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PMC:1860061 / 14759-17125 JSONTXT 4 Projects

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Id Subject Object Predicate Lexical cue
T9552 0-7 NN denotes Disease
T9554 7-8 HYPH denotes -
T9553 8-16 JJ denotes specific
T9556 17-31 RB denotes differentially
T9557 32-41 VBN denotes expressed
T9555 42-47 NNS denotes genes
T9558 47-221 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 48-50 TO denotes To
T9560 51-59 VB denotes identify
T9562 60-63 DT denotes the
T9564 64-71 NN denotes disease
T9566 71-72 HYPH denotes -
T9565 72-80 JJ denotes specific
T9567 81-95 RB denotes differentially
T9568 96-105 VBN denotes expressed
T9563 106-111 NNS denotes genes
T9569 112-114 IN denotes in
T9570 115-118 NN denotes CIA
T9571 118-120 , denotes ,
T9572 120-122 PRP denotes we
T9561 123-131 VBD denotes detected
T9573 132-135 DT denotes the
T9574 136-141 NNS denotes genes
T9575 142-146 WDT denotes that
T9577 147-151 VBD denotes were
T9578 152-166 RB denotes differentially
T9576 167-176 VBN denotes expressed
T9579 177-179 IN denotes in
T9580 180-183 NNS denotes LNs
T9581 184-190 IN denotes during
T9582 191-194 NN denotes CIA
T9583 195-197 IN denotes in
T9584 198-201 DT denotes the
T9586 202-213 JJ denotes susceptible
T9585 214-220 NN denotes strain
T9587 220-221 . denotes .
T9588 221-300 sentence denotes Three experimental conditions, PI, OA and CA, were compared with the NC group.
T9589 222-227 CD denotes Three
T9591 228-240 JJ denotes experimental
T9590 241-251 NNS denotes conditions
T9593 251-253 , denotes ,
T9594 253-255 NN denotes PI
T9595 255-257 , denotes ,
T9596 257-259 NN denotes OA
T9597 260-263 CC denotes and
T9598 264-266 NN denotes CA
T9599 266-268 , denotes ,
T9600 268-272 VBD denotes were
T9592 273-281 VBN denotes compared
T9601 282-286 IN denotes with
T9602 287-290 DT denotes the
T9604 291-293 NN denotes NC
T9603 294-299 NN denotes group
T9605 299-300 . denotes .
T9606 300-506 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 301-303 IN denotes On
T9609 304-307 NN denotes day
T9610 308-310 CD denotes 10
T9611 311-316 IN denotes after
T9612 317-329 NN denotes immunisation
T9613 329-331 , denotes ,
T9614 331-334 CD denotes 102
T9615 335-340 NNS denotes genes
T9617 341-345 VBD denotes were
T9618 346-360 RB denotes differentially
T9616 361-370 VBN denotes expressed
T9619 371-372 , denotes –
T9620 373-377 JJS denotes most
T9621 378-380 IN denotes of
T9622 381-385 PRP denotes them
T9623 386-390 VBD denotes were
T9608 391-402 VBN denotes upregulated
T9624 403-404 -LRB- denotes (
T9626 404-406 CD denotes 78
T9627 407-410 IN denotes out
T9628 411-413 IN denotes of
T9625 414-417 CD denotes 102
T9629 417-418 -RRB- denotes )
T9630 419-420 , denotes –
T9631 421-426 IN denotes while
T9633 427-429 IN denotes at
T9634 430-433 DT denotes the
T9636 434-439 NN denotes onset
T9635 440-445 NN denotes phase
T9637 446-448 IN denotes of
T9638 449-452 DT denotes the
T9639 453-460 NN denotes disease
T9640 460-462 , denotes ,
T9641 462-466 RB denotes only
T9643 467-469 CD denotes 26
T9642 470-475 NNS denotes genes
T9644 476-480 VBD denotes were
T9645 481-495 RB denotes differentially
T9632 496-505 VBN denotes expressed
T9646 505-506 . denotes .
T9647 506-625 sentence denotes At the chronic phase of the disease, 184 differentially expressed genes were identified, with 156 downregulated genes.
T9648 507-509 IN denotes At
T9650 510-513 DT denotes the
T9652 514-521 JJ denotes chronic
T9651 522-527 NN denotes phase
T9653 528-530 IN denotes of
T9654 531-534 DT denotes the
T9655 535-542 NN denotes disease
T9656 542-544 , denotes ,
T9657 544-547 CD denotes 184
T9659 548-562 RB denotes differentially
T9660 563-572 VBN denotes expressed
T9658 573-578 NNS denotes genes
T9661 579-583 VBD denotes were
T9649 584-594 VBN denotes identified
T9662 594-596 , denotes ,
T9663 596-600 IN denotes with
T9664 601-604 CD denotes 156
T9666 605-618 VBN denotes downregulated
T9665 619-624 NNS denotes genes
T9667 624-625 . denotes .
T9668 625-696 sentence denotes Only one gene was differentially expressed at all three phases of CIA.
T9669 626-630 RB denotes Only
T9671 631-634 CD denotes one
T9670 635-639 NN denotes gene
T9673 640-643 VBD denotes was
T9674 644-658 RB denotes differentially
T9672 659-668 VBN denotes expressed
T9675 669-671 IN denotes at
T9676 672-675 DT denotes all
T9678 676-681 CD denotes three
T9677 682-688 NNS denotes phases
T9679 689-691 IN denotes of
T9680 692-695 NN denotes CIA
T9681 695-696 . denotes .
T9682 696-844 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 697-704 IN denotes Besides
T9685 705-709 DT denotes this
T9686 710-714 NN denotes gene
T9687 714-716 , denotes ,
T9688 716-720 CD denotes five
T9690 720-722 , denotes ,
T9691 722-725 CD denotes one
T9692 726-729 CC denotes and
T9693 730-733 CD denotes six
T9694 734-748 RB denotes differentially
T9695 749-758 VBN denotes expressed
T9689 759-764 NNS denotes genes
T9696 765-769 VBD denotes were
T9684 770-776 VBN denotes shared
T9697 777-779 IN denotes by
T9698 780-782 NN denotes PI
T9699 783-787 IN denotes with
T9700 788-790 NN denotes OA
T9701 790-792 , denotes ,
T9702 792-794 NN denotes PI
T9703 795-799 IN denotes with
T9704 800-802 NN denotes CA
T9705 803-806 CC denotes and
T9706 807-809 NN denotes OA
T9707 810-814 IN denotes with
T9708 815-817 NN denotes CA
T9709 817-819 , denotes ,
T9710 819-831 RB denotes respectively
T9711 832-833 -LRB- denotes (
T9713 833-839 NN denotes Figure
T9712 840-842 NN denotes 2a
T9714 842-843 -RRB- denotes )
T9715 843-844 . denotes .
T9716 844-988 sentence denotes Taken together, 310 disease-specific differentially expressed genes were differentially regulated during CIA in DBA/1 mice (Additional file 2).
T9717 845-850 VBN denotes Taken
T9719 851-859 RB denotes together
T9720 859-861 , denotes ,
T9721 861-864 CD denotes 310
T9723 865-872 NN denotes disease
T9725 872-873 HYPH denotes -
T9724 873-881 JJ denotes specific
T9726 882-896 RB denotes differentially
T9727 897-906 VBN denotes expressed
T9722 907-912 NNS denotes genes
T9728 913-917 VBD denotes were
T9729 918-932 RB denotes differentially
T9718 933-942 VBN denotes regulated
T9730 943-949 IN denotes during
T9731 950-953 NN denotes CIA
T9732 954-956 IN denotes in
T9733 957-960 NN denotes DBA
T9735 960-961 HYPH denotes /
T9736 961-962 CD denotes 1
T9734 963-967 NNS denotes mice
T9737 968-969 -LRB- denotes (
T9739 969-979 JJ denotes Additional
T9738 980-984 NN denotes file
T9740 985-986 CD denotes 2
T9741 986-987 -RRB- denotes )
T9742 987-988 . denotes .
T9743 988-1116 sentence denotes To further characterise the gene expression pattern during CIA, we performed hierarchical cluster analysis for these 310 genes.
T9744 989-991 TO denotes To
T9746 992-999 RB denotes further
T9745 1000-1012 VB denotes characterise
T9748 1013-1016 DT denotes the
T9750 1017-1021 NN denotes gene
T9751 1022-1032 NN denotes expression
T9749 1033-1040 NN denotes pattern
T9752 1041-1047 IN denotes during
T9753 1048-1051 NN denotes CIA
T9754 1051-1053 , denotes ,
T9755 1053-1055 PRP denotes we
T9747 1056-1065 VBD denotes performed
T9756 1066-1078 JJ denotes hierarchical
T9758 1079-1086 NN denotes cluster
T9757 1087-1095 NN denotes analysis
T9759 1096-1099 IN denotes for
T9760 1100-1105 DT denotes these
T9762 1106-1109 CD denotes 310
T9761 1110-1115 NNS denotes genes
T9763 1115-1116 . denotes .
T9764 1116-1238 sentence denotes Six gene clusters were identified (clusters I to VI, Figure 2b), each with a distinct gene expression pattern during CIA.
T9765 1117-1120 CD denotes Six
T9767 1121-1125 NN denotes gene
T9766 1126-1134 NNS denotes clusters
T9769 1135-1139 VBD denotes were
T9768 1140-1150 VBN denotes identified
T9770 1151-1152 -LRB- denotes (
T9772 1152-1160 NNS denotes clusters
T9771 1161-1162 CD denotes I
T9773 1163-1165 IN denotes to
T9774 1166-1168 CD denotes VI
T9775 1168-1170 , denotes ,
T9776 1170-1176 NN denotes Figure
T9777 1177-1179 NN denotes 2b
T9778 1179-1180 -RRB- denotes )
T9779 1180-1182 , denotes ,
T9780 1182-1186 DT denotes each
T9781 1187-1191 IN denotes with
T9782 1192-1193 DT denotes a
T9784 1194-1202 JJ denotes distinct
T9785 1203-1207 NN denotes gene
T9786 1208-1218 NN denotes expression
T9783 1219-1226 NN denotes pattern
T9787 1227-1233 IN denotes during
T9788 1234-1237 NN denotes CIA
T9789 1237-1238 . denotes .
T9790 1238-1332 sentence denotes Cluster I contains 16 genes, representing genes that were upregulated after induction of CIA.
T9791 1239-1246 NN denotes Cluster
T9793 1247-1248 CD denotes I
T9792 1249-1257 VBZ denotes contains
T9794 1258-1260 CD denotes 16
T9795 1261-1266 NNS denotes genes
T9796 1266-1268 , denotes ,
T9797 1268-1280 VBG denotes representing
T9798 1281-1286 NNS denotes genes
T9799 1287-1291 WDT denotes that
T9801 1292-1296 VBD denotes were
T9800 1297-1308 VBN denotes upregulated
T9802 1309-1314 IN denotes after
T9803 1315-1324 NN denotes induction
T9804 1325-1327 IN denotes of
T9805 1328-1331 NN denotes CIA
T9806 1331-1332 . denotes .
T9807 1332-1500 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 1333-1336 DT denotes The
T9809 1337-1347 NN denotes expression
T9811 1348-1350 IN denotes of
T9812 1351-1356 DT denotes these
T9813 1357-1362 NNS denotes genes
T9810 1363-1370 VBD denotes reached
T9814 1371-1372 DT denotes a
T9815 1373-1377 NN denotes peak
T9816 1378-1380 IN denotes at
T9817 1381-1384 DT denotes the
T9819 1385-1390 NN denotes onset
T9818 1391-1396 NN denotes phase
T9820 1397-1399 IN denotes of
T9821 1400-1403 DT denotes the
T9822 1404-1411 NN denotes disease
T9823 1412-1415 CC denotes and
T9824 1416-1426 JJ denotes functional
T9826 1427-1437 NN denotes clustering
T9825 1438-1445 NNS denotes results
T9827 1446-1454 VBD denotes revealed
T9828 1455-1459 IN denotes that
T9830 1460-1464 PRP denotes they
T9831 1465-1468 VBP denotes are
T9829 1469-1476 VBN denotes related
T9832 1477-1479 IN denotes to
T9833 1480-1483 DT denotes the
T9835 1484-1490 JJ denotes immune
T9834 1491-1499 NN denotes response
T9836 1499-1500 . denotes .
T9837 1500-1620 sentence denotes Cluster II contains 12 genes whose expression was gradually upregulated and reached a peak at the chronic phase of CIA.
T9838 1501-1508 NN denotes Cluster
T9840 1509-1511 CD denotes II
T9839 1512-1520 VBZ denotes contains
T9841 1521-1523 CD denotes 12
T9842 1524-1529 NNS denotes genes
T9843 1530-1535 WP$ denotes whose
T9844 1536-1546 NN denotes expression
T9846 1547-1550 VBD denotes was
T9847 1551-1560 RB denotes gradually
T9845 1561-1572 VBN denotes upregulated
T9848 1573-1576 CC denotes and
T9849 1577-1584 VBN denotes reached
T9850 1585-1586 DT denotes a
T9851 1587-1591 NN denotes peak
T9852 1592-1594 IN denotes at
T9853 1595-1598 DT denotes the
T9855 1599-1606 JJ denotes chronic
T9854 1607-1612 NN denotes phase
T9856 1613-1615 IN denotes of
T9857 1616-1619 NN denotes CIA
T9858 1619-1620 . denotes .
T9859 1620-1730 sentence denotes These genes are mainly related to the immune response, organelle membrane and extracellular region and space.
T9860 1621-1626 DT denotes These
T9861 1627-1632 NNS denotes genes
T9863 1633-1636 VBP denotes are
T9864 1637-1643 RB denotes mainly
T9862 1644-1651 VBN denotes related
T9865 1652-1654 IN denotes to
T9866 1655-1658 DT denotes the
T9868 1659-1665 JJ denotes immune
T9867 1666-1674 NN denotes response
T9869 1674-1676 , denotes ,
T9870 1676-1685 NN denotes organelle
T9871 1686-1694 NN denotes membrane
T9872 1695-1698 CC denotes and
T9873 1699-1712 JJ denotes extracellular
T9874 1713-1719 NN denotes region
T9875 1720-1723 CC denotes and
T9876 1724-1729 NN denotes space
T9877 1729-1730 . denotes .
T9878 1730-1804 sentence denotes Cluster III contains 78 genes that were only upregulated at the PI phase.
T9879 1731-1738 NN denotes Cluster
T9881 1739-1742 CD denotes III
T9880 1743-1751 VBZ denotes contains
T9882 1752-1754 CD denotes 78
T9883 1755-1760 NNS denotes genes
T9884 1761-1765 WDT denotes that
T9886 1766-1770 VBD denotes were
T9887 1771-1775 RB denotes only
T9885 1776-1787 VBN denotes upregulated
T9888 1788-1790 IN denotes at
T9889 1791-1794 DT denotes the
T9891 1795-1797 NN denotes PI
T9890 1798-1803 NN denotes phase
T9892 1803-1804 . denotes .
T9893 1804-1859 sentence denotes These genes are related to the intercellular junction.
T9894 1805-1810 DT denotes These
T9895 1811-1816 NNS denotes genes
T9897 1817-1820 VBP denotes are
T9896 1821-1828 VBN denotes related
T9898 1829-1831 IN denotes to
T9899 1832-1835 DT denotes the
T9901 1836-1849 JJ denotes intercellular
T9900 1850-1858 NN denotes junction
T9902 1858-1859 . denotes .
T9903 1859-1990 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 1860-1864 JJR denotes More
T9906 1865-1869 IN denotes than
T9905 1870-1874 NN denotes half
T9908 1875-1877 IN denotes of
T9909 1878-1881 DT denotes the
T9910 1882-1887 NNS denotes genes
T9911 1888-1889 -LRB- denotes (
T9913 1889-1892 CD denotes 156
T9914 1893-1895 IN denotes of
T9912 1896-1899 CD denotes 310
T9915 1899-1900 -RRB- denotes )
T9907 1901-1907 VBP denotes belong
T9916 1908-1910 IN denotes to
T9917 1911-1918 NN denotes cluster
T9918 1919-1921 CD denotes IV
T9919 1922-1925 CC denotes and
T9920 1926-1935 VBP denotes represent
T9921 1936-1941 NNS denotes genes
T9922 1942-1954 RB denotes specifically
T9923 1955-1968 VBN denotes downregultaed
T9924 1969-1971 IN denotes at
T9925 1972-1975 DT denotes the
T9927 1976-1983 JJ denotes chronic
T9926 1984-1989 NN denotes phase
T9928 1989-1990 . denotes .
T9929 1990-2128 sentence denotes These genes are functionally related to lymphocyte proliferation, T cell activation, protein binding as well as the notch signal pathway.
T9930 1991-1996 DT denotes These
T9931 1997-2002 NNS denotes genes
T9933 2003-2006 VBP denotes are
T9934 2007-2019 RB denotes functionally
T9932 2020-2027 VBN denotes related
T9935 2028-2030 IN denotes to
T9936 2031-2041 NN denotes lymphocyte
T9937 2042-2055 NN denotes proliferation
T9938 2055-2057 , denotes ,
T9939 2057-2058 NN denotes T
T9940 2059-2063 NN denotes cell
T9941 2064-2074 NN denotes activation
T9942 2074-2076 , denotes ,
T9943 2076-2083 NN denotes protein
T9944 2084-2091 NN denotes binding
T9945 2092-2094 RB denotes as
T9947 2095-2099 RB denotes well
T9946 2100-2102 IN denotes as
T9948 2103-2106 DT denotes the
T9950 2107-2112 NN denotes notch
T9951 2113-2119 NN denotes signal
T9949 2120-2127 NN denotes pathway
T9952 2127-2128 . denotes .
T9953 2128-2190 sentence denotes Cluster V contains eight genes downregulated at the PI phase.
T9954 2129-2136 NN denotes Cluster
T9956 2137-2138 CD denotes V
T9955 2139-2147 VBZ denotes contains
T9957 2148-2153 CD denotes eight
T9958 2154-2159 NNS denotes genes
T9959 2160-2173 VBN denotes downregulated
T9960 2174-2176 IN denotes at
T9961 2177-2180 DT denotes the
T9963 2181-2183 NN denotes PI
T9962 2184-2189 NN denotes phase
T9964 2189-2190 . denotes .
T9965 2190-2250 sentence denotes Cluster VI contains 18 genes downregulated at the OA phase.
T9966 2191-2198 NN denotes Cluster
T9968 2199-2201 CD denotes VI
T9967 2202-2210 VBZ denotes contains
T9969 2211-2213 CD denotes 18
T9970 2214-2219 NNS denotes genes
T9971 2220-2233 VBN denotes downregulated
T9972 2234-2236 IN denotes at
T9973 2237-2240 DT denotes the
T9975 2241-2243 NN denotes OA
T9974 2244-2249 NN denotes phase
T9976 2249-2250 . denotes .
T9977 2250-2366 sentence denotes The GO term classification showed no functional cluster that was significantly enriched in these two gene clusters.
T9978 2251-2254 DT denotes The
T9980 2255-2257 NN denotes GO
T9981 2258-2262 NN denotes term
T9979 2263-2277 NN denotes classification
T9982 2278-2284 VBD denotes showed
T9983 2285-2287 DT denotes no
T9985 2288-2298 JJ denotes functional
T9984 2299-2306 NN denotes cluster
T9986 2307-2311 WDT denotes that
T9988 2312-2315 VBD denotes was
T9989 2316-2329 RB denotes significantly
T9987 2330-2338 VBN denotes enriched
T9990 2339-2341 IN denotes in
T9991 2342-2347 DT denotes these
T9993 2348-2351 CD denotes two
T9994 2352-2356 NN denotes gene
T9992 2357-2365 NNS denotes clusters
T9995 2365-2366 . denotes .
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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