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Id Subject Object Predicate Lexical cue
T5781 4134-4144 NN denotes expression
T5782 4152-4154 IN denotes of
T5783 4155-4158 DT denotes the
T5784 4163-4168 NNS denotes genes
T5785 4159-4162 CD denotes two
T5786 4169-4175 IN denotes across
T5787 4176-4179 DT denotes the
T5788 4180-4187 NNS denotes samples
T4075 193-204 NN denotes environment
T4076 174-181 NN denotes climate
T4077 182-192 VBN denotes controlled
T4078 181-182 HYPH denotes -
T4079 205-209 IN denotes with
T4080 210-212 CD denotes 12
T4044 23-30 NNS denotes Animals
T4045 30-32 , denotes ,
T4046 32-44 NN denotes immunisation
T4047 45-48 CC denotes and
T4048 49-59 NN denotes assessment
T4049 60-62 IN denotes of
T4050 63-72 NN denotes arthritis
T4051 72-288 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 73-77 CC denotes Both
T4053 78-81 NN denotes DBA
T4054 94-98 NNS denotes mice
T4055 81-82 HYPH denotes /
T4056 82-83 CD denotes 1
T4057 84-87 CC denotes and
T4058 88-91 NN denotes FVB
T4059 92-93 NN denotes N
T4060 91-92 HYPH denotes /
T4061 123-131 VBN denotes obtained
T4062 99-103 VBN denotes used
T4063 104-106 IN denotes in
T4064 107-111 DT denotes this
T4065 112-117 NN denotes study
T4066 118-122 VBD denotes were
T4067 132-136 IN denotes from
T4068 137-140 DT denotes the
T4069 149-159 NNP denotes Laboratory
T4070 141-148 NNP denotes Jackson
T4071 160-163 CC denotes and
T4072 164-168 VBN denotes kept
T4073 169-171 IN denotes in
T4074 172-173 DT denotes a
T4081 213-217 NN denotes hour
T4082 229-235 NNS denotes cycles
T4083 218-223 NN denotes light
T4084 224-228 NN denotes dark
T4085 223-224 HYPH denotes /
T4086 236-238 IN denotes in
T4087 239-242 DT denotes the
T4088 250-258 NN denotes facility
T4089 243-249 NN denotes animal
T4090 259-261 IN denotes at
T4091 262-265 DT denotes the
T4092 266-276 NNP denotes University
T4093 277-279 IN denotes of
T4094 280-287 NNP denotes Rostock
T4095 287-288 . denotes .
T4096 288-365 sentence denotes All animal experiments were pre-approved by the State Animal Care Committee.
T4097 289-292 DT denotes All
T4098 300-311 NNS denotes experiments
T4099 293-299 NN denotes animal
T4100 317-329 VBN denotes pre-approved
T4101 312-316 VBD denotes were
T4102 330-332 IN denotes by
T4103 333-336 DT denotes the
T4104 355-364 NNP denotes Committee
T4105 337-342 NNP denotes State
T4106 343-349 NNP denotes Animal
T4107 350-354 NNP denotes Care
T4108 364-365 . denotes .
T4109 365-479 sentence denotes CIA was induced in control and experimental animals according to established protocols described previously [10].
T4110 366-369 NN denotes CIA
T4111 374-381 VBN denotes induced
T4112 370-373 VBD denotes was
T4113 382-384 IN denotes in
T4114 385-392 NN denotes control
T4115 410-417 NNS denotes animals
T4116 393-396 CC denotes and
T4117 397-409 JJ denotes experimental
T4118 418-427 VBG denotes according
T4119 428-430 IN denotes to
T4120 431-442 VBN denotes established
T4121 443-452 NNS denotes protocols
T4122 453-462 VBN denotes described
T4123 463-473 RB denotes previously
T4124 474-475 -LRB- denotes [
T4125 475-477 CD denotes 10
T4126 477-478 -RRB- denotes ]
T4127 478-479 . denotes .
T4128 479-698 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 480-482 IN denotes In
T4130 540-549 VBN denotes immunised
T4131 483-488 NN denotes brief
T4132 488-490 , denotes ,
T4133 490-493 NN denotes DBA
T4134 494-496 NN denotes 1J
T4135 493-494 HYPH denotes /
T4136 527-534 NN denotes progeny
T4137 496-498 , denotes ,
T4138 498-501 NN denotes FVB
T4139 502-503 NN denotes N
T4140 501-502 HYPH denotes /
T4141 504-507 CC denotes and
T4142 508-509 -LRB- denotes (
T4143 513-515 NN denotes 1J
T4144 509-512 NN denotes DBA
T4145 512-513 HYPH denotes /
T4146 516-517 SYM denotes ×
T4147 518-521 NN denotes FVB
T4148 522-523 NN denotes N
T4149 521-522 HYPH denotes /
T4150 523-524 -RRB- denotes )
T4151 524-526 NN denotes F2
T4152 535-539 VBD denotes were
T4153 550-552 IN denotes at
T4154 553-554 CD denotes 8
T4155 558-560 CD denotes 12
T4156 555-557 IN denotes to
T4157 561-566 NNS denotes weeks
T4158 567-569 IN denotes at
T4159 570-573 DT denotes the
T4160 574-578 NN denotes base
T4161 579-581 IN denotes of
T4162 582-585 DT denotes the
T4163 586-590 NN denotes tail
T4164 591-595 IN denotes with
T4165 596-599 CD denotes 125
T4166 600-602 NN denotes μg
T4167 603-605 IN denotes of
T4168 606-612 JJ denotes bovine
T4169 613-621 NN denotes Collagen
T4170 622-624 CD denotes II
T4171 625-626 -LRB- denotes (
T4172 626-634 NNP denotes Chondrex
T4173 634-636 , denotes ,
T4174 636-643 NNP denotes Redmond
T4175 643-645 , denotes ,
T4176 645-647 NNP denotes WA
T4177 647-649 , denotes ,
T4178 649-652 NNP denotes USA
T4179 652-653 -RRB- denotes )
T4180 654-664 VBN denotes emulsified
T4181 665-667 IN denotes in
T4182 668-671 NN denotes CFA
T4183 672-673 -LRB- denotes (
T4184 673-678 NNP denotes DIFCO
T4185 678-680 , denotes ,
T4186 680-687 NNP denotes Detroit
T4187 687-689 , denotes ,
T4188 689-691 NNP denotes MI
T4189 691-693 , denotes ,
T4190 693-696 NNP denotes USA
T4191 696-697 -RRB- denotes )
T4192 697-698 . denotes .
T4193 698-834 sentence denotes The clinical scoring of arthritis commenced 18 days after immunisation, and animals were monitored three times weekly for signs of CIA.
T4194 699-702 DT denotes The
T4195 712-719 NN denotes scoring
T4196 703-711 JJ denotes clinical
T4197 733-742 VBD denotes commenced
T4198 720-722 IN denotes of
T4199 723-732 NN denotes arthritis
T4200 743-745 CD denotes 18
T4201 746-750 NNS denotes days
T4202 751-756 IN denotes after
T4203 757-769 NN denotes immunisation
T4204 769-771 , denotes ,
T4205 771-774 CC denotes and
T4206 775-782 NNS denotes animals
T4207 788-797 VBN denotes monitored
T4208 783-787 VBD denotes were
T4209 798-803 CD denotes three
T4210 804-809 NNS denotes times
T4211 810-816 RB denotes weekly
T4212 817-820 IN denotes for
T4213 821-826 NNS denotes signs
T4214 827-829 IN denotes of
T4215 830-833 NN denotes CIA
T4216 833-834 . denotes .
T4217 834-954 sentence denotes Arthritis development was monitored in all four limbs using a three-score system per limb as described previously [10].
T4218 835-844 NN denotes Arthritis
T4219 845-856 NN denotes development
T4220 861-870 VBN denotes monitored
T4221 857-860 VBD denotes was
T4222 871-873 IN denotes in
T4223 874-877 DT denotes all
T4224 883-888 NNS denotes limbs
T4225 878-882 CD denotes four
T4226 889-894 VBG denotes using
T4227 895-896 DT denotes a
T4228 909-915 NN denotes system
T4229 897-902 CD denotes three
T4230 903-908 NN denotes score
T4231 902-903 HYPH denotes -
T4232 916-919 IN denotes per
T4233 920-924 NN denotes limb
T4234 925-927 IN denotes as
T4235 928-937 VBN denotes described
T4236 938-948 RB denotes previously
T4237 949-950 -LRB- denotes [
T4238 950-952 CD denotes 10
T4239 952-953 -RRB- denotes ]
T4240 953-954 . denotes .
T4241 954-1039 sentence denotes Eight-week old FVB/N and DBA/1J mice were used for the detection of gene expression.
T4242 955-960 CD denotes Eight
T4243 961-965 NN denotes week
T4244 960-961 HYPH denotes -
T4245 966-969 JJ denotes old
T4246 987-991 NNS denotes mice
T4247 970-973 NN denotes FVB
T4248 974-975 NN denotes N
T4249 973-974 HYPH denotes /
T4250 976-979 CC denotes and
T4251 980-983 NN denotes DBA
T4252 984-986 NN denotes 1J
T4253 983-984 HYPH denotes /
T4254 997-1001 VBN denotes used
T4255 992-996 VBD denotes were
T4256 1002-1005 IN denotes for
T4257 1006-1009 DT denotes the
T4258 1010-1019 NN denotes detection
T4259 1020-1022 IN denotes of
T4260 1023-1027 NN denotes gene
T4261 1028-1038 NN denotes expression
T4262 1038-1039 . denotes .
T4263 1039-1242 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 1040-1044 PRP denotes They
T4265 1050-1057 VBN denotes divided
T4266 1045-1049 VBD denotes were
T4267 1058-1062 IN denotes into
T4268 1063-1067 CD denotes four
T4269 1081-1087 NNS denotes groups
T4270 1068-1080 JJ denotes experimental
T4271 1088-1097 VBG denotes according
T4272 1098-1100 IN denotes to
T4273 1101-1104 DT denotes the
T4274 1115-1121 NNS denotes phases
T4275 1105-1114 JJ denotes different
T4276 1122-1124 IN denotes of
T4277 1125-1128 NN denotes CIA
T4278 1128-1130 , denotes ,
T4279 1130-1136 RB denotes namely
T4280 1143-1150 NN denotes control
T4281 1137-1142 JJ denotes naive
T4282 1151-1152 -LRB- denotes (
T4283 1152-1154 NN denotes NC
T4284 1154-1155 -RRB- denotes )
T4285 1155-1157 , denotes ,
T4286 1157-1174 NN denotes post-immunisation
T4287 1175-1176 -LRB- denotes (
T4288 1176-1178 NN denotes PI
T4289 1178-1179 -RRB- denotes )
T4290 1179-1181 , denotes ,
T4291 1181-1186 NN denotes onset
T4292 1187-1189 IN denotes of
T4293 1190-1199 NN denotes arthritis
T4294 1200-1201 -LRB- denotes (
T4295 1201-1203 NN denotes OA
T4296 1203-1204 -RRB- denotes )
T4297 1205-1208 CC denotes and
T4298 1209-1216 JJ denotes chronic
T4299 1217-1226 NN denotes arthritis
T4300 1227-1228 -LRB- denotes (
T4301 1228-1230 NN denotes CA
T4302 1230-1231 -RRB- denotes )
T4303 1232-1233 -LRB- denotes (
T4304 1233-1238 NN denotes Table
T4305 1239-1240 CD denotes 1
T4306 1240-1241 -RRB- denotes )
T4307 1241-1242 . denotes .
T4308 1242-1328 sentence denotes The NC group contained non-immunised mice that were sacrificed at the age of 8 weeks.
T4309 1243-1246 DT denotes The
T4310 1250-1255 NN denotes group
T4311 1247-1249 NN denotes NC
T4312 1256-1265 VBD denotes contained
T4313 1266-1279 JJ denotes non-immunised
T4314 1280-1284 NNS denotes mice
T4315 1285-1289 WDT denotes that
T4316 1295-1305 VBN denotes sacrificed
T4317 1290-1294 VBD denotes were
T4318 1306-1308 IN denotes at
T4319 1309-1312 DT denotes the
T4320 1313-1316 NN denotes age
T4321 1317-1319 IN denotes of
T4322 1320-1321 CD denotes 8
T4323 1322-1327 NNS denotes weeks
T4324 1327-1328 . denotes .
T4325 1328-1399 sentence denotes The mice in the PI group were sacrificed on day 10 after immunisation.
T4326 1329-1332 DT denotes The
T4327 1333-1337 NNS denotes mice
T4328 1359-1369 VBN denotes sacrificed
T4329 1338-1340 IN denotes in
T4330 1341-1344 DT denotes the
T4331 1348-1353 NN denotes group
T4332 1345-1347 NN denotes PI
T4333 1354-1358 VBD denotes were
T4334 1370-1372 IN denotes on
T4335 1373-1376 NN denotes day
T4336 1377-1379 CD denotes 10
T4337 1380-1385 IN denotes after
T4338 1386-1398 NN denotes immunisation
T4339 1398-1399 . denotes .
T4340 1399-1470 sentence denotes The mice in the OA group were sacrificed on day 35 after immunisation.
T4341 1400-1403 DT denotes The
T4342 1404-1408 NNS denotes mice
T4343 1430-1440 VBN denotes sacrificed
T4344 1409-1411 IN denotes in
T4345 1412-1415 DT denotes the
T4346 1419-1424 NN denotes group
T4347 1416-1418 NN denotes OA
T4348 1425-1429 VBD denotes were
T4349 1441-1443 IN denotes on
T4350 1444-1447 NN denotes day
T4351 1448-1450 CD denotes 35
T4352 1451-1456 IN denotes after
T4353 1457-1469 NN denotes immunisation
T4354 1469-1470 . denotes .
T4355 1470-1634 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 1471-1476 CD denotes Three
T4357 1497-1501 NNS denotes mice
T4358 1477-1480 NN denotes FVB
T4359 1481-1482 NN denotes N
T4360 1480-1481 HYPH denotes /
T4361 1483-1496 JJ denotes non-arthritic
T4362 1594-1604 VBN denotes sacrificed
T4363 1502-1505 CC denotes and
T4364 1506-1511 CD denotes three
T4365 1518-1522 NNS denotes mice
T4366 1512-1515 NN denotes DBA
T4367 1515-1516 HYPH denotes /
T4368 1516-1517 CD denotes 1
T4369 1523-1527 WDT denotes that
T4370 1528-1534 VBD denotes showed
T4371 1535-1540 NNS denotes signs
T4372 1541-1543 IN denotes of
T4373 1544-1553 NN denotes arthritis
T4374 1554-1556 IN denotes on
T4375 1557-1560 NN denotes day
T4376 1561-1563 CD denotes 33
T4377 1564-1566 CC denotes or
T4378 1567-1569 CD denotes 34
T4379 1570-1575 IN denotes after
T4380 1576-1588 NN denotes immunisation
T4381 1589-1593 VBD denotes were
T4382 1605-1607 IN denotes on
T4383 1608-1611 NN denotes day
T4384 1612-1614 CD denotes 35
T4385 1615-1620 IN denotes after
T4386 1621-1633 NN denotes immunisation
T4387 1633-1634 . denotes .
T4388 1634-1705 sentence denotes The mice in the CA group were sacrificed on day 95 after immunisation.
T4389 1635-1638 DT denotes The
T4390 1639-1643 NNS denotes mice
T4391 1665-1675 VBN denotes sacrificed
T4392 1644-1646 IN denotes in
T4393 1647-1650 DT denotes the
T4394 1654-1659 NN denotes group
T4395 1651-1653 NN denotes CA
T4396 1660-1664 VBD denotes were
T4397 1676-1678 IN denotes on
T4398 1679-1682 NN denotes day
T4399 1683-1685 CD denotes 95
T4400 1686-1691 IN denotes after
T4401 1692-1704 NN denotes immunisation
T4402 1704-1705 . denotes .
T4403 1705-1856 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 1706-1711 CD denotes Three
T4405 1732-1736 NNS denotes mice
T4406 1712-1725 JJ denotes non-arthritic
T4407 1726-1729 NN denotes FVB
T4408 1730-1731 NN denotes N
T4409 1729-1730 HYPH denotes /
T4410 1816-1826 VBN denotes sacrificed
T4411 1737-1740 CC denotes and
T4412 1741-1746 CD denotes three
T4413 1753-1757 NNS denotes mice
T4414 1747-1750 NN denotes DBA
T4415 1750-1751 HYPH denotes /
T4416 1751-1752 CD denotes 1
T4417 1758-1762 WDT denotes that
T4418 1767-1776 VBN denotes developed
T4419 1763-1766 VBD denotes had
T4420 1777-1786 NN denotes arthritis
T4421 1787-1790 IN denotes for
T4422 1791-1793 RB denotes at
T4423 1800-1803 CD denotes two
T4424 1794-1799 RBS denotes least
T4425 1804-1810 NNS denotes months
T4426 1811-1815 VBD denotes were
T4427 1827-1829 IN denotes on
T4428 1830-1833 NN denotes day
T4429 1834-1836 CD denotes 95
T4430 1837-1842 IN denotes after
T4431 1843-1855 NN denotes immunisation
T4432 1855-1856 . denotes .
T4689 2203-2205 CD denotes 23
T4628 1858-1865 NN denotes Linkage
T4629 1866-1874 NN denotes analysis
T4630 1874-1966 sentence denotes Detailed information on genotyping of the genome screen has been described previously [10].
T4631 1875-1883 JJ denotes Detailed
T4632 1884-1895 NN denotes information
T4633 1940-1949 VBN denotes described
T4634 1896-1898 IN denotes on
T4635 1899-1909 NN denotes genotyping
T4636 1910-1912 IN denotes of
T4637 1913-1916 DT denotes the
T4638 1924-1930 NN denotes screen
T4639 1917-1923 NN denotes genome
T4640 1931-1934 VBZ denotes has
T4641 1935-1939 VBN denotes been
T4642 1950-1960 RB denotes previously
T4643 1961-1962 -LRB- denotes [
T4644 1962-1964 CD denotes 10
T4645 1964-1965 -RRB- denotes ]
T4646 1965-1966 . denotes .
T4647 1966-2135 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 1967-1969 IN denotes In
T4649 1980-1989 VBD denotes genotyped
T4650 1970-1975 JJ denotes short
T4651 1975-1977 , denotes ,
T4652 1977-1979 PRP denotes we
T4653 1990-1993 CD denotes 290
T4654 1997-2001 NNS denotes mice
T4655 1994-1996 NN denotes F2
T4656 2002-2007 VBG denotes using
T4657 2008-2011 CD denotes 126
T4658 2039-2046 NNS denotes markers
T4659 2012-2023 JJ denotes informative
T4660 2024-2038 NN denotes microsatellite
T4661 2047-2055 VBG denotes covering
T4662 2056-2059 DT denotes the
T4663 2060-2066 NN denotes genome
T4664 2067-2071 IN denotes with
T4665 2072-2074 DT denotes an
T4666 2096-2104 NN denotes distance
T4667 2075-2082 JJ denotes average
T4668 2083-2095 JJ denotes inter-marker
T4669 2105-2107 IN denotes of
T4670 2108-2112 CD denotes 11.5
T4671 2113-2115 NN denotes cM
T4672 2116-2119 IN denotes for
T4673 2120-2123 CD denotes 290
T4674 2127-2134 NN denotes progeny
T4675 2124-2126 NN denotes F2
T4676 2134-2135 . denotes .
T4677 2135-2207 sentence denotes All linkage analyses were performed with QTX Map manager software [23].
T4678 2136-2139 DT denotes All
T4679 2148-2156 NNS denotes analyses
T4680 2140-2147 NN denotes linkage
T4681 2162-2171 VBN denotes performed
T4682 2157-2161 VBD denotes were
T4683 2172-2176 IN denotes with
T4684 2177-2180 NN denotes QTX
T4685 2193-2201 NN denotes software
T4686 2181-2184 NN denotes Map
T4687 2185-2192 NN denotes manager
T4688 2202-2203 -LRB- denotes [
T4690 2205-2206 -RRB- denotes ]
T4691 2206-2207 . denotes .
T4692 2207-2287 sentence denotes The main clinical phenotype of CIA, arthritis severity, was taken as phenotype.
T4693 2208-2211 DT denotes The
T4694 2226-2235 NN denotes phenotype
T4695 2212-2216 JJ denotes main
T4696 2217-2225 JJ denotes clinical
T4697 2268-2273 VBN denotes taken
T4698 2236-2238 IN denotes of
T4699 2239-2242 NN denotes CIA
T4700 2242-2244 , denotes ,
T4701 2244-2253 NN denotes arthritis
T4702 2254-2262 NN denotes severity
T4703 2262-2264 , denotes ,
T4704 2264-2267 VBD denotes was
T4705 2274-2276 IN denotes as
T4706 2277-2286 NN denotes phenotype
T4707 2286-2287 . denotes .
T4708 2287-2389 sentence denotes To detect the small-effect QTL, the threshold value of linkage was set as P = 0.05 (Chi-square test).
T4709 2288-2290 TO denotes To
T4710 2291-2297 VB denotes detect
T4711 2355-2358 VBN denotes set
T4712 2298-2301 DT denotes the
T4713 2315-2318 NN denotes QTL
T4714 2302-2307 JJ denotes small
T4715 2308-2314 NN denotes effect
T4716 2307-2308 HYPH denotes -
T4717 2318-2320 , denotes ,
T4718 2320-2323 DT denotes the
T4719 2334-2339 NN denotes value
T4720 2324-2333 NN denotes threshold
T4721 2340-2342 IN denotes of
T4722 2343-2350 NN denotes linkage
T4723 2351-2354 VBD denotes was
T4724 2359-2361 IN denotes as
T4725 2362-2363 NN denotes P
T4726 2366-2370 CD denotes 0.05
T4727 2364-2365 SYM denotes =
T4728 2371-2372 -LRB- denotes (
T4729 2383-2387 NN denotes test
T4730 2372-2375 NN denotes Chi
T4731 2376-2382 NN denotes square
T4732 2375-2376 HYPH denotes -
T4733 2387-2388 -RRB- denotes )
T4734 2388-2389 . denotes .
T5000 2391-2397 NN denotes Sample
T5001 2398-2409 NN denotes preparation
T5002 2410-2413 CC denotes and
T5003 2414-2424 NN denotes microarray
T5004 2425-2438 NN denotes hybridisation
T5005 2438-2524 sentence denotes Lymph nodes (LNs) draining the immunisation site were used for total RNA preparation.
T5006 2439-2444 NN denotes Lymph
T5007 2445-2450 NNS denotes nodes
T5008 2493-2497 VBN denotes used
T5009 2451-2452 -LRB- denotes (
T5010 2452-2455 NNS denotes LNs
T5011 2455-2456 -RRB- denotes )
T5012 2457-2465 VBG denotes draining
T5013 2466-2469 DT denotes the
T5014 2483-2487 NN denotes site
T5015 2470-2482 NN denotes immunisation
T5016 2488-2492 VBD denotes were
T5017 2498-2501 IN denotes for
T5018 2502-2507 JJ denotes total
T5019 2512-2523 NN denotes preparation
T5020 2508-2511 NN denotes RNA
T5021 2523-2524 . denotes .
T5022 2524-2670 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 2525-2528 DT denotes The
T5024 2535-2538 NN denotes RNA
T5025 2529-2534 JJ denotes total
T5026 2543-2552 VBN denotes extracted
T5027 2539-2542 VBD denotes was
T5028 2553-2557 IN denotes from
T5029 2558-2561 DT denotes the
T5030 2569-2580 NNS denotes homogenates
T5031 2562-2568 NN denotes tissue
T5032 2581-2586 VBG denotes using
T5033 2587-2588 DT denotes a
T5034 2600-2603 NN denotes kit
T5035 2589-2599 JJ denotes commercial
T5036 2604-2606 IN denotes in
T5037 2607-2617 NN denotes accordance
T5038 2618-2622 IN denotes with
T5039 2623-2626 DT denotes the
T5040 2636-2644 NN denotes protocol
T5041 2627-2635 VBN denotes provided
T5042 2645-2646 -LRB- denotes (
T5043 2646-2651 NNP denotes QIGEN
T5044 2651-2653 , denotes ,
T5045 2653-2659 NNP denotes Hilden
T5046 2659-2661 , denotes ,
T5047 2661-2668 NNP denotes Germany
T5048 2668-2669 -RRB- denotes )
T5049 2669-2670 . denotes .
T5050 2670-2805 sentence denotes Analysis of gene expression was conducted using a U430A array (Affymetrix, Santa Clara, CA, USA) interrogating more than 22,000 genes.
T5051 2671-2679 NN denotes Analysis
T5052 2703-2712 VBN denotes conducted
T5053 2680-2682 IN denotes of
T5054 2683-2687 NN denotes gene
T5055 2688-2698 NN denotes expression
T5056 2699-2702 VBD denotes was
T5057 2713-2718 VBG denotes using
T5058 2719-2720 DT denotes a
T5059 2727-2732 NN denotes array
T5060 2721-2726 NN denotes U430A
T5061 2733-2734 -LRB- denotes (
T5062 2734-2744 NNP denotes Affymetrix
T5063 2744-2746 , denotes ,
T5064 2746-2751 NNP denotes Santa
T5065 2752-2757 NNP denotes Clara
T5066 2757-2759 , denotes ,
T5067 2759-2761 NNP denotes CA
T5068 2761-2763 , denotes ,
T5069 2763-2766 NNP denotes USA
T5070 2766-2767 -RRB- denotes )
T5071 2768-2781 VBG denotes interrogating
T5072 2782-2786 JJR denotes more
T5073 2792-2798 CD denotes 22,000
T5074 2787-2791 IN denotes than
T5075 2799-2804 NNS denotes genes
T5076 2804-2805 . denotes .
T5077 2805-2882 sentence denotes RNA probes were labelled in accordance with the manufacturer's instructions.
T5078 2806-2809 NN denotes RNA
T5079 2810-2816 NNS denotes probes
T5080 2822-2830 VBN denotes labelled
T5081 2817-2821 VBD denotes were
T5082 2831-2833 IN denotes in
T5083 2834-2844 NN denotes accordance
T5084 2845-2849 IN denotes with
T5085 2850-2853 DT denotes the
T5086 2854-2866 NN denotes manufacturer
T5087 2869-2881 NNS denotes instructions
T5088 2866-2868 POS denotes 's
T5089 2881-2882 . denotes .
T5090 2882-2951 sentence denotes Samples from individual mice were hybridised onto individual arrays.
T5091 2883-2890 NNS denotes Samples
T5092 2917-2927 VBN denotes hybridised
T5093 2891-2895 IN denotes from
T5094 2896-2906 JJ denotes individual
T5095 2907-2911 NNS denotes mice
T5096 2912-2916 VBD denotes were
T5097 2928-2932 IN denotes onto
T5098 2933-2943 JJ denotes individual
T5099 2944-2950 NNS denotes arrays
T5100 2950-2951 . denotes .
T5101 2951-3031 sentence denotes Hybridisation and washing of gene chips were done as previously described [16].
T5102 2952-2965 NN denotes Hybridisation
T5103 2997-3001 VBN denotes done
T5104 2966-2969 CC denotes and
T5105 2970-2977 NN denotes washing
T5106 2978-2980 IN denotes of
T5107 2981-2985 NN denotes gene
T5108 2986-2991 NNS denotes chips
T5109 2992-2996 VBD denotes were
T5110 3002-3004 IN denotes as
T5111 3016-3025 VBN denotes described
T5112 3005-3015 RB denotes previously
T5113 3026-3027 -LRB- denotes [
T5114 3027-3029 CD denotes 16
T5115 3029-3030 -RRB- denotes ]
T5116 3030-3031 . denotes .
T5117 3031-3112 sentence denotes Fluorescent signals were collected by laser scan (Hewlett-Packard Gene Scanner).
T5118 3032-3043 JJ denotes Fluorescent
T5119 3044-3051 NNS denotes signals
T5120 3057-3066 VBN denotes collected
T5121 3052-3056 VBD denotes were
T5122 3067-3069 IN denotes by
T5123 3070-3075 NN denotes laser
T5124 3076-3080 NN denotes scan
T5125 3081-3082 -LRB- denotes (
T5126 3103-3110 NNP denotes Scanner
T5127 3082-3089 NNP denotes Hewlett
T5128 3090-3097 NNP denotes Packard
T5129 3089-3090 HYPH denotes -
T5130 3098-3102 NNP denotes Gene
T5131 3110-3111 -RRB- denotes )
T5132 3111-3112 . denotes .
T5603 3114-3124 NN denotes Microarray
T5604 3125-3133 NN denotes analysis
T5605 3133-3293 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 3134-3147 NN denotes Normalisation
T5607 3176-3180 VBN denotes done
T5608 3148-3150 IN denotes of
T5609 3151-3154 DT denotes the
T5610 3166-3171 NN denotes level
T5611 3155-3165 NN denotes expression
T5612 3172-3175 VBD denotes was
T5613 3181-3186 VBG denotes using
T5614 3187-3197 NNP denotes Affymetrix
T5615 3207-3210 NN denotes MAS
T5616 3198-3206 NN denotes software
T5617 3211-3212 CD denotes 5
T5618 3212-3214 , denotes ,
T5619 3214-3219 WDT denotes which
T5620 3223-3228 VBN denotes based
T5621 3220-3222 VBZ denotes is
T5622 3229-3231 IN denotes on
T5623 3232-3238 JJ denotes global
T5624 3239-3246 NN denotes scaling
T5625 3247-3249 IN denotes of
T5626 3250-3255 JJ denotes total
T5627 3272-3277 NN denotes level
T5628 3256-3260 NN denotes gene
T5629 3261-3271 NN denotes expression
T5630 3278-3281 IN denotes per
T5631 3282-3292 NN denotes microarray
T5632 3292-3293 . denotes .
T5633 3293-3371 sentence denotes The normalised expression values were imported to and analysed by dCHIP [24].
T5634 3294-3297 DT denotes The
T5635 3320-3326 NNS denotes values
T5636 3298-3308 JJ denotes normalised
T5637 3309-3319 NN denotes expression
T5638 3332-3340 VBN denotes imported
T5639 3327-3331 VBD denotes were
T5640 3341-3343 IN denotes to
T5641 3344-3347 CC denotes and
T5642 3348-3356 VBN denotes analysed
T5643 3357-3359 IN denotes by
T5644 3360-3365 NN denotes dCHIP
T5645 3366-3367 -LRB- denotes [
T5646 3367-3369 CD denotes 24
T5647 3369-3370 -RRB- denotes ]
T5648 3370-3371 . denotes .
T5649 3371-3694 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 3372-3386 RB denotes Differentially
T5651 3387-3396 VBN denotes expressed
T5652 3397-3402 NNS denotes genes
T5653 3408-3418 VBN denotes identified
T5654 3403-3407 VBD denotes were
T5655 3419-3421 IN denotes by
T5656 3422-3430 VBG denotes defining
T5657 3431-3434 DT denotes the
T5658 3457-3465 NNS denotes criteria
T5659 3435-3446 JJ denotes appropriate
T5660 3447-3456 NN denotes filtering
T5661 3466-3468 IN denotes in
T5662 3469-3472 DT denotes the
T5663 3479-3487 NN denotes software
T5664 3473-3478 NN denotes dCHIP
T5665 3488-3490 IN denotes as
T5666 3490-3492 : denotes :
T5667 3492-3497 JJ denotes lower
T5668 3500-3501 NN denotes %
T5669 3498-3500 CD denotes 90
T5670 3513-3521 NN denotes boundary
T5671 3502-3512 NN denotes confidence
T5672 3561-3569 VBN denotes exceeded
T5673 3522-3524 IN denotes of
T5674 3525-3529 NN denotes fold
T5675 3530-3536 NN denotes change
T5676 3537-3544 IN denotes between
T5677 3545-3548 DT denotes the
T5678 3555-3560 NNS denotes means
T5679 3549-3554 NN denotes group
T5680 3685-3688 VBD denotes was
T5681 3570-3577 RB denotes twofold
T5682 3577-3578 : denotes ;
T5683 3579-3582 DT denotes the
T5684 3592-3602 NN denotes difference
T5685 3583-3591 JJ denotes absolute
T5686 3626-3634 VBD denotes exceeded
T5687 3603-3610 IN denotes between
T5688 3611-3614 DT denotes the
T5689 3619-3625 NNS denotes groups
T5690 3615-3618 CD denotes two
T5691 3635-3638 CD denotes 100
T5692 3638-3639 : denotes ;
T5693 3640-3643 DT denotes the
T5694 3652-3661 NN denotes threshold
T5695 3644-3645 NN denotes P
T5696 3646-3651 NN denotes value
T5697 3662-3664 IN denotes of
T5698 3665-3668 DT denotes the
T5699 3680-3684 NN denotes test
T5700 3669-3677 JJ denotes unpaired
T5701 3678-3679 NN denotes t
T5702 3679-3680 HYPH denotes -
T5703 3689-3693 CD denotes 0.05
T5704 3693-3694 . denotes .
T5705 3694-3840 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 3695-3698 DT denotes The
T5707 3715-3719 NN denotes rate
T5708 3699-3704 JJ denotes false
T5709 3705-3714 NN denotes discovery
T5710 3724-3735 VBN denotes established
T5711 3720-3723 VBD denotes was
T5712 3736-3740 IN denotes with
T5713 3741-3742 DT denotes a
T5714 3755-3759 NN denotes test
T5715 3743-3754 NN denotes permutation
T5716 3760-3763 IN denotes for
T5717 3764-3768 DT denotes each
T5718 3778-3788 NN denotes comparison
T5719 3769-3777 JJ denotes pairwise
T5720 3789-3791 TO denotes to
T5721 3792-3800 VB denotes estimate
T5722 3801-3804 DT denotes the
T5723 3805-3815 NN denotes proportion
T5724 3816-3818 IN denotes of
T5725 3819-3824 JJ denotes false
T5726 3825-3833 JJ denotes positive
T5727 3824-3825 HYPH denotes -
T5728 3834-3839 NNS denotes genes
T5729 3839-3840 . denotes .
T5730 3840-3951 sentence denotes Hierarchical gene clustering was performed with dCHIP to characterise the gene expression patterns during CIA.
T5731 3841-3853 JJ denotes Hierarchical
T5732 3859-3869 NN denotes clustering
T5733 3854-3858 NN denotes gene
T5734 3874-3883 VBN denotes performed
T5735 3870-3873 VBD denotes was
T5736 3884-3888 IN denotes with
T5737 3889-3894 NN denotes dCHIP
T5738 3895-3897 TO denotes to
T5739 3898-3910 VB denotes characterise
T5740 3911-3914 DT denotes the
T5741 3931-3939 NNS denotes patterns
T5742 3915-3919 NN denotes gene
T5743 3920-3930 NN denotes expression
T5744 3940-3946 IN denotes during
T5745 3947-3950 NN denotes CIA
T5746 3950-3951 . denotes .
T5747 3951-4193 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 3952-3955 DT denotes The
T5749 3975-3984 NN denotes algorithm
T5750 3956-3963 NN denotes default
T5751 3964-3974 NN denotes clustering
T5752 3994-3997 VBD denotes was
T5753 3985-3987 IN denotes of
T5754 3988-3993 NNS denotes genes
T5755 4044-4051 VBN denotes defined
T5756 3998-4000 IN denotes as
T5757 4001-4008 VBZ denotes follows
T5758 4008-4010 : denotes :
T5759 4010-4013 DT denotes the
T5760 4014-4022 NN denotes distance
T5761 4023-4030 IN denotes between
T5762 4031-4034 CD denotes two
T5763 4035-4040 NNS denotes genes
T5764 4041-4043 VBZ denotes is
T5765 4052-4054 IN denotes as
T5766 4055-4056 CD denotes 1
T5767 4059-4060 NN denotes r
T5768 4057-4058 HYPH denotes –
T5769 4060-4062 , denotes ,
T5770 4062-4067 WRB denotes where
T5771 4070-4072 VBZ denotes is
T5772 4068-4069 NN denotes r
T5773 4073-4076 DT denotes the
T5774 4097-4108 NN denotes coefficient
T5775 4077-4084 NNP denotes Pearson
T5776 4085-4096 NN denotes correlation
T5777 4109-4116 IN denotes between
T5778 4117-4120 DT denotes the
T5779 4145-4151 NNS denotes values
T5780 4121-4133 VBN denotes standardised
T5789 4188-4192 VBN denotes used
T5790 4192-4193 . denotes .
T5791 4193-4365 sentence denotes To characterise the functional relationship between differentially expressed genes, Gene Ontology (GO) term classification incorporated in DNA-Chip Analyzer was performed.
T5792 4194-4196 TO denotes To
T5793 4197-4209 VB denotes characterise
T5794 4355-4364 VBN denotes performed
T5795 4210-4213 DT denotes the
T5796 4225-4237 NN denotes relationship
T5797 4214-4224 JJ denotes functional
T5798 4238-4245 IN denotes between
T5799 4246-4260 RB denotes differentially
T5800 4271-4276 NNS denotes genes
T5801 4261-4270 VBN denotes expressed
T5802 4276-4278 , denotes ,
T5803 4278-4282 NN denotes Gene
T5804 4283-4291 NN denotes Ontology
T5805 4302-4316 NN denotes classification
T5806 4292-4293 -LRB- denotes (
T5807 4293-4295 NN denotes GO
T5808 4295-4296 -RRB- denotes )
T5809 4297-4301 NN denotes term
T5810 4317-4329 VBN denotes incorporated
T5811 4330-4332 IN denotes in
T5812 4333-4336 NNP denotes DNA
T5813 4337-4341 NNP denotes Chip
T5814 4336-4337 HYPH denotes -
T5815 4342-4350 NNP denotes Analyzer
T5816 4351-4354 VBD denotes was
T5817 4364-4365 . denotes .
T5818 4365-4483 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 4366-4369 DT denotes The
T5820 4382-4387 NN denotes level
T5821 4370-4381 JJ denotes significant
T5822 4415-4418 VBN denotes set
T5823 4388-4391 IN denotes for
T5824 4392-4393 DT denotes a
T5825 4403-4410 NN denotes cluster
T5826 4394-4402 NN denotes function
T5827 4411-4414 VBD denotes was
T5828 4419-4421 IN denotes at
T5829 4422-4423 NN denotes P
T5830 4424-4425 SYM denotes <
T5831 4426-4431 CD denotes 0.005
T5832 4431-4433 , denotes ,
T5833 4433-4436 CC denotes and
T5834 4437-4440 DT denotes the
T5835 4449-4453 NN denotes size
T5836 4441-4448 JJ denotes minimum
T5837 4467-4470 VBD denotes was
T5838 4454-4456 IN denotes of
T5839 4457-4458 DT denotes a
T5840 4459-4466 NN denotes cluster
T5841 4471-4476 CD denotes three
T5842 4477-4482 NNS denotes genes
T5843 4482-4483 . denotes .
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
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
R1037 T4062 T4054 acl used,mice
R1038 T4063 T4062 prep in,used
R1039 T4064 T4065 det this,study
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
R1050 T4075 T4073 pobj environment,in
R1051 T4076 T4077 npadvmod climate,controlled
R1052 T4077 T4075 amod controlled,environment
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
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
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
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
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
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
R1110 T4141 T4139 cc and,N
R1111 T4142 T4143 punct (,1J
R1112 T4143 T4139 conj 1J,N
R1115 T4146 T4143 punct ×,1J
R1116 T4147 T4148 compound FVB,N
R1117 T4148 T4143 appos N,1J
R1119 T4150 T4143 punct ),1J
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
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
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
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
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
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
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
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
R1197 T4232 T4228 prep per,system
R1198 T4233 T4232 pobj limb,per
R1199 T4234 T4235 mark as,described
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
R1210 T4246 T4254 nsubjpass mice,used
R1211 T4247 T4248 nmod FVB,N
R1212 T4248 T4246 nmod N,mice
R1214 T4250 T4248 cc and,N
R1215 T4251 T4252 compound DBA,1J
R1216 T4252 T4248 conj 1J,N
R1218 T4255 T4254 auxpass were,used
R1219 T4256 T4254 prep for,used
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
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
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
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
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
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
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
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
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
R1310 T4356 T4357 nummod Three,mice
R1311 T4357 T4362 nsubjpass mice,sacrificed
R1312 T4358 T4359 nmod FVB,N
R1313 T4359 T4357 nmod N,mice
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
R1476 T4733 T4729 punct ),test
R1477 T4734 T4711 punct .,set
R1478 T5000 T5001 compound Sample,preparation
R1479 T5002 T5001 cc and,preparation
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
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
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
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
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
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
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
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
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
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
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
R1590 T5127 T5128 compound Hewlett,Packard
R1591 T5128 T5126 compound Packard,Scanner
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
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
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
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
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
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
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
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
R1666 T5680 T5665 pcomp was,as
R1667 T5681 T5672 advmod twofold,exceeded
R1668 T5682 T5680 punct ;,was
R1669 T5683 T5684 det the,difference
R1670 T5684 T5686 nsubj difference,exceeded
R1672 T5686 T5680 ccomp exceeded,was
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
R1680 T5694 T5680 nsubj threshold,was
R1683 T5697 T5694 prep of,threshold
R1684 T5698 T5699 det the,test
R1685 T5699 T5697 pobj test,of
R1689 T5703 T5680 attr 0.05,was
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
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
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
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
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
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
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
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
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
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
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
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
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
R1459 T4716 T4715 punct -,effect
R1475 T4732 T4731 punct -,square
R1592 T5129 T5128 punct -,Packard
R1665 T5679 T5678 compound group,means
R1671 T5685 T5684 amod absolute,difference
R1673 T5687 T5684 prep between,difference
R1674 T5688 T5689 det the,groups
R1681 T5695 T5696 compound P,value
R1682 T5696 T5694 compound value,threshold
R1686 T5700 T5699 amod unpaired,test
R1687 T5701 T5699 compound t,test
R1688 T5702 T5699 punct -,test
R1036 T4060 T4059 punct /,N
R1053 T4078 T4077 punct -,controlled
R1060 T4085 T4084 punct /,dark
R1109 T4140 T4139 punct /,N
R1113 T4144 T4143 compound DBA,1J
R1114 T4145 T4143 punct /,1J
R1118 T4149 T4148 punct /,N
R1196 T4231 T4230 punct -,score
R1213 T4249 T4248 punct /,N
R1217 T4253 T4252 punct /,1J
R1314 T4360 T4359 punct /,N
R1359 T4409 T4408 punct /,N

craft-ca-core-ex-dev

Below, discontinuous spans are shown in the chain model. You can change it to the bag model.

Id Subject Object Predicate Lexical cue
T4014 23-30 NCBITaxon:33208 denotes Animals
T4015 94-98 NCBITaxon:10088 denotes mice
T4016 243-249 NCBITaxon:33208 denotes animal
T4017 293-299 NCBITaxon:33208 denotes animal
T4018 343-349 NCBITaxon:33208 denotes Animal
T4019 410-417 NCBITaxon:33208 denotes animals
T4020 586-590 UBERON:0002415 denotes tail
T4021 606-612 NCBITaxon:27592 denotes bovine
T4022 613-621 CHEBI_PR_EXT:collagen denotes Collagen
T4023 613-624 PR_EXT:000003266 denotes Collagen II
T4024 775-782 NCBITaxon:33208 denotes animals
T4025 883-888 UBERON:0002101 denotes limbs
T4026 920-924 UBERON:0002101 denotes limb
T4027 987-991 NCBITaxon:10088 denotes mice
T4028 1023-1027 SO_EXT:0000704 denotes gene
T4029 1023-1038 GO:0010467 denotes gene expression
T4030 1280-1284 NCBITaxon:10088 denotes mice
T4031 1295-1305 GO_EXT:killing denotes sacrificed
T4032 1333-1337 NCBITaxon:10088 denotes mice
T4033 1359-1369 GO_EXT:killing denotes sacrificed
T4034 1404-1408 NCBITaxon:10088 denotes mice
T4035 1430-1440 GO_EXT:killing denotes sacrificed
T4036 1497-1501 NCBITaxon:10088 denotes mice
T4037 1518-1522 NCBITaxon:10088 denotes mice
T4038 1594-1604 GO_EXT:killing denotes sacrificed
T4039 1639-1643 NCBITaxon:10088 denotes mice
T4040 1665-1675 GO_EXT:killing denotes sacrificed
T4041 1732-1736 NCBITaxon:10088 denotes mice
T4042 1753-1757 NCBITaxon:10088 denotes mice
T4043 1816-1826 GO_EXT:killing denotes sacrificed
T4621 1917-1923 SO_EXT:0001026 denotes genome
T4622 1997-2001 NCBITaxon:10088 denotes mice
T4623 2024-2038 SO_EXT:microsatellite_unit_or_region denotes microsatellite
T4624 2039-2046 CHEBI_SO_EXT:molecular_indicator_or_label_or_marker_or_tag denotes markers
T4625 2060-2066 SO_EXT:0001026 denotes genome
T4626 2089-2095 CHEBI_SO_EXT:molecular_indicator_or_label_or_marker_or_tag denotes marker
T4627 2315-2318 SO_EXT:0000771 denotes QTL
T4986 2452-2455 UBERON:0000029 denotes LNs
T4987 2508-2511 CHEBI_SO_EXT:RNA denotes RNA
T4984 2425-2438 GO:0097617 denotes hybridisation
T4985 2439-2450 UBERON:0000029 denotes Lymph nodes
T4988 2535-2538 CHEBI_SO_EXT:RNA denotes RNA
T4989 2562-2568 UBERON:0000479 denotes tissue
T4990 2683-2687 SO_EXT:0000704 denotes gene
T4991 2683-2698 GO:0010467 denotes gene expression
T4992 2799-2804 SO_EXT:0000704 denotes genes
T4993 2806-2816 CHEBI_SO_EXT:riboprobe denotes RNA probes
T4994 2822-2830 CHEBI_SO_EXT:molecular_label_or_mark_or_tag_process denotes labelled
T4995 2907-2911 NCBITaxon:10088 denotes mice
T4996 2917-2927 GO:0097617 denotes hybridised
T4997 2952-2965 GO:0097617 denotes Hybridisation
T4998 2981-2985 SO_EXT:0000704 denotes gene
T4999 3098-3102 SO_EXT:0000704 denotes Gene
T5584 3155-3165 GO:0010467 denotes expression
T5585 3256-3260 SO_EXT:0000704 denotes gene
T5586 3256-3271 GO:0010467 denotes gene expression
T5587 3309-3319 GO:0010467 denotes expression
T5588 3387-3396 GO:0010467 denotes expressed
T5589 3397-3402 SO_EXT:0000704 denotes genes
T5590 3834-3839 SO_EXT:0000704 denotes genes
T5591 3854-3858 SO_EXT:0000704 denotes gene
T5592 3915-3919 SO_EXT:0000704 denotes gene
T5593 3915-3930 GO:0010467 denotes gene expression
T5594 3988-3993 SO_EXT:0000704 denotes genes
T5595 4035-4040 SO_EXT:0000704 denotes genes
T5596 4134-4144 GO:0010467 denotes expression
T5597 4163-4168 SO_EXT:0000704 denotes genes
T5598 4261-4270 GO:0010467 denotes expressed
T5599 4271-4276 SO_EXT:0000704 denotes genes
T5600 4278-4282 SO_EXT:0000704 denotes Gene
T5601 4333-4336 CHEBI_SO_EXT:DNA denotes DNA
T5602 4477-4482 SO_EXT:0000704 denotes genes

2_test

Id Subject Object Predicate Lexical cue
17244351-15529344-4361124 475-477 15529344 denotes 10
17244351-15529344-4361125 950-952 15529344 denotes 10
17244351-15529344-4361126 1962-1964 15529344 denotes 10
17244351-11707780-4361127 2203-2205 11707780 denotes 23
17244351-11908948-4361128 3027-3029 11908948 denotes 16
17244351-11134512-4361129 3367-3369 11134512 denotes 24

craft-ca-core-dev

Below, discontinuous spans are shown in the chain model. You can change it to the bag model.

Id Subject Object Predicate Lexical cue
T3991 23-30 NCBITaxon:33208 denotes Animals
T3992 94-98 NCBITaxon:10088 denotes mice
T3993 243-249 NCBITaxon:33208 denotes animal
T3994 293-299 NCBITaxon:33208 denotes animal
T3995 343-349 NCBITaxon:33208 denotes Animal
T3996 410-417 NCBITaxon:33208 denotes animals
T3997 586-590 UBERON:0002415 denotes tail
T3998 606-612 NCBITaxon:27592 denotes bovine
T3999 613-624 PR:000003266 denotes Collagen II
T4000 775-782 NCBITaxon:33208 denotes animals
T4001 883-888 UBERON:0002101 denotes limbs
T4002 920-924 UBERON:0002101 denotes limb
T4003 987-991 NCBITaxon:10088 denotes mice
T4004 1023-1027 SO:0000704 denotes gene
T4005 1023-1038 GO:0010467 denotes gene expression
T4006 1280-1284 NCBITaxon:10088 denotes mice
T4007 1333-1337 NCBITaxon:10088 denotes mice
T4008 1404-1408 NCBITaxon:10088 denotes mice
T4009 1497-1501 NCBITaxon:10088 denotes mice
T4010 1518-1522 NCBITaxon:10088 denotes mice
T4011 1639-1643 NCBITaxon:10088 denotes mice
T4012 1732-1736 NCBITaxon:10088 denotes mice
T4013 1753-1757 NCBITaxon:10088 denotes mice
T4617 1917-1923 SO:0001026 denotes genome
T4618 1997-2001 NCBITaxon:10088 denotes mice
T4619 2060-2066 SO:0001026 denotes genome
T4620 2315-2318 SO:0000771 denotes QTL
T4972 2425-2438 GO:0097617 denotes hybridisation
T4973 2439-2450 UBERON:0000029 denotes Lymph nodes
T4974 2452-2455 UBERON:0000029 denotes LNs
T4975 2562-2568 UBERON:0000479 denotes tissue
T4976 2683-2687 SO:0000704 denotes gene
T4977 2683-2698 GO:0010467 denotes gene expression
T4978 2799-2804 SO:0000704 denotes genes
T4979 2907-2911 NCBITaxon:10088 denotes mice
T4980 2917-2927 GO:0097617 denotes hybridised
T4981 2952-2965 GO:0097617 denotes Hybridisation
T4982 2981-2985 SO:0000704 denotes gene
T4983 3098-3102 SO:0000704 denotes Gene
T5583 4477-4482 SO:0000704 denotes genes
T5566 3155-3165 GO:0010467 denotes expression
T5567 3256-3260 SO:0000704 denotes gene
T5568 3256-3271 GO:0010467 denotes gene expression
T5569 3309-3319 GO:0010467 denotes expression
T5570 3387-3396 GO:0010467 denotes expressed
T5571 3397-3402 SO:0000704 denotes genes
T5572 3834-3839 SO:0000704 denotes genes
T5573 3854-3858 SO:0000704 denotes gene
T5574 3915-3919 SO:0000704 denotes gene
T5575 3915-3930 GO:0010467 denotes gene expression
T5576 3988-3993 SO:0000704 denotes genes
T5577 4035-4040 SO:0000704 denotes genes
T5578 4134-4144 GO:0010467 denotes expression
T5579 4163-4168 SO:0000704 denotes genes
T5580 4261-4270 GO:0010467 denotes expressed
T5581 4271-4276 SO:0000704 denotes genes
T5582 4278-4282 SO:0000704 denotes Gene