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PMC:1860061 / 8965-10334 JSONTXT 5 Projects

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Id Subject Object Predicate Lexical cue
T5603 0-10 NN denotes Microarray
T5604 11-19 NN denotes analysis
T5605 19-179 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 20-33 NN denotes Normalisation
T5608 34-36 IN denotes of
T5609 37-40 DT denotes the
T5611 41-51 NN denotes expression
T5610 52-57 NN denotes level
T5612 58-61 VBD denotes was
T5607 62-66 VBN denotes done
T5613 67-72 VBG denotes using
T5614 73-83 NNP denotes Affymetrix
T5616 84-92 NN denotes software
T5615 93-96 NN denotes MAS
T5617 97-98 CD denotes 5
T5618 98-100 , denotes ,
T5619 100-105 WDT denotes which
T5621 106-108 VBZ denotes is
T5620 109-114 VBN denotes based
T5622 115-117 IN denotes on
T5623 118-124 JJ denotes global
T5624 125-132 NN denotes scaling
T5625 133-135 IN denotes of
T5626 136-141 JJ denotes total
T5628 142-146 NN denotes gene
T5629 147-157 NN denotes expression
T5627 158-163 NN denotes level
T5630 164-167 IN denotes per
T5631 168-178 NN denotes microarray
T5632 178-179 . denotes .
T5633 179-257 sentence denotes The normalised expression values were imported to and analysed by dCHIP [24].
T5634 180-183 DT denotes The
T5636 184-194 JJ denotes normalised
T5637 195-205 NN denotes expression
T5635 206-212 NNS denotes values
T5639 213-217 VBD denotes were
T5638 218-226 VBN denotes imported
T5640 227-229 IN denotes to
T5641 230-233 CC denotes and
T5642 234-242 VBN denotes analysed
T5643 243-245 IN denotes by
T5644 246-251 NN denotes dCHIP
T5645 252-253 -LRB- denotes [
T5646 253-255 CD denotes 24
T5647 255-256 -RRB- denotes ]
T5648 256-257 . denotes .
T5649 257-580 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 258-272 RB denotes Differentially
T5651 273-282 VBN denotes expressed
T5652 283-288 NNS denotes genes
T5654 289-293 VBD denotes were
T5653 294-304 VBN denotes identified
T5655 305-307 IN denotes by
T5656 308-316 VBG denotes defining
T5657 317-320 DT denotes the
T5659 321-332 JJ denotes appropriate
T5660 333-342 NN denotes filtering
T5658 343-351 NNS denotes criteria
T5661 352-354 IN denotes in
T5662 355-358 DT denotes the
T5664 359-364 NN denotes dCHIP
T5663 365-373 NN denotes software
T5665 374-376 IN denotes as
T5666 376-378 : denotes :
T5667 378-383 JJ denotes lower
T5669 384-386 CD denotes 90
T5668 386-387 NN denotes %
T5671 388-398 NN denotes confidence
T5670 399-407 NN denotes boundary
T5673 408-410 IN denotes of
T5674 411-415 NN denotes fold
T5675 416-422 NN denotes change
T5676 423-430 IN denotes between
T5677 431-434 DT denotes the
T5679 435-440 NN denotes group
T5678 441-446 NNS denotes means
T5672 447-455 VBN denotes exceeded
T5681 456-463 RB denotes twofold
T5682 463-464 : denotes ;
T5683 465-468 DT denotes the
T5685 469-477 JJ denotes absolute
T5684 478-488 NN denotes difference
T5687 489-496 IN denotes between
T5688 497-500 DT denotes the
T5690 501-504 CD denotes two
T5689 505-511 NNS denotes groups
T5686 512-520 VBD denotes exceeded
T5691 521-524 CD denotes 100
T5692 524-525 : denotes ;
T5693 526-529 DT denotes the
T5695 530-531 NN denotes P
T5696 532-537 NN denotes value
T5694 538-547 NN denotes threshold
T5697 548-550 IN denotes of
T5698 551-554 DT denotes the
T5700 555-563 JJ denotes unpaired
T5701 564-565 NN denotes t
T5702 565-566 HYPH denotes -
T5699 566-570 NN denotes test
T5680 571-574 VBD denotes was
T5703 575-579 CD denotes 0.05
T5704 579-580 . denotes .
T5705 580-726 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 581-584 DT denotes The
T5708 585-590 JJ denotes false
T5709 591-600 NN denotes discovery
T5707 601-605 NN denotes rate
T5711 606-609 VBD denotes was
T5710 610-621 VBN denotes established
T5712 622-626 IN denotes with
T5713 627-628 DT denotes a
T5715 629-640 NN denotes permutation
T5714 641-645 NN denotes test
T5716 646-649 IN denotes for
T5717 650-654 DT denotes each
T5719 655-663 JJ denotes pairwise
T5718 664-674 NN denotes comparison
T5720 675-677 TO denotes to
T5721 678-686 VB denotes estimate
T5722 687-690 DT denotes the
T5723 691-701 NN denotes proportion
T5724 702-704 IN denotes of
T5725 705-710 JJ denotes false
T5727 710-711 HYPH denotes -
T5726 711-719 JJ denotes positive
T5728 720-725 NNS denotes genes
T5729 725-726 . denotes .
T5730 726-837 sentence denotes Hierarchical gene clustering was performed with dCHIP to characterise the gene expression patterns during CIA.
T5731 727-739 JJ denotes Hierarchical
T5733 740-744 NN denotes gene
T5732 745-755 NN denotes clustering
T5735 756-759 VBD denotes was
T5734 760-769 VBN denotes performed
T5736 770-774 IN denotes with
T5737 775-780 NN denotes dCHIP
T5738 781-783 TO denotes to
T5739 784-796 VB denotes characterise
T5740 797-800 DT denotes the
T5742 801-805 NN denotes gene
T5743 806-816 NN denotes expression
T5741 817-825 NNS denotes patterns
T5744 826-832 IN denotes during
T5745 833-836 NN denotes CIA
T5746 836-837 . denotes .
T5747 837-1079 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 838-841 DT denotes The
T5750 842-849 NN denotes default
T5751 850-860 NN denotes clustering
T5749 861-870 NN denotes algorithm
T5753 871-873 IN denotes of
T5754 874-879 NNS denotes genes
T5752 880-883 VBD denotes was
T5756 884-886 IN denotes as
T5757 887-894 VBZ denotes follows
T5758 894-896 : denotes :
T5759 896-899 DT denotes the
T5760 900-908 NN denotes distance
T5761 909-916 IN denotes between
T5762 917-920 CD denotes two
T5763 921-926 NNS denotes genes
T5764 927-929 VBZ denotes is
T5755 930-937 VBN denotes defined
T5765 938-940 IN denotes as
T5766 941-942 CD denotes 1
T5768 943-944 HYPH denotes –
T5767 945-946 NN denotes r
T5769 946-948 , denotes ,
T5770 948-953 WRB denotes where
T5772 954-955 NN denotes r
T5771 956-958 VBZ denotes is
T5773 959-962 DT denotes the
T5775 963-970 NNP denotes Pearson
T5776 971-982 NN denotes correlation
T5774 983-994 NN denotes coefficient
T5777 995-1002 IN denotes between
T5778 1003-1006 DT denotes the
T5780 1007-1019 VBN denotes standardised
T5781 1020-1030 NN denotes expression
T5779 1031-1037 NNS denotes values
T5782 1038-1040 IN denotes of
T5783 1041-1044 DT denotes the
T5785 1045-1048 CD denotes two
T5784 1049-1054 NNS denotes genes
T5786 1055-1061 IN denotes across
T5787 1062-1065 DT denotes the
T5788 1066-1073 NNS denotes samples
T5789 1074-1078 VBN denotes used
T5790 1078-1079 . denotes .
T5791 1079-1251 sentence denotes To characterise the functional relationship between differentially expressed genes, Gene Ontology (GO) term classification incorporated in DNA-Chip Analyzer was performed.
T5792 1080-1082 TO denotes To
T5793 1083-1095 VB denotes characterise
T5795 1096-1099 DT denotes the
T5797 1100-1110 JJ denotes functional
T5796 1111-1123 NN denotes relationship
T5798 1124-1131 IN denotes between
T5799 1132-1146 RB denotes differentially
T5801 1147-1156 VBN denotes expressed
T5800 1157-1162 NNS denotes genes
T5802 1162-1164 , denotes ,
T5803 1164-1168 NN denotes Gene
T5804 1169-1177 NN denotes Ontology
T5806 1178-1179 -LRB- denotes (
T5807 1179-1181 NN denotes GO
T5808 1181-1182 -RRB- denotes )
T5809 1183-1187 NN denotes term
T5805 1188-1202 NN denotes classification
T5810 1203-1215 VBN denotes incorporated
T5811 1216-1218 IN denotes in
T5812 1219-1222 NNP denotes DNA
T5814 1222-1223 HYPH denotes -
T5813 1223-1227 NNP denotes Chip
T5815 1228-1236 NNP denotes Analyzer
T5816 1237-1240 VBD denotes was
T5794 1241-1250 VBN denotes performed
T5817 1250-1251 . denotes .
T5818 1251-1369 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 1252-1255 DT denotes The
T5821 1256-1267 JJ denotes significant
T5820 1268-1273 NN denotes level
T5823 1274-1277 IN denotes for
T5824 1278-1279 DT denotes a
T5826 1280-1288 NN denotes function
T5825 1289-1296 NN denotes cluster
T5827 1297-1300 VBD denotes was
T5822 1301-1304 VBN denotes set
T5828 1305-1307 IN denotes at
T5829 1308-1309 NN denotes P
T5830 1310-1311 SYM denotes <
T5831 1312-1317 CD denotes 0.005
T5832 1317-1319 , denotes ,
T5833 1319-1322 CC denotes and
T5834 1323-1326 DT denotes the
T5836 1327-1334 JJ denotes minimum
T5835 1335-1339 NN denotes size
T5838 1340-1342 IN denotes of
T5839 1343-1344 DT denotes a
T5840 1345-1352 NN denotes cluster
T5837 1353-1356 VBD denotes was
T5841 1357-1362 CD denotes three
T5842 1363-1368 NNS denotes genes
T5843 1368-1369 . denotes .
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
R1665 T5679 T5678 compound group,means
R1666 T5680 T5665 pcomp was,as
R1667 T5681 T5672 advmod twofold,exceeded
R1668 T5682 T5680 punct ;,was
R1669 T5683 T5684 det the,difference
R1670 T5684 T5686 nsubj difference,exceeded
R1671 T5685 T5684 amod absolute,difference
R1672 T5686 T5680 ccomp exceeded,was
R1673 T5687 T5684 prep between,difference
R1674 T5688 T5689 det the,groups
R1675 T5689 T5687 pobj groups,between
R1676 T5690 T5689 nummod two,groups
R1677 T5691 T5686 dobj 100,exceeded
R1678 T5692 T5680 punct ;,was
R1679 T5693 T5694 det the,threshold
R1680 T5694 T5680 nsubj threshold,was
R1681 T5695 T5696 compound P,value
R1682 T5696 T5694 compound value,threshold
R1683 T5697 T5694 prep of,threshold
R1684 T5698 T5699 det the,test
R1685 T5699 T5697 pobj test,of
R1686 T5700 T5699 amod unpaired,test
R1687 T5701 T5699 compound t,test
R1688 T5702 T5699 punct -,test
R1689 T5703 T5680 attr 0.05,was
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