T2732	dobj	basis,detect
R4670	T15035	T15030	dobj	mice,generate
R4671	T15036	T15034	punct	-,knock
R4672	T15037	T15034	prt	out,knock
R4673	T15038	T15039	aux	to,investigate
R4674	T15039	T15030	advcl	investigate,generate
R4675	T15040	T15041	det	the,role
R4676	T15041	T15039	dobj	role,investigate
R4677	T15042	T15041	prep	of,role
R4678	T15043	T15044	det	the,genes
R4679	T15044	T15042	pobj	genes,of
R468	T2735	T2734	amod	genetic,basis
R4680	T15045	T15039	prep	in,investigate
R4681	T15046	T15045	pobj	CIA,in
R4682	T15047	T15030	punct	.,generate
R4683	T15049	T15050	prep	For,investigate
R4684	T15051	T15052	det	the,loci
R4685	T15052	T15049	pobj	loci,For
R4686	T15053	T15054	poss	whose,counterparts
R4687	T15054	T15055	dep	counterparts,linked
R4688	T15055	T15052	relcl	linked,loci
R4689	T15056	T15054	prep	on,counterparts
R469	T2736	T2734	prep	of,basis
R4690	T15057	T15058	det	the,genome
R4691	T15058	T15056	pobj	genome,on
R4692	T15059	T15058	amod	human,genome
R4693	T15060	T15055	auxpass	are,linked
R4694	T15061	T15055	prep	to,linked
R4695	T15062	T15061	pobj	RA,to
R4696	T15063	T15050	punct	", ",investigate
R4697	T15064	T15050	nsubj	we,investigate
R4698	T15065	T15050	aux	will,investigate
R4699	T15066	T15067	det	the,genes
R47	T509	T510	aux	to,identify
R470	T2737	T2738	det	these,diseases
R4700	T15067	T15050	dobj	genes,investigate
R4701	T15068	T15067	compound	candidate,genes
R4702	T15069	T15050	advcl	using,investigate
R4703	T15070	T15071	compound	case,control
R4704	T15071	T15073	compound	control,studies
R4705	T15072	T15071	punct	-,control
R4706	T15073	T15069	dobj	studies,using
R4707	T15074	T15073	compound	association,studies
R4708	T15075	T15069	prep	in,using
R4709	T15076	T15077	compound	RA,cohorts
R471	T2738	T2736	pobj	diseases,of
R4710	T15077	T15075	pobj	cohorts,in
R4711	T15078	T15050	punct	.,investigate
R472	T2739	T2723	punct	.,is
R473	T2626	T2625	compound	genome,screen
R474	T2741	T2742	prep	With,are
R475	T2627	T2628	aux	to,identify
R476	T2743	T2744	amod	controllable,factors
R477	T2744	T2741	pobj	factors,With
R478	T2628	T2614	advcl	identify,carried
R479	T2745	T2744	amod	environmental,factors
R48	T510	T507	advcl	identify,strategy
R480	T2746	T2747	advmod	as,as
R481	T2747	T2744	cc	as,factors
R482	T2629	T2630	det	the,loci
R483	T2748	T2747	advmod	well,as
R484	T2749	T2750	det	the,background
R485	T2750	T2744	conj	background,factors
R486	T2630	T2628	dobj	loci,identify
R487	T2751	T2750	amod	known,background
R488	T2752	T2750	amod	genetic,background
R489	T2753	T2742	punct	", ",are
R49	T511	T512	det	the,genes
R490	T2631	T2632	amod	quantitative,trait
R491	T2754	T2755	compound	animal,models
R492	T2755	T2742	nsubj	models,are
R493	T2756	T2757	amod	powerful,tools
R494	T2632	T2630	compound	trait,loci
R495	T2633	T2630	punct	(,loci
R496	T2757	T2742	attr	tools,are
R497	T2634	T2630	appos	QTL,loci
R498	T2758	T2759	aux	to,search
R499	T2759	T2757	advcl	search,tools
R5	T462	T460	conj	transcriptome,genome
R50	T512	T510	dobj	genes,identify
R500	T2635	T2628	punct	),identify
R501	T2760	T2759	prep	for,search
R502	T2761	T2762	compound	susceptibility,genes
R503	T2762	T2760	pobj	genes,for
R504	T2636	T2628	prep	in,identify
R505	T2763	T2762	prep	for,genes
R506	T2764	T2765	amod	complex,diseases
R507	T2765	T2763	pobj	diseases,for
R508	T2637	T2638	npadvmod	collagen,induced
R509	T2638	T2640	amod	induced,arthritis
R51	T513	T512	compound	candidate,genes
R510	T2639	T2638	punct	-,induced
R511	T2640	T2636	pobj	arthritis,in
R512	T2766	T2742	punct	", ",are
R513	T2767	T2742	cc	and,are
R514	T2768	T2769	aux	have,employed
R515	T2641	T2640	punct	(,arthritis
R516	T2769	T2742	conj	employed,are
R517	T2770	T2769	auxpass	been,employed
R518	T2642	T2640	appos	CIA,arthritis
R519	T2771	T2769	advmod	intensively,employed
R52	T514	T512	prep	for,genes
R520	T2772	T2769	prep	for,employed
R521	T2773	T2774	det	that,purpose
R522	T2774	T2772	pobj	purpose,for
R523	T2775	T2742	punct	.,are
R524	T2643	T2640	punct	),arthritis
R525	T2644	T2640	punct	", ",arthritis
R526	T2777	T2778	amod	More,"27,000"
R527	T2778	T2780	nummod	"27,000",QTL
R528	T2779	T2778	quantmod	than,"27,000"
R529	T2645	T2646	dep	which,is
R53	T515	T516	amod	small,effect
R530	T2780	T2781	nsubjpass	QTL,identified
R531	T2646	T2640	relcl	is,arthritis
R532	T2782	T2781	aux	have,identified
R533	T2783	T2781	auxpass	been,identified
R534	T2784	T2781	prep	in,identified
R535	T2647	T2648	det	a,model
R536	T2785	T2786	det	the,genome
R537	T2786	T2784	pobj	genome,in
R538	T2648	T2646	attr	model,is
R539	T2787	T2786	compound	mouse,genome
R54	T516	T514	pobj	effect,for
R540	T2788	T2789	mark	since,identified
R541	T2789	T2781	advcl	identified,identified
R542	T2649	T2650	advmod	widely,used
R543	T2790	T2791	det	the,QTL
R544	T2791	T2789	nsubjpass	QTL,identified
R545	T2792	T2791	amod	first,QTL
R546	T2650	T2648	amod	used,model
R547	T2793	T2789	auxpass	was,identified
R548	T2794	T2789	prep	at,identified
R549	T2651	T2648	compound	animal,model
R55	T517	T516	punct	-,effect
R550	T2795	T2796	det	the,beginning
R551	T2796	T2794	pobj	beginning,at
R552	T2797	T2796	prep	of,beginning
R553	T2798	T2799	det	the,1990s
R554	T2652	T2648	prep	of,model
R555	T2799	T2797	pobj	1990s,of
R556	T2800	T2801	punct	[,11
R557	T2653	T2652	pobj	RA,of
R558	T2801	T2781	parataxis	11,identified
R559	T2802	T2801	punct	],11
R56	T518	T519	amod	quantitative,trait
R560	T2803	T2781	punct	.,identified
R561	T2654	T2614	punct	.,carried
R562	T2805	T2806	prep	By,identified
R563	T2656	T2657	advmod	Only,QTL
R564	T2807	T2805	pobj	2005,By
R565	T2808	T2806	punct	", ",identified
R566	T2809	T2810	advmod	approximately,20
R567	T2810	T2811	nummod	20,genes
R568	T2657	T2659	nsubjpass	QTL,identified
R569	T2811	T2806	nsubjpass	genes,identified
R57	T519	T520	compound	trait,loci
R570	T2812	T2813	amod	quantitative,trait
R571	T2813	T2811	compound	trait,genes
R572	T2658	T2657	nummod	one,QTL
R573	T2814	T2811	punct	(,genes
R574	T2815	T2811	appos	QTGs,genes
R575	T2816	T2811	punct	),genes
R576	T2817	T2811	prep	in,genes
R577	T2818	T2819	det	the,genome
R578	T2819	T2817	pobj	genome,in
R579	T2872	T2873	amod	small,effect
R58	T520	T516	appos	loci,effect
R580	T2820	T2819	compound	mouse,genome
R581	T2821	T2806	aux	had,identified
R582	T2822	T2806	auxpass	been,identified
R583	T2823	T2824	punct	[,13
R584	T2824	T2806	parataxis	13,identified
R585	T2825	T2824	nummod	12,13
R586	T2873	T2875	compound	effect,QTL
R587	T2826	T2824	punct	",",13
R588	T2827	T2824	punct	],13
R589	T2828	T2806	punct	.,identified
R59	T521	T520	punct	(,loci
R590	T2874	T2873	punct	-,effect
R591	T2830	T2831	advmod	Interestingly,have
R592	T2875	T2866	nsubj	QTL,are
R593	T2832	T2831	punct	", ",have
R594	T2833	T2834	amod	most,QTGs
R595	T2876	T2866	acomp	difficult,are
R596	T2834	T2831	nsubj	QTGs,have
R597	T2835	T2834	acl	identified,QTGs
R598	T2877	T2878	aux	to,identify
R599	T2836	T2835	prep	in,identified
R6	T463	T464	aux	to,identify
R60	T522	T520	appos	QTL,loci
R600	T2837	T2838	compound	animal,models
R601	T2838	T2836	pobj	models,in
R602	T2878	T2876	advcl	identify,difficult
R603	T2839	T2840	det	the,polymorphisms
R604	T2840	T2831	dobj	polymorphisms,have
R605	T2879	T2878	prep	with,identify
R606	T2841	T2840	amod	causal,polymorphisms
R607	T2842	T2840	prep	in,polymorphisms
R608	T2843	T2844	det	the,region
R609	T2880	T2881	amod	traditional,strategies
R61	T523	T516	punct	),effect
R610	T2844	T2842	pobj	region,in
R611	T2845	T2846	npadvmod	protein,coding
R612	T2846	T2844	amod	coding,region
R613	T2881	T2879	pobj	strategies,with
R614	T2847	T2846	punct	-,coding
R615	T2848	T2849	punct	[,14
R616	T2849	T2844	parataxis	14,region
R617	T2882	T2866	cc	and,are
R618	T2850	T2849	punct	],14
R619	T2851	T2840	punct	", ",polymorphisms
R62	T524	T516	prep	in,effect
R620	T2852	T2853	dep	which,provoke
R621	T2883	T2866	punct	", ",are
R622	T2853	T2840	relcl	provoke,polymorphisms
R623	T2854	T2855	compound	protein,changes
R624	T2884	T2885	prep	on,affect
R625	T2855	T2853	dobj	changes,provoke
R626	T2856	T2855	compound	structure,changes
R627	T2857	T2855	cc	or,changes
R628	T2858	T2859	compound	protein,deficiency
R629	T2859	T2855	conj	deficiency,changes
R63	T525	T526	npadvmod	collagen,induced
R630	T2860	T2831	punct	.,have
R631	T2885	T2866	conj	affect,are
R632	T2862	T2863	nsubj	This,suggests
R633	T2886	T2887	det	the,hand
R634	T2864	T2863	punct	", ",suggests
R635	T2887	T2884	pobj	hand,on
R636	T2865	T2866	prep	on,are
R637	T2888	T2887	amod	other,hand
R638	T2866	T2863	advcl	are,suggests
R639	T2867	T2868	det	the,hand
R64	T526	T527	amod	induced,arthritis
R640	T2889	T2885	punct	", ",affect
R641	T2868	T2865	pobj	hand,on
R642	T2869	T2868	nummod	one,hand
R643	T2870	T2866	punct	", ",are
R644	T2890	T2885	mark	that,affect
R645	T2871	T2866	mark	that,are
R646	T2891	T2892	det	the,polymorphisms
R647	T2892	T2885	nsubj	polymorphisms,affect
R648	T2893	T2892	acl	regulating,polymorphisms
R649	T2894	T2895	compound	gene,expression
R65	T527	T524	pobj	arthritis,in
R650	T2978	T2977	amod	past,decade
R651	T2979	T2975	punct	", ",applied
R652	T2895	T2893	dobj	expression,regulating
R653	T2980	T2981	amod	many,studies
R654	T2981	T2975	nsubj	studies,applied
R655	T2896	T2885	aux	might,affect
R656	T2982	T2983	det	this,technique
R657	T2983	T2975	dobj	technique,applied
R658	T2897	T2898	advmod	only,slightly
R659	T2984	T2985	aux	to,study
R66	T528	T527	punct	(,arthritis
R660	T2985	T2975	advcl	study,applied
R661	T2986	T2987	preconj	both,RA
R662	T2987	T2985	dobj	RA,study
R663	T2898	T2885	advmod	slightly,affect
R664	T2988	T2987	cc	and,RA
R665	T2989	T2990	poss	its,models
R666	T2899	T2900	det	the,traits
R667	T2990	T2987	conj	models,RA
R668	T2991	T2990	compound	animal,models
R669	T2992	T2993	punct	[,15
R67	T529	T527	appos	CIA,arthritis
R670	T2900	T2885	dobj	traits,affect
R671	T2993	T2975	parataxis	15,applied
R672	T2994	T2995	punct	-,22
R673	T2995	T2993	prep	22,15
R674	T2901	T2900	amod	quantitative,traits
R675	T2996	T2993	punct	],15
R676	T2997	T2975	punct	.,applied
R677	T2902	T2885	punct	", ",affect
R678	T2999	T3000	advmod	Indeed,show
R679	T3001	T3000	punct	", ",show
R68	T530	T510	punct	),identify
R680	T3002	T3000	nsubj	genes,show
R681	T3003	T3002	acl	involved,genes
R682	T2903	T2885	cc	and,affect
R683	T3004	T3003	prep	in,involved
R684	T3005	T3004	pobj	arthritis,in
R685	T3006	T3007	amod	distinct,patterns
R686	T3007	T3000	dobj	patterns,show
R687	T2904	T2905	advmod	thus,are
R688	T3008	T3007	compound	expression,patterns
R689	T3009	T3007	prep	in,patterns
R69	T531	T510	advcl	using,identify
R690	T3010	T3011	amod	certain,tissues
R691	T2905	T2885	conj	are,affect
R692	T3011	T3009	pobj	tissues,in
R693	T3012	T3011	cc	and,tissues
R694	T3013	T3014	amod	pathological,stages
R695	T2906	T2907	advmod	more,difficult
R696	T3014	T3011	conj	stages,tissues
R697	T3015	T3014	prep	of,stages
R698	T3016	T3017	det	the,disease
R699	T2907	T2905	acomp	difficult,are
R7	T464	T456	advcl	identify,Combining
R70	T532	T533	amod	global,approaches
R700	T3017	T3015	pobj	disease,of
R701	T3018	T3000	punct	.,show
R702	T2908	T2909	aux	to,identify
R703	T3020	T3021	nsubjpass	Genes,expressed
R704	T2909	T2907	advcl	identify,difficult
R705	T3022	T3020	acl	involved,Genes
R706	T3023	T3022	prep	in,involved
R707	T3024	T3025	amod	immunoinflammatory,responses
R708	T3025	T3023	pobj	responses,in
R709	T2910	T2863	punct	.,suggests
R71	T533	T531	dobj	approaches,using
R710	T3026	T3021	auxpass	were,expressed
R711	T3027	T3021	advmod	differentially,expressed
R712	T3028	T3021	prep	in,expressed
R713	T2912	T2913	npadvmod	Microarray,based
R714	T3029	T3030	det	the,cells
R715	T3030	T3028	pobj	cells,in
R716	T3031	T3030	compound	blood,cells
R717	T3032	T3021	prep	in,expressed
R718	T2913	T2915	amod	based,expression
R719	T3033	T3034	compound	RA,patients
R72	T534	T533	nmod	genome,approaches
R720	T3034	T3032	pobj	patients,in
R721	T3035	T3036	punct	[,18
R722	T2914	T2913	punct	-,based
R723	T3036	T3021	parataxis	18,expressed
R724	T3037	T3036	punct	],18
R725	T3038	T3021	punct	.,expressed
R726	T2915	T2918	nsubj	expression,is
R727	T2916	T2915	amod	global,expression
R728	T2917	T2915	compound	gene,expression
R729	T3040	T3041	nsubjpass	Chemokines,upregulated
R73	T535	T534	cc	and,genome
R730	T2919	T2920	det	a,technique
R731	T3042	T3040	cc	and,Chemokines
R732	T3043	T3044	compound	adhesion,molecules
R733	T3044	T3040	conj	molecules,Chemokines
R734	T3045	T3041	auxpass	were,upregulated
R735	T3046	T3041	prep	in,upregulated
R736	T3047	T3048	det	the,joint
R737	T3048	T3046	pobj	joint,in
R738	T2920	T2918	attr	technique,is
R739	T3049	T3041	prep	at,upregulated
R74	T536	T534	conj	transcriptome,genome
R740	T3050	T3051	det	the,phase
R741	T3051	T3049	pobj	phase,at
R742	T2921	T2920	amod	powerful,technique
R743	T3052	T3051	compound	initiation,phase
R744	T2922	T2920	prep	for,technique
R745	T3053	T3051	prep	of,phase
R746	T3054	T3053	pobj	arthritis,of
R747	T3055	T3041	prep	in,upregulated
R748	T3056	T3057	compound	animal,models
R749	T2923	T2922	pcomp	investigating,for
R75	T537	T504	punct	.,present
R750	T3057	T3055	pobj	models,in
R751	T3058	T3059	punct	[,22
R752	T3059	T3041	parataxis	22,upregulated
R753	T2924	T2925	amod	complex,diseases
R754	T3060	T3059	nummod	21,22
R755	T3061	T3059	punct	",",22
R756	T3062	T3059	punct	],22
R757	T2925	T2923	dobj	diseases,investigating
R758	T3063	T3041	punct	", ",upregulated
R759	T3064	T3065	mark	while,expressed
R76	T539	T540	advmod	First,performed
R760	T2926	T2918	punct	.,is
R761	T3065	T3041	advcl	expressed,upregulated
R762	T3066	T3065	nsubjpass	genes,expressed
R763	T3067	T3066	acl	involved,genes
R764	T3068	T3067	prep	in,involved
R765	T2928	T2929	prep	During,are
R766	T3069	T3070	compound	cartilage,destruction
R767	T3070	T3068	pobj	destruction,in
R768	T3071	T3070	cc	and,destruction
R769	T3072	T3073	compound	bone,erosion
R77	T541	T540	punct	", ",performed
R770	T2930	T2931	compound	disease,development
R771	T3073	T3070	conj	erosion,destruction
R772	T3074	T3065	auxpass	were,expressed
R773	T3075	T3065	advmod	differentially,expressed
R774	T3076	T3065	prep	at,expressed
R775	T2931	T2928	pobj	development,During
R776	T3077	T3078	det	the,phase
R777	T3078	T3076	pobj	phase,at
R778	T3079	T3078	amod	late,phase
R779	T2932	T2929	punct	", ",are
R78	T542	T540	nsubj	we,performed
R780	T3080	T3078	prep	of,phase
R781	T3081	T3080	pobj	arthritis,of
R782	T3082	T3065	prep	in,expressed
R783	T2933	T2929	nsubj	genes,are
R784	T3083	T3084	compound	animal,models
R785	T2934	T2933	acl	involved,genes
R786	T2935	T2934	prep	in,involved
R787	T3084	T3082	pobj	models,in
R788	T2936	T2937	det	the,disease
R789	T3085	T3084	prep	of,models
R79	T543	T544	compound	genome,linkage
R790	T3086	T3085	pobj	RA,of
R791	T3087	T3088	punct	[,16
R792	T2937	T2935	pobj	disease,in
R793	T3088	T3065	parataxis	16,expressed
R794	T3089	T3088	nummod	15,16
R795	T2938	T2929	acomp	likely,are
R796	T3090	T3088	punct	",",16
R797	T2939	T2940	aux	to,regulated
R798	T3091	T3088	punct	],16
R799	T3092	T3041	punct	.,upregulated
R8	T465	T466	det	the,genes
R80	T544	T545	compound	linkage,analysis
R800	T3094	T3095	mark	Besides,detecting
R801	T2940	T2938	xcomp	regulated,likely
R802	T3095	T3096	advcl	detecting,used
R803	T2941	T2940	auxpass	be,regulated
R804	T3097	T3095	dobj	genes,detecting
R805	T3098	T3097	acl	involved,genes
R806	T3099	T3098	prep	in,involved
R807	T2942	T2940	advmod	differentially,regulated
R808	T3100	T3101	amod	complex,diseases
R809	T3101	T3099	pobj	diseases,in
R81	T545	T540	dobj	analysis,performed
R810	T3102	T3096	punct	", ",used
R811	T3103	T3096	nsubjpass	microarrays,used
R812	T2943	T2929	punct	.,are
R813	T3104	T3096	aux	could,used
R814	T3105	T3096	advmod	also,used
R815	T3106	T3096	auxpass	be,used
R816	T2945	T2946	advmod	Therefore,identified
R817	T3107	T3108	aux	to,detect
R818	T3108	T3096	advcl	detect,used
R819	T3109	T3110	det	the,polymorphisms
R82	T546	T540	prep	in,performed
R820	T3110	T3108	dobj	polymorphisms,detect
R821	T2947	T2946	punct	", ",identified
R822	T3111	T3110	amod	genetic,polymorphisms
R823	T3112	T3110	acl	regulating,polymorphisms
R824	T3113	T3114	compound	gene,expression
R825	T3114	T3112	dobj	expression,regulating
R826	T3115	T3116	mark	because,be
R827	T2948	T2949	compound	signature,genes
R828	T3116	T3108	advcl	be,detect
R829	T3117	T3118	amod	differential,expressions
R83	T547	T548	compound	F2,progeny
R830	T2949	T2946	nsubjpass	genes,identified
R831	T3118	T3116	nsubj	expressions,be
R832	T3119	T3118	prep	between,expressions
R833	T3120	T3121	nummod	two,strains
R834	T2950	T2949	prep	of,genes
R835	T3121	T3119	pobj	strains,between
R836	T3122	T3116	aux	might,be
R837	T3123	T3124	det	the,result
R838	T3124	T3116	attr	result,be
R839	T2951	T2952	det	the,diseases
R84	T548	T546	pobj	progeny,in
R840	T3125	T3124	prep	of,result
R841	T3126	T3127	det	a,polymorphism
R842	T3127	T3125	pobj	polymorphism,of
R843	T2952	T2950	pobj	diseases,of
R844	T3128	T3127	acl	located,polymorphism
R845	T3129	T3128	prep	in,located
R846	T3130	T3131	amod	regulatory,elements
R847	T2953	T2946	aux	could,identified
R848	T3131	T3129	pobj	elements,in
R849	T3132	T3096	punct	.,used
R85	T549	T548	prep	of,progeny
R850	T2954	T2946	auxpass	be,identified
R851	T3134	T3135	aux	To,identify
R852	T3135	T3136	advcl	identify,investigated
R853	T2955	T2946	prep	by,identified
R854	T3137	T3138	det	the,QTL
R855	T3138	T3135	dobj	QTL,identify
R856	T2956	T2955	pcomp	detecting,by
R857	T3139	T3140	amod	small,effect
R858	T3140	T3138	compound	effect,QTL
R859	T3141	T3140	punct	-,effect
R86	T550	T551	det	the,strains
R860	T3142	T3138	prep	of,QTL
R861	T2957	T2958	det	the,patterns
R862	T3143	T3142	pobj	CIA,of
R863	T3144	T3145	advmod	as,as
R864	T3145	T3138	cc	as,QTL
R865	T2958	T2956	dobj	patterns,detecting
R866	T3146	T3145	advmod	well,as
R867	T3147	T3148	det	the,genes
R868	T3148	T3138	conj	genes,QTL
R869	T2959	T2958	compound	expression,patterns
R87	T551	T549	pobj	strains,of
R870	T2960	T2958	prep	of,patterns
R871	T3149	T3148	amod	potential,genes
R872	T2961	T2962	det	the,tissues
R873	T3150	T3148	compound	candidate,genes
R874	T3151	T3148	prep	inside,genes
R875	T3152	T3151	pobj	them,inside
R876	T2962	T2960	pobj	tissues,of
R877	T3153	T3136	punct	", ",investigated
R878	T3154	T3136	nsubj	we,investigated
R879	T2963	T2964	npadvmod	disease,related
R88	T552	T553	npadvmod	CIA,susceptible
R880	T3155	T3156	npadvmod	CIA,susceptible
R881	T3156	T3158	amod	susceptible,strains
R882	T3157	T3156	advmod	genetically,susceptible
R883	T2964	T2962	amod	related,tissues
R884	T3158	T3136	dobj	strains,investigated
R885	T3159	T3156	cc	and,susceptible
R886	T3160	T3156	conj	resistant,susceptible
R887	T2965	T2964	punct	-,related
R888	T3161	T3136	prep	at,investigated
R889	T3162	T3163	preconj	both,genome
R89	T553	T551	amod	susceptible,strains
R890	T3163	T3165	nmod	genome,levels
R891	T3164	T3163	det	the,genome
R892	T3165	T3161	pobj	levels,at
R893	T3166	T3163	cc	and,genome
R894	T3167	T3163	conj	transcriptome,genome
R895	T2966	T2962	compound	cells,tissues
R896	T3168	T3136	punct	.,investigated
R897	T3170	T3171	prep	At,generated
R898	T2967	T2962	punct	/,tissues
R899	T3172	T3173	det	the,level
R9	T466	T464	dobj	genes,identify
R90	T554	T553	cc	and,susceptible
R900	T3173	T3170	pobj	level,At
R901	T2968	T2962	cc	and,tissues
R902	T3174	T3173	compound	genome,level
R903	T2969	T2970	poss	their,controls
R904	T3175	T3171	punct	", ",generated
R905	T3176	T3177	compound	F2,progeny
R906	T3177	T3171	nsubjpass	progeny,generated
R907	T3178	T3177	prep	of,progeny
R908	T2970	T2962	conj	controls,tissues
R909	T3179	T3180	det	the,strains
R91	T555	T553	conj	resistant,susceptible
R910	T3180	T3178	pobj	strains,of
R911	T3181	T3180	amod	CIA,strains
R912	T2971	T2970	amod	ideal,controls
R913	T3182	T3181	amod	susceptible,CIA
R914	T3183	T3184	punct	(,DBA
R915	T3184	T3182	parataxis	DBA,susceptible
R916	T2972	T2946	punct	.,identified
R917	T3185	T3184	punct	/,DBA
R918	T3186	T3184	nummod	1,DBA
R919	T3187	T3184	punct	),DBA
R92	T556	T557	aux	to,search
R920	T2974	T2975	prep	In,applied
R921	T3188	T3181	cc	and,CIA
R922	T3189	T3181	conj	resistant,CIA
R923	T2976	T2977	det	the,decade
R924	T2977	T2974	pobj	decade,In
R925	T3190	T3191	punct	(,N
R926	T3191	T3189	parataxis	N,resistant
R927	T3192	T3191	compound	FVB,N
R928	T3193	T3191	punct	/,N
R929	T3194	T3191	punct	),N
R93	T557	T540	advcl	search,performed
R930	T3195	T3171	auxpass	were,generated
R931	T3196	T3171	cc	and,generated
R932	T3197	T3198	det	a,analysis
R933	T3198	T3203	nsubjpass	analysis,performed
R934	T3199	T3200	npadvmod	genome,wide
R935	T3200	T3198	amod	wide,analysis
R936	T3201	T3200	punct	-,wide
R937	T3202	T3198	compound	linkage,analysis
R938	T3203	T3171	conj	performed,generated
R939	T3204	T3203	auxpass	was,performed
R94	T558	T557	prep	for,search
R940	T3205	T3206	aux	to,identify
R941	T3206	T3203	advcl	identify,performed
R942	T3207	T3208	amod	small,effect
R943	T3208	T3210	compound	effect,QTL
R944	T3209	T3208	punct	-,effect
R945	T3210	T3206	dobj	QTL,identify
R946	T3211	T3203	punct	.,performed
R947	T3213	T3214	prep	At,detected
R948	T3215	T3216	det	the,level
R949	T3216	T3213	pobj	level,At
R95	T559	T560	amod	small,effect
R950	T3217	T3216	compound	transcriptome,level
R951	T3218	T3214	punct	", ",detected
R952	T3219	T3214	nsubj	we,detected
R953	T3220	T3221	det	the,patterns
R954	T3221	T3214	dobj	patterns,detected
R955	T3222	T3223	compound	gene,expression
R956	T3223	T3221	compound	expression,patterns
R957	T3224	T3221	prep	of,patterns
R958	T3225	T3226	preconj	both,strains
R959	T3226	T3224	pobj	strains,of
R96	T560	T562	compound	effect,QTL
R960	T3227	T3226	det	the,strains
R961	T3228	T3226	nmod	DBA,strains
R962	T3229	T3228	punct	/,DBA
R963	T3230	T3228	nummod	1,DBA
R964	T3231	T3228	cc	and,DBA
R965	T3232	T3233	compound	FVB,N
R966	T3233	T3228	conj	N,DBA
R967	T3234	T3233	punct	/,N
R968	T3235	T3214	prep	at,detected
R969	T3236	T3237	nummod	four,phases
R97	T561	T560	punct	-,effect
R970	T3237	T3235	pobj	phases,at
R971	T3238	T3237	amod	different,phases
R972	T3239	T3237	prep	of,phases
R973	T3240	T3239	pobj	CIA,of
R974	T3241	T3214	punct	.,detected
R975	T3243	T3244	det	The,genes
R976	T3244	T3247	nsubjpass	genes,identified
R977	T3245	T3244	amod	potential,genes
R978	T3246	T3244	compound	candidate,genes
R979	T3247	T3249	ccomp	identified,located
R98	T562	T558	pobj	QTL,for
R980	T3248	T3247	auxpass	were,identified
R981	T3250	T3247	prep	based,identified
R982	T3251	T3250	prep	on,based
R983	T3252	T3253	nummod	three,criteria
R984	T3253	T3251	pobj	criteria,on
R985	T3254	T3249	punct	: ,located
R986	T3255	T3249	nsubjpass	they,located
R987	T3256	T3249	auxpass	are,located
R988	T3257	T3249	prep	within,located
R989	T3258	T3259	det	the,region
R99	T563	T540	punct	.,performed
R990	T3259	T3257	pobj	region,within
R991	T3260	T3259	amod	genomic,region
R992	T3261	T3259	acl	linked,region
R993	T3262	T3261	prep	to,linked
R994	T3263	T3262	pobj	CIA,to
R995	T3264	T3249	punct	;,located
R996	T3265	T3266	nsubjpass	they,expressed
R997	T3266	T3249	conj	expressed,located
R998	T3267	T3266	auxpass	are,expressed
R999	T3268	T3269	npadvmod	disease,specific

PMC:1860061 JSONTXT 8 Projects

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PMC:1860061 JSON TXT 8 Projects