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PMC:1860061 / 8985-9691 JSONTXT

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craft-sa-dev

Id Subject Object Predicate Lexical cue
T5606 0-13 NN denotes Normalisation
T5607 42-46 VBN denotes done
T5608 14-16 IN denotes of
T5609 17-20 DT denotes the
T5610 32-37 NN denotes level
T5611 21-31 NN denotes expression
T5612 38-41 VBD denotes was
T5613 47-52 VBG denotes using
T5614 53-63 NNP denotes Affymetrix
T5615 73-76 NN denotes MAS
T5616 64-72 NN denotes software
T5617 77-78 CD denotes 5
T5618 78-80 , denotes ,
T5619 80-85 WDT denotes which
T5620 89-94 VBN denotes based
T5621 86-88 VBZ denotes is
T5622 95-97 IN denotes on
T5623 98-104 JJ denotes global
T5624 105-112 NN denotes scaling
T5625 113-115 IN denotes of
T5626 116-121 JJ denotes total
T5627 138-143 NN denotes level
T5628 122-126 NN denotes gene
T5629 127-137 NN denotes expression
T5630 144-147 IN denotes per
T5631 148-158 NN denotes microarray
T5632 158-159 . denotes .
T5633 159-237 sentence denotes The normalised expression values were imported to and analysed by dCHIP [24].
T5634 160-163 DT denotes The
T5635 186-192 NNS denotes values
T5636 164-174 JJ denotes normalised
T5637 175-185 NN denotes expression
T5638 198-206 VBN denotes imported
T5639 193-197 VBD denotes were
T5640 207-209 IN denotes to
T5641 210-213 CC denotes and
T5642 214-222 VBN denotes analysed
T5643 223-225 IN denotes by
T5644 226-231 NN denotes dCHIP
T5645 232-233 -LRB- denotes [
T5646 233-235 CD denotes 24
T5647 235-236 -RRB- denotes ]
T5648 236-237 . denotes .
T5649 237-560 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 238-252 RB denotes Differentially
T5651 253-262 VBN denotes expressed
T5652 263-268 NNS denotes genes
T5653 274-284 VBN denotes identified
T5654 269-273 VBD denotes were
T5655 285-287 IN denotes by
T5656 288-296 VBG denotes defining
T5657 297-300 DT denotes the
T5658 323-331 NNS denotes criteria
T5659 301-312 JJ denotes appropriate
T5660 313-322 NN denotes filtering
T5661 332-334 IN denotes in
T5662 335-338 DT denotes the
T5663 345-353 NN denotes software
T5664 339-344 NN denotes dCHIP
T5665 354-356 IN denotes as
T5666 356-358 : denotes :
T5667 358-363 JJ denotes lower
T5668 366-367 NN denotes %
T5669 364-366 CD denotes 90
T5670 379-387 NN denotes boundary
T5671 368-378 NN denotes confidence
T5672 427-435 VBN denotes exceeded
T5673 388-390 IN denotes of
T5674 391-395 NN denotes fold
T5675 396-402 NN denotes change
T5676 403-410 IN denotes between
T5677 411-414 DT denotes the
T5678 421-426 NNS denotes means
T5679 415-420 NN denotes group
T5680 551-554 VBD denotes was
T5681 436-443 RB denotes twofold
T5682 443-444 : denotes ;
T5683 445-448 DT denotes the
T5684 458-468 NN denotes difference
T5685 449-457 JJ denotes absolute
T5686 492-500 VBD denotes exceeded
T5687 469-476 IN denotes between
T5688 477-480 DT denotes the
T5689 485-491 NNS denotes groups
T5690 481-484 CD denotes two
T5691 501-504 CD denotes 100
T5692 504-505 : denotes ;
T5693 506-509 DT denotes the
T5694 518-527 NN denotes threshold
T5695 510-511 NN denotes P
T5696 512-517 NN denotes value
T5697 528-530 IN denotes of
T5698 531-534 DT denotes the
T5699 546-550 NN denotes test
T5700 535-543 JJ denotes unpaired
T5701 544-545 NN denotes t
T5702 545-546 HYPH denotes -
T5703 555-559 CD denotes 0.05
T5704 559-560 . denotes .
T5705 560-706 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 561-564 DT denotes The
T5707 581-585 NN denotes rate
T5708 565-570 JJ denotes false
T5709 571-580 NN denotes discovery
T5710 590-601 VBN denotes established
T5711 586-589 VBD denotes was
T5712 602-606 IN denotes with
T5713 607-608 DT denotes a
T5714 621-625 NN denotes test
T5715 609-620 NN denotes permutation
T5716 626-629 IN denotes for
T5717 630-634 DT denotes each
T5718 644-654 NN denotes comparison
T5719 635-643 JJ denotes pairwise
T5720 655-657 TO denotes to
T5721 658-666 VB denotes estimate
T5722 667-670 DT denotes the
T5723 671-681 NN denotes proportion
T5724 682-684 IN denotes of
T5725 685-690 JJ denotes false
T5726 691-699 JJ denotes positive
T5727 690-691 HYPH denotes -
T5728 700-705 NNS denotes genes
T5729 705-706 . denotes .
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
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

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
T5584 21-31 GO:0010467 denotes expression
T5585 122-126 SO_EXT:0000704 denotes gene
T5586 122-137 GO:0010467 denotes gene expression
T5587 175-185 GO:0010467 denotes expression
T5588 253-262 GO:0010467 denotes expressed
T5589 263-268 SO_EXT:0000704 denotes genes
T5590 700-705 SO_EXT:0000704 denotes genes

2_test

Id Subject Object Predicate Lexical cue
17244351-11134512-4361129 233-235 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
T5566 21-31 GO:0010467 denotes expression
T5567 122-126 SO:0000704 denotes gene
T5568 122-137 GO:0010467 denotes gene expression
T5569 175-185 GO:0010467 denotes expression
T5570 253-262 GO:0010467 denotes expressed
T5571 263-268 SO:0000704 denotes genes
T5572 700-705 SO:0000704 denotes genes