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PMC:1860061 / 14807-15747 JSONTXT

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Id Subject Object Predicate Lexical cue
T9559 0-2 TO denotes To
T9560 3-11 VB denotes identify
T9561 75-83 VBD denotes detected
T9562 12-15 DT denotes the
T9563 58-63 NNS denotes genes
T9564 16-23 NN denotes disease
T9565 24-32 JJ denotes specific
T9566 23-24 HYPH denotes -
T9567 33-47 RB denotes differentially
T9568 48-57 VBN denotes expressed
T9569 64-66 IN denotes in
T9570 67-70 NN denotes CIA
T9571 70-72 , denotes ,
T9572 72-74 PRP denotes we
T9573 84-87 DT denotes the
T9574 88-93 NNS denotes genes
T9575 94-98 WDT denotes that
T9576 119-128 VBN denotes expressed
T9577 99-103 VBD denotes were
T9578 104-118 RB denotes differentially
T9579 129-131 IN denotes in
T9580 132-135 NNS denotes LNs
T9581 136-142 IN denotes during
T9582 143-146 NN denotes CIA
T9583 147-149 IN denotes in
T9584 150-153 DT denotes the
T9585 166-172 NN denotes strain
T9586 154-165 JJ denotes susceptible
T9587 172-173 . denotes .
T9588 173-252 sentence denotes Three experimental conditions, PI, OA and CA, were compared with the NC group.
T9589 174-179 CD denotes Three
T9590 193-203 NNS denotes conditions
T9591 180-192 JJ denotes experimental
T9592 225-233 VBN denotes compared
T9593 203-205 , denotes ,
T9594 205-207 NN denotes PI
T9595 207-209 , denotes ,
T9596 209-211 NN denotes OA
T9597 212-215 CC denotes and
T9598 216-218 NN denotes CA
T9599 218-220 , denotes ,
T9600 220-224 VBD denotes were
T9601 234-238 IN denotes with
T9602 239-242 DT denotes the
T9603 246-251 NN denotes group
T9604 243-245 NN denotes NC
T9605 251-252 . denotes .
T9606 252-458 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 253-255 IN denotes On
T9608 343-354 VBN denotes upregulated
T9609 256-259 NN denotes day
T9610 260-262 CD denotes 10
T9611 263-268 IN denotes after
T9612 269-281 NN denotes immunisation
T9613 281-283 , denotes ,
T9614 283-286 CD denotes 102
T9615 287-292 NNS denotes genes
T9616 313-322 VBN denotes expressed
T9617 293-297 VBD denotes were
T9618 298-312 RB denotes differentially
T9619 323-324 , denotes –
T9620 325-329 JJS denotes most
T9621 330-332 IN denotes of
T9622 333-337 PRP denotes them
T9623 338-342 VBD denotes were
T9624 355-356 -LRB- denotes (
T9625 366-369 CD denotes 102
T9626 356-358 CD denotes 78
T9627 359-362 IN denotes out
T9628 363-365 IN denotes of
T9629 369-370 -RRB- denotes )
T9630 371-372 , denotes –
T9631 373-378 IN denotes while
T9632 448-457 VBN denotes expressed
T9633 379-381 IN denotes at
T9634 382-385 DT denotes the
T9635 392-397 NN denotes phase
T9636 386-391 NN denotes onset
T9637 398-400 IN denotes of
T9638 401-404 DT denotes the
T9639 405-412 NN denotes disease
T9640 412-414 , denotes ,
T9641 414-418 RB denotes only
T9642 422-427 NNS denotes genes
T9643 419-421 CD denotes 26
T9644 428-432 VBD denotes were
T9645 433-447 RB denotes differentially
T9646 457-458 . denotes .
T9647 458-577 sentence denotes At the chronic phase of the disease, 184 differentially expressed genes were identified, with 156 downregulated genes.
T9648 459-461 IN denotes At
T9649 536-546 VBN denotes identified
T9650 462-465 DT denotes the
T9651 474-479 NN denotes phase
T9652 466-473 JJ denotes chronic
T9653 480-482 IN denotes of
T9654 483-486 DT denotes the
T9655 487-494 NN denotes disease
T9656 494-496 , denotes ,
T9657 496-499 CD denotes 184
T9658 525-530 NNS denotes genes
T9659 500-514 RB denotes differentially
T9660 515-524 VBN denotes expressed
T9661 531-535 VBD denotes were
T9662 546-548 , denotes ,
T9663 548-552 IN denotes with
T9664 553-556 CD denotes 156
T9665 571-576 NNS denotes genes
T9666 557-570 VBN denotes downregulated
T9667 576-577 . denotes .
T9668 577-648 sentence denotes Only one gene was differentially expressed at all three phases of CIA.
T9669 578-582 RB denotes Only
T9670 587-591 NN denotes gene
T9671 583-586 CD denotes one
T9672 611-620 VBN denotes expressed
T9673 592-595 VBD denotes was
T9674 596-610 RB denotes differentially
T9675 621-623 IN denotes at
T9676 624-627 DT denotes all
T9677 634-640 NNS denotes phases
T9678 628-633 CD denotes three
T9679 641-643 IN denotes of
T9680 644-647 NN denotes CIA
T9681 647-648 . denotes .
T9682 648-796 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 649-656 IN denotes Besides
T9684 722-728 VBN denotes shared
T9685 657-661 DT denotes this
T9686 662-666 NN denotes gene
T9687 666-668 , denotes ,
T9688 668-672 CD denotes five
T9689 711-716 NNS denotes genes
T9690 672-674 , denotes ,
T9691 674-677 CD denotes one
T9692 678-681 CC denotes and
T9693 682-685 CD denotes six
T9694 686-700 RB denotes differentially
T9695 701-710 VBN denotes expressed
T9696 717-721 VBD denotes were
T9697 729-731 IN denotes by
T9698 732-734 NN denotes PI
T9699 735-739 IN denotes with
T9700 740-742 NN denotes OA
T9701 742-744 , denotes ,
T9702 744-746 NN denotes PI
T9703 747-751 IN denotes with
T9704 752-754 NN denotes CA
T9705 755-758 CC denotes and
T9706 759-761 NN denotes OA
T9707 762-766 IN denotes with
T9708 767-769 NN denotes CA
T9709 769-771 , denotes ,
T9710 771-783 RB denotes respectively
T9711 784-785 -LRB- denotes (
T9712 792-794 NN denotes 2a
T9713 785-791 NN denotes Figure
T9714 794-795 -RRB- denotes )
T9715 795-796 . denotes .
T9716 796-940 sentence denotes Taken together, 310 disease-specific differentially expressed genes were differentially regulated during CIA in DBA/1 mice (Additional file 2).
T9717 797-802 VBN denotes Taken
T9718 885-894 VBN denotes regulated
T9719 803-811 RB denotes together
T9720 811-813 , denotes ,
T9721 813-816 CD denotes 310
T9722 859-864 NNS denotes genes
T9723 817-824 NN denotes disease
T9724 825-833 JJ denotes specific
T9725 824-825 HYPH denotes -
T9726 834-848 RB denotes differentially
T9727 849-858 VBN denotes expressed
T9728 865-869 VBD denotes were
T9729 870-884 RB denotes differentially
T9730 895-901 IN denotes during
T9731 902-905 NN denotes CIA
T9732 906-908 IN denotes in
T9733 909-912 NN denotes DBA
T9734 915-919 NNS denotes mice
T9735 912-913 HYPH denotes /
T9736 913-914 CD denotes 1
T9737 920-921 -LRB- denotes (
T9738 932-936 NN denotes file
T9739 921-931 JJ denotes Additional
T9740 937-938 CD denotes 2
T9741 938-939 -RRB- denotes )
T9742 939-940 . denotes .
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

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
T9495 571-576 SO_EXT:0000704 denotes genes
T9496 587-591 SO_EXT:0000704 denotes gene
T9497 611-620 GO:0010467 denotes expressed
T9498 662-666 SO_EXT:0000704 denotes gene
T9499 701-710 GO:0010467 denotes expressed
T9500 711-716 SO_EXT:0000704 denotes genes
T9482 48-57 GO:0010467 denotes expressed
T9483 58-63 SO_EXT:0000704 denotes genes
T9484 88-93 SO_EXT:0000704 denotes genes
T9485 119-128 GO:0010467 denotes expressed
T9486 132-135 UBERON:0000029 denotes LNs
T9487 287-292 SO_EXT:0000704 denotes genes
T9488 313-322 GO:0010467 denotes expressed
T9489 343-354 GO_EXT:positive_regulation denotes upregulated
T9490 422-427 SO_EXT:0000704 denotes genes
T9491 448-457 GO:0010467 denotes expressed
T9492 515-524 GO:0010467 denotes expressed
T9493 525-530 SO_EXT:0000704 denotes genes
T9494 557-570 GO_EXT:negative_regulation denotes downregulated
T9501 849-858 GO:0010467 denotes expressed
T9502 859-864 SO_EXT:0000704 denotes genes
T9503 885-894 GO:0065007 denotes regulated
T9504 915-919 NCBITaxon:10088 denotes mice

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
T9424 48-57 GO:0010467 denotes expressed
T9425 58-63 SO:0000704 denotes genes
T9426 88-93 SO:0000704 denotes genes
T9427 119-128 GO:0010467 denotes expressed
T9428 132-135 UBERON:0000029 denotes LNs
T9429 287-292 SO:0000704 denotes genes
T9430 313-322 GO:0010467 denotes expressed
T9431 422-427 SO:0000704 denotes genes
T9432 448-457 GO:0010467 denotes expressed
T9433 515-524 GO:0010467 denotes expressed
T9434 525-530 SO:0000704 denotes genes
T9435 571-576 SO:0000704 denotes genes
T9436 587-591 SO:0000704 denotes gene
T9437 611-620 GO:0010467 denotes expressed
T9438 662-666 SO:0000704 denotes gene
T9439 701-710 GO:0010467 denotes expressed
T9440 711-716 SO:0000704 denotes genes
T9441 849-858 GO:0010467 denotes expressed
T9442 859-864 SO:0000704 denotes genes
T9443 885-894 GO:0065007 denotes regulated
T9444 915-919 NCBITaxon:10088 denotes mice