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PMC:1253828 / 7706-9665 JSONTXT

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Id Subject Object Predicate Lexical cue
T2531 0-10 NN denotes Microarray
T2532 11-19 NN denotes analysis
T2533 20-23 CC denotes and
T2534 24-28 NNS denotes data
T2535 29-39 NN denotes processing
T2536 39-265 sentence denotes Total RNA was isolated from liver tissue of pI–pC-induced, mock- or cadmium-treated Mtf1Mx-cre and Mtf1loxP mice (n = 3 per genotype and respective treatment; all male) essentially as described by Chomczynski and Sacchi (27).
T2537 40-45 JJ denotes Total
T2538 46-49 NN denotes RNA
T2539 54-62 VBN denotes isolated
T2540 50-53 VBD denotes was
T2541 63-67 IN denotes from
T2542 68-73 NN denotes liver
T2543 74-80 NN denotes tissue
T2544 81-83 IN denotes of
T2545 84-86 NN denotes pI
T2546 87-89 NN denotes pC
T2547 86-87 HYPH denotes –
T2548 90-97 VBN denotes induced
T2549 89-90 HYPH denotes -
T2550 148-152 NNS denotes mice
T2551 97-99 , denotes ,
T2552 99-103 JJ denotes mock
T2553 116-123 VBN denotes treated
T2554 103-104 HYPH denotes -
T2555 105-107 CC denotes or
T2556 108-115 NN denotes cadmium
T2557 115-116 HYPH denotes -
T2558 124-130 NN denotes Mtf1Mx
T2559 131-134 NN denotes cre
T2560 130-131 HYPH denotes -
T2561 135-138 CC denotes and
T2562 139-147 NN denotes Mtf1loxP
T2563 153-154 -LRB- denotes (
T2564 203-207 JJ denotes male
T2565 154-155 NN denotes n
T2566 158-159 CD denotes 3
T2567 156-157 SYM denotes =
T2568 160-163 IN denotes per
T2569 164-172 NN denotes genotype
T2570 173-176 CC denotes and
T2571 177-187 JJ denotes respective
T2572 188-197 NN denotes treatment
T2573 197-198 : denotes ;
T2574 199-202 DT denotes all
T2575 207-208 -RRB- denotes )
T2576 209-220 RB denotes essentially
T2577 224-233 VBN denotes described
T2578 221-223 IN denotes as
T2579 234-236 IN denotes by
T2580 237-248 NNP denotes Chomczynski
T2581 249-252 CC denotes and
T2582 253-259 NNP denotes Sacchi
T2583 260-261 -LRB- denotes (
T2584 261-263 CD denotes 27
T2585 263-264 -RRB- denotes )
T2586 264-265 . denotes .
T2587 265-490 sentence denotes Gene expression analysis was performed in the Functional Genomics Center Zurich using GeneChip® Mouse Genome 430 2.0 Arrays (Affymetrix) according to the manufacturer's instructions and the following reagents and conditions.
T2588 266-270 NN denotes Gene
T2589 271-281 NN denotes expression
T2590 282-290 NN denotes analysis
T2591 295-304 VBN denotes performed
T2592 291-294 VBD denotes was
T2593 305-307 IN denotes in
T2594 308-311 DT denotes the
T2595 332-338 NNP denotes Center
T2596 312-322 NNP denotes Functional
T2597 323-331 NNP denotes Genomics
T2598 339-345 NNP denotes Zurich
T2599 346-351 VBG denotes using
T2600 352-361 NNP denotes GeneChip®
T2601 383-389 NNS denotes Arrays
T2602 362-367 NNP denotes Mouse
T2603 368-374 NNP denotes Genome
T2604 375-378 CD denotes 430
T2605 379-382 CD denotes 2.0
T2606 390-391 -LRB- denotes (
T2607 391-401 NNP denotes Affymetrix
T2608 401-402 -RRB- denotes )
T2609 403-412 VBG denotes according
T2610 413-415 IN denotes to
T2611 416-419 DT denotes the
T2612 420-432 NN denotes manufacturer
T2613 435-447 NNS denotes instructions
T2614 432-434 POS denotes 's
T2615 448-451 CC denotes and
T2616 452-455 DT denotes the
T2617 466-474 NNS denotes reagents
T2618 456-465 VBG denotes following
T2619 475-478 CC denotes and
T2620 479-489 NNS denotes conditions
T2621 489-490 . denotes .
T2622 490-601 sentence denotes cDNA was synthesized with SuperScript™ Double-Stranded cDNA Synthesis Kit (Invitrogen), using 15 µg total RNA.
T2623 491-495 NN denotes cDNA
T2624 500-511 VBN denotes synthesized
T2625 496-499 VBD denotes was
T2626 512-516 IN denotes with
T2627 517-528 NNP denotes SuperScript
T2628 561-564 NN denotes Kit
T2629 528-529 SYM denotes ™
T2630 530-536 JJ denotes Double
T2631 537-545 VBN denotes Stranded
T2632 536-537 HYPH denotes -
T2633 546-550 NN denotes cDNA
T2634 551-560 NN denotes Synthesis
T2635 565-566 -LRB- denotes (
T2636 566-576 NNP denotes Invitrogen
T2637 576-577 -RRB- denotes )
T2638 577-579 , denotes ,
T2639 579-584 VBG denotes using
T2640 585-587 CD denotes 15
T2641 588-590 NN denotes µg
T2642 597-600 NN denotes RNA
T2643 591-596 JJ denotes total
T2644 600-601 . denotes .
T2645 601-730 sentence denotes In vitro transcription was performed with BioArray™ High Yield™ RNA Transcript Labeling Kit (Enzo) and 3.5 to 6 µg of each cDNA.
T2646 602-604 FW denotes In
T2647 605-610 FW denotes vitro
T2648 611-624 NN denotes transcription
T2649 629-638 VBN denotes performed
T2650 625-628 VBD denotes was
T2651 639-643 IN denotes with
T2652 644-652 NNP denotes BioArray
T2653 690-693 NN denotes Kit
T2654 652-653 SYM denotes ™
T2655 654-658 NNP denotes High
T2656 659-664 NNP denotes Yield
T2657 664-665 SYM denotes ™
T2658 666-669 NN denotes RNA
T2659 670-680 NN denotes Transcript
T2660 681-689 NN denotes Labeling
T2661 694-695 -LRB- denotes (
T2662 695-699 NNP denotes Enzo
T2663 699-700 -RRB- denotes )
T2664 701-704 CC denotes and
T2665 705-708 CD denotes 3.5
T2666 712-713 CD denotes 6
T2667 709-711 IN denotes to
T2668 714-716 NN denotes µg
T2669 717-719 IN denotes of
T2670 720-724 DT denotes each
T2671 725-729 NN denotes cDNA
T2672 729-730 . denotes .
T2673 730-831 sentence denotes Clean-up of both cDNA and cRNA samples was done using GeneChip® Sample Clean-up Module (Affymetrix).
T2674 731-736 NN denotes Clean
T2675 737-739 NN denotes up
T2676 736-737 HYPH denotes -
T2677 774-778 VBN denotes done
T2678 740-742 IN denotes of
T2679 743-747 CC denotes both
T2680 748-752 NN denotes cDNA
T2681 762-769 NNS denotes samples
T2682 753-756 CC denotes and
T2683 757-761 NN denotes cRNA
T2684 770-773 VBD denotes was
T2685 779-784 VBG denotes using
T2686 785-794 NNP denotes GeneChip®
T2687 811-817 NNP denotes Module
T2688 795-801 NNP denotes Sample
T2689 802-807 NNP denotes Clean
T2690 808-810 NNP denotes up
T2691 807-808 HYPH denotes -
T2692 818-819 -LRB- denotes (
T2693 819-829 NNP denotes Affymetrix
T2694 829-830 -RRB- denotes )
T2695 830-831 . denotes .
T2696 831-949 sentence denotes For the automated washing and staining in the Affymetrix fluidics station 450, the protocol EukGE-Ws2v4_450 was used.
T2697 832-835 IN denotes For
T2698 944-948 VBN denotes used
T2699 836-839 DT denotes the
T2700 850-857 NN denotes washing
T2701 840-849 VBN denotes automated
T2702 858-861 CC denotes and
T2703 862-870 NN denotes staining
T2704 871-873 IN denotes in
T2705 874-877 DT denotes the
T2706 898-905 NN denotes station
T2707 878-888 NNP denotes Affymetrix
T2708 889-897 NN denotes fluidics
T2709 906-909 CD denotes 450
T2710 909-911 , denotes ,
T2711 911-914 DT denotes the
T2712 930-939 NN denotes Ws2v4_450
T2713 915-923 NN denotes protocol
T2714 924-929 NN denotes EukGE
T2715 929-930 HYPH denotes -
T2716 940-943 VBD denotes was
T2717 948-949 . denotes .
T2718 949-1016 sentence denotes The probe arrays were scanned with the Affymetrix GS 3000 scanner.
T2719 950-953 DT denotes The
T2720 960-966 NNS denotes arrays
T2721 954-959 NN denotes probe
T2722 972-979 VBN denotes scanned
T2723 967-971 VBD denotes were
T2724 980-984 IN denotes with
T2725 985-988 DT denotes the
T2726 1008-1015 NN denotes scanner
T2727 989-999 NNP denotes Affymetrix
T2728 1000-1002 NNP denotes GS
T2729 1003-1007 CD denotes 3000
T2730 1015-1016 . denotes .
T2731 1016-1088 sentence denotes Raw data are available at ArrayExpress (, accession number E-MEXP-438).
T2732 1017-1020 JJ denotes Raw
T2733 1021-1025 NNS denotes data
T2734 1026-1029 VBP denotes are
T2735 1030-1039 JJ denotes available
T2736 1040-1042 IN denotes at
T2737 1043-1055 NNP denotes ArrayExpress
T2738 1056-1057 -LRB- denotes (
T2739 1078-1082 NN denotes MEXP
T2740 1057-1059 , denotes ,
T2741 1059-1068 NN denotes accession
T2742 1069-1075 NN denotes number
T2743 1076-1077 NN denotes E
T2744 1077-1078 HYPH denotes -
T2745 1082-1083 HYPH denotes -
T2746 1083-1086 CD denotes 438
T2747 1086-1087 -RRB- denotes )
T2748 1087-1088 . denotes .
T2749 1088-1205 sentence denotes Data analysis was performed with GeneSpring 6.1 software (Silicon Genetics), applying a significance level P ≤ 0.05.
T2750 1089-1093 NNS denotes Data
T2751 1094-1102 NN denotes analysis
T2752 1107-1116 VBN denotes performed
T2753 1103-1106 VBD denotes was
T2754 1117-1121 IN denotes with
T2755 1122-1132 NNP denotes GeneSpring
T2756 1137-1145 NN denotes software
T2757 1133-1136 CD denotes 6.1
T2758 1146-1147 -LRB- denotes (
T2759 1155-1163 NNP denotes Genetics
T2760 1147-1154 NNP denotes Silicon
T2761 1163-1164 -RRB- denotes )
T2762 1164-1166 , denotes ,
T2763 1166-1174 VBG denotes applying
T2764 1175-1176 DT denotes a
T2765 1190-1195 NN denotes level
T2766 1177-1189 NN denotes significance
T2767 1196-1197 NN denotes P
T2768 1200-1204 CD denotes 0.05
T2769 1198-1199 SYM denotes ≤
T2770 1204-1205 . denotes .
T2771 1205-1322 sentence denotes Furthermore, multiple testing correction was used in addition to obtain cadmium-responsive, MTF-1-independent genes.
T2772 1206-1217 RB denotes Furthermore
T2773 1251-1255 VBN denotes used
T2774 1217-1219 , denotes ,
T2775 1219-1227 JJ denotes multiple
T2776 1236-1246 NN denotes correction
T2777 1228-1235 NN denotes testing
T2778 1247-1250 VBD denotes was
T2779 1256-1258 IN denotes in
T2780 1259-1267 NN denotes addition
T2781 1268-1270 TO denotes to
T2782 1271-1277 VB denotes obtain
T2783 1278-1285 NN denotes cadmium
T2784 1286-1296 JJ denotes responsive
T2785 1285-1286 HYPH denotes -
T2786 1316-1321 NNS denotes genes
T2787 1296-1298 , denotes ,
T2788 1298-1301 NN denotes MTF
T2789 1304-1315 JJ denotes independent
T2790 1301-1302 HYPH denotes -
T2791 1302-1303 CD denotes 1
T2792 1303-1304 HYPH denotes -
T2793 1321-1322 . denotes .
T2794 1322-1511 sentence denotes Genes were considered to be differentially expressed if there was at least a 2-fold difference in expression levels of the compared experimental groups (genotype and respective treatment).
T2795 1323-1328 NNS denotes Genes
T2796 1334-1344 VBN denotes considered
T2797 1329-1333 VBD denotes were
T2798 1345-1347 TO denotes to
T2799 1366-1375 VBN denotes expressed
T2800 1348-1350 VB denotes be
T2801 1351-1365 RB denotes differentially
T2802 1376-1378 IN denotes if
T2803 1385-1388 VBD denotes was
T2804 1379-1384 EX denotes there
T2805 1389-1391 RB denotes at
T2806 1392-1397 RBS denotes least
T2807 1400-1406 JJ denotes 2-fold
T2808 1398-1399 DT denotes a
T2809 1407-1417 NN denotes difference
T2810 1418-1420 IN denotes in
T2811 1421-1431 NN denotes expression
T2812 1432-1438 NNS denotes levels
T2813 1439-1441 IN denotes of
T2814 1442-1445 DT denotes the
T2815 1468-1474 NNS denotes groups
T2816 1446-1454 VBN denotes compared
T2817 1455-1467 JJ denotes experimental
T2818 1475-1476 -LRB- denotes (
T2819 1476-1484 NN denotes genotype
T2820 1485-1488 CC denotes and
T2821 1489-1499 JJ denotes respective
T2822 1500-1509 NN denotes treatment
T2823 1509-1510 -RRB- denotes )
T2824 1510-1511 . denotes .
T2825 1511-1696 sentence denotes The result was considered reliable if signal values for the respective gene were scored ‘present’ at least for all mice in one experimental group or for two mice in each of two groups.
T2826 1512-1515 DT denotes The
T2827 1516-1522 NN denotes result
T2828 1527-1537 VBN denotes considered
T2829 1523-1526 VBD denotes was
T2830 1538-1546 JJ denotes reliable
T2831 1547-1549 IN denotes if
T2832 1593-1599 VBN denotes scored
T2833 1550-1556 NN denotes signal
T2834 1557-1563 NNS denotes values
T2835 1564-1567 IN denotes for
T2836 1568-1571 DT denotes the
T2837 1583-1587 NN denotes gene
T2838 1572-1582 JJ denotes respective
T2839 1588-1592 VBD denotes were
T2840 1600-1601 `` denotes ‘
T2841 1601-1608 JJ denotes present
T2842 1608-1609 '' denotes ’
T2843 1610-1612 RB denotes at
T2844 1613-1618 RBS denotes least
T2845 1619-1622 IN denotes for
T2846 1623-1626 DT denotes all
T2847 1627-1631 NNS denotes mice
T2848 1632-1634 IN denotes in
T2849 1635-1638 CD denotes one
T2850 1652-1657 NN denotes group
T2851 1639-1651 JJ denotes experimental
T2852 1658-1660 CC denotes or
T2853 1661-1664 IN denotes for
T2854 1665-1668 CD denotes two
T2855 1669-1673 NNS denotes mice
T2856 1674-1676 IN denotes in
T2857 1677-1681 DT denotes each
T2858 1682-1684 IN denotes of
T2859 1685-1688 CD denotes two
T2860 1689-1695 NNS denotes groups
T2861 1695-1696 . denotes .
T2862 1696-1959 sentence denotes To screen for the presence of the MRE core consensus sequence TGCRCNC in the promoter region, the upstream sequences of the respective genes were obtained from the University of California Santa Cruz (UCSC) Genome Browser Database (; October/November 2004) (28).
T2863 1697-1699 TO denotes To
T2864 1700-1706 VB denotes screen
T2865 1843-1851 VBN denotes obtained
T2866 1707-1710 IN denotes for
T2867 1711-1714 DT denotes the
T2868 1715-1723 NN denotes presence
T2869 1724-1726 IN denotes of
T2870 1727-1730 DT denotes the
T2871 1750-1758 NN denotes sequence
T2872 1731-1734 NN denotes MRE
T2873 1735-1739 NN denotes core
T2874 1740-1749 NN denotes consensus
T2875 1759-1766 NN denotes TGCRCNC
T2876 1767-1769 IN denotes in
T2877 1770-1773 DT denotes the
T2878 1783-1789 NN denotes region
T2879 1774-1782 NN denotes promoter
T2880 1789-1791 , denotes ,
T2881 1791-1794 DT denotes the
T2882 1804-1813 NNS denotes sequences
T2883 1795-1803 JJ denotes upstream
T2884 1814-1816 IN denotes of
T2885 1817-1820 DT denotes the
T2886 1832-1837 NNS denotes genes
T2887 1821-1831 JJ denotes respective
T2888 1838-1842 VBD denotes were
T2889 1852-1856 IN denotes from
T2890 1857-1860 DT denotes the
T2891 1919-1927 NNP denotes Database
T2892 1861-1871 NNP denotes University
T2893 1872-1874 IN denotes of
T2894 1875-1885 NNP denotes California
T2895 1892-1896 NNP denotes Cruz
T2896 1886-1891 NNP denotes Santa
T2897 1897-1898 -LRB- denotes (
T2898 1898-1902 NNP denotes UCSC
T2899 1902-1903 -RRB- denotes )
T2900 1904-1910 NNP denotes Genome
T2901 1911-1918 NNP denotes Browser
T2902 1928-1929 -LRB- denotes (
T2903 1939-1947 NNP denotes November
T2904 1929-1930 : denotes ;
T2905 1931-1938 NNP denotes October
T2906 1938-1939 SYM denotes /
T2907 1948-1952 CD denotes 2004
T2908 1952-1953 -RRB- denotes )
T2909 1954-1955 -LRB- denotes (
T2910 1955-1957 CD denotes 28
T2911 1957-1958 -RRB- denotes )
T2912 1958-1959 . denotes .
R1487 T2531 T2532 compound Microarray,analysis
R1488 T2533 T2532 cc and,analysis
R1489 T2534 T2535 compound data,processing
R1490 T2535 T2532 conj processing,analysis
R1491 T2537 T2538 amod Total,RNA
R1492 T2538 T2539 nsubjpass RNA,isolated
R1493 T2540 T2539 auxpass was,isolated
R1494 T2541 T2539 prep from,isolated
R1495 T2542 T2543 compound liver,tissue
R1496 T2543 T2541 pobj tissue,from
R1497 T2544 T2543 prep of,tissue
R1498 T2545 T2546 compound pI,pC
R1499 T2546 T2548 npadvmod pC,induced
R1500 T2547 T2546 punct –,pC
R1501 T2548 T2550 amod induced,mice
R1502 T2549 T2548 punct -,induced
R1503 T2550 T2544 pobj mice,of
R1504 T2551 T2550 punct ", ",mice
R1505 T2552 T2553 amod mock,treated
R1506 T2553 T2550 amod treated,mice
R1507 T2554 T2552 punct -,mock
R1508 T2555 T2552 cc or,mock
R1509 T2556 T2552 conj cadmium,mock
R1510 T2557 T2553 punct -,treated
R1511 T2558 T2559 nmod Mtf1Mx,cre
R1512 T2559 T2550 nmod cre,mice
R1513 T2560 T2559 punct -,cre
R1514 T2561 T2559 cc and,cre
R1515 T2562 T2559 conj Mtf1loxP,cre
R1516 T2563 T2564 punct (,male
R1517 T2564 T2544 parataxis male,of
R1518 T2565 T2566 nsubj n,3
R1519 T2566 T2564 ccomp 3,male
R1520 T2567 T2566 punct =,3
R1521 T2568 T2566 prep per,3
R1522 T2569 T2568 pobj genotype,per
R1523 T2570 T2569 cc and,genotype
R1524 T2571 T2572 amod respective,treatment
R1525 T2572 T2569 conj treatment,genotype
R1526 T2573 T2564 punct ;,male
R1527 T2574 T2564 det all,male
R1528 T2575 T2564 punct ),male
R1529 T2576 T2577 advmod essentially,described
R1530 T2577 T2539 advcl described,isolated
R1531 T2578 T2577 mark as,described
R1532 T2579 T2577 agent by,described
R1533 T2580 T2579 pobj Chomczynski,by
R1534 T2581 T2580 cc and,Chomczynski
R1535 T2582 T2580 conj Sacchi,Chomczynski
R1536 T2583 T2584 punct (,27
R1537 T2584 T2577 parataxis 27,described
R1538 T2585 T2584 punct ),27
R1539 T2586 T2539 punct .,isolated
R1540 T2588 T2589 compound Gene,expression
R1541 T2589 T2590 compound expression,analysis
R1542 T2590 T2591 nsubjpass analysis,performed
R1543 T2592 T2591 auxpass was,performed
R1544 T2593 T2591 prep in,performed
R1545 T2594 T2595 det the,Center
R1546 T2595 T2593 pobj Center,in
R1547 T2596 T2597 compound Functional,Genomics
R1548 T2597 T2595 compound Genomics,Center
R1549 T2598 T2595 npadvmod Zurich,Center
R1550 T2599 T2591 advcl using,performed
R1551 T2600 T2601 nmod GeneChip®,Arrays
R1552 T2601 T2599 dobj Arrays,using
R1553 T2602 T2603 nmod Mouse,Genome
R1554 T2603 T2601 nmod Genome,Arrays
R1555 T2604 T2603 nummod 430,Genome
R1556 T2605 T2601 nummod 2.0,Arrays
R1557 T2606 T2607 punct (,Affymetrix
R1558 T2607 T2601 parataxis Affymetrix,Arrays
R1559 T2608 T2607 punct ),Affymetrix
R1560 T2609 T2599 prep according,using
R1561 T2610 T2609 prep to,according
R1562 T2611 T2612 det the,manufacturer
R1563 T2612 T2613 poss manufacturer,instructions
R1564 T2613 T2610 pobj instructions,to
R1565 T2614 T2612 case 's,manufacturer
R1566 T2615 T2613 cc and,instructions
R1567 T2616 T2617 det the,reagents
R1568 T2617 T2613 conj reagents,instructions
R1569 T2618 T2617 amod following,reagents
R1570 T2619 T2617 cc and,reagents
R1571 T2620 T2617 conj conditions,reagents
R1572 T2621 T2591 punct .,performed
R1573 T2623 T2624 nsubjpass cDNA,synthesized
R1574 T2625 T2624 auxpass was,synthesized
R1575 T2626 T2624 prep with,synthesized
R1576 T2627 T2628 nmod SuperScript,Kit
R1578 T2629 T2627 punct ™,SuperScript
R1579 T2630 T2631 amod Double,Stranded
R1580 T2631 T2628 amod Stranded,Kit
R1581 T2632 T2631 punct -,Stranded
R1582 T2633 T2628 compound cDNA,Kit
R1583 T2634 T2628 compound Synthesis,Kit
R1584 T2635 T2636 punct (,Invitrogen
R1585 T2636 T2628 parataxis Invitrogen,Kit
R1586 T2637 T2636 punct ),Invitrogen
R1587 T2638 T2624 punct ", ",synthesized
R1588 T2639 T2624 advcl using,synthesized
R1589 T2640 T2641 nummod 15,µg
R1590 T2641 T2642 nmod µg,RNA
R1591 T2642 T2639 dobj RNA,using
R1592 T2643 T2642 amod total,RNA
R1593 T2644 T2624 punct .,synthesized
R1594 T2646 T2647 advmod In,vitro
R1595 T2647 T2648 amod vitro,transcription
R1596 T2648 T2649 nsubjpass transcription,performed
R1597 T2650 T2649 auxpass was,performed
R1598 T2651 T2649 prep with,performed
R1599 T2652 T2653 nmod BioArray,Kit
R1600 T2653 T2651 pobj Kit,with
R1601 T2654 T2652 punct ™,BioArray
R1602 T2655 T2656 nmod High,Yield
R1603 T2656 T2653 nmod Yield,Kit
R1604 T2657 T2656 punct ™,Yield
R1605 T2658 T2653 compound RNA,Kit
R1606 T2659 T2653 compound Transcript,Kit
R1607 T2660 T2653 compound Labeling,Kit
R1608 T2661 T2662 punct (,Enzo
R1609 T2662 T2653 parataxis Enzo,Kit
R1610 T2663 T2662 punct ),Enzo
R1611 T2664 T2653 cc and,Kit
R1612 T2665 T2666 quantmod 3.5,6
R1613 T2666 T2668 nummod 6,µg
R1614 T2667 T2666 quantmod to,6
R1615 T2668 T2653 conj µg,Kit
R1616 T2669 T2668 prep of,µg
R1617 T2670 T2671 det each,cDNA
R1618 T2671 T2669 pobj cDNA,of
R1619 T2672 T2649 punct .,performed
R1620 T2674 T2675 compound Clean,up
R1621 T2675 T2677 nsubjpass up,done
R1622 T2676 T2675 punct -,up
R1623 T2678 T2675 prep of,up
R1624 T2679 T2680 preconj both,cDNA
R1625 T2680 T2681 nmod cDNA,samples
R1626 T2681 T2678 pobj samples,of
R1627 T2682 T2680 cc and,cDNA
R1628 T2683 T2680 conj cRNA,cDNA
R1629 T2684 T2677 auxpass was,done
R1630 T2685 T2677 advcl using,done
R1631 T2686 T2687 compound GeneChip®,Module
R1632 T2687 T2685 dobj Module,using
R1633 T2688 T2687 compound Sample,Module
R1634 T2689 T2690 compound Clean,up
R1635 T2690 T2687 compound up,Module
R1636 T2691 T2690 punct -,up
R1637 T2692 T2693 punct (,Affymetrix
R1638 T2693 T2687 parataxis Affymetrix,Module
R1639 T2694 T2693 punct ),Affymetrix
R1640 T2695 T2677 punct .,done
R1641 T2697 T2698 prep For,used
R1642 T2699 T2700 det the,washing
R1643 T2700 T2697 pobj washing,For
R1644 T2701 T2700 amod automated,washing
R1645 T2702 T2700 cc and,washing
R1646 T2703 T2700 conj staining,washing
R1647 T2704 T2700 prep in,washing
R1648 T2705 T2706 det the,station
R1649 T2706 T2704 pobj station,in
R1650 T2707 T2706 compound Affymetrix,station
R1651 T2708 T2706 compound fluidics,station
R1652 T2709 T2706 nummod 450,station
R1653 T2710 T2698 punct ", ",used
R1654 T2711 T2712 det the,Ws2v4_450
R1655 T2712 T2698 nsubjpass Ws2v4_450,used
R1656 T2713 T2712 compound protocol,Ws2v4_450
R1657 T2714 T2712 compound EukGE,Ws2v4_450
R1658 T2715 T2712 punct -,Ws2v4_450
R1659 T2716 T2698 auxpass was,used
R1660 T2717 T2698 punct .,used
R1661 T2719 T2720 det The,arrays
R1662 T2720 T2722 nsubjpass arrays,scanned
R1663 T2721 T2720 compound probe,arrays
R1664 T2723 T2722 auxpass were,scanned
R1665 T2724 T2722 prep with,scanned
R1666 T2725 T2726 det the,scanner
R1667 T2726 T2724 pobj scanner,with
R1668 T2727 T2728 nmod Affymetrix,GS
R1669 T2728 T2726 nmod GS,scanner
R1670 T2729 T2728 nummod 3000,GS
R1671 T2730 T2722 punct .,scanned
R1672 T2732 T2733 amod Raw,data
R1673 T2733 T2734 nsubj data,are
R1674 T2735 T2734 acomp available,are
R1675 T2736 T2734 prep at,are
R1676 T2737 T2736 pobj ArrayExpress,at
R1677 T2738 T2739 punct (,MEXP
R1678 T2739 T2734 parataxis MEXP,are
R1679 T2740 T2739 punct ", ",MEXP
R1680 T2741 T2742 compound accession,number
R1681 T2742 T2739 compound number,MEXP
R1682 T2743 T2739 compound E,MEXP
R1683 T2744 T2739 punct -,MEXP
R1684 T2745 T2739 punct -,MEXP
R1685 T2746 T2739 nummod 438,MEXP
R1686 T2747 T2739 punct ),MEXP
R1687 T2748 T2734 punct .,are
R1688 T2750 T2751 compound Data,analysis
R1689 T2751 T2752 nsubjpass analysis,performed
R1690 T2753 T2752 auxpass was,performed
R1691 T2754 T2752 prep with,performed
R1692 T2755 T2756 nmod GeneSpring,software
R1693 T2756 T2754 pobj software,with
R1694 T2757 T2756 nummod 6.1,software
R1695 T2758 T2759 punct (,Genetics
R1696 T2759 T2756 parataxis Genetics,software
R1697 T2760 T2759 compound Silicon,Genetics
R1698 T2761 T2759 punct ),Genetics
R1699 T2762 T2752 punct ", ",performed
R1700 T2763 T2752 advcl applying,performed
R1701 T2764 T2765 det a,level
R1702 T2765 T2763 dobj level,applying
R1703 T2766 T2765 compound significance,level
R1704 T2767 T2768 nsubj P,0.05
R1705 T2768 T2765 appos 0.05,level
R1706 T2769 T2768 punct ≤,0.05
R1707 T2770 T2752 punct .,performed
R1708 T2772 T2773 advmod Furthermore,used
R1709 T2774 T2773 punct ", ",used
R1710 T2775 T2776 amod multiple,correction
R1711 T2776 T2773 nsubjpass correction,used
R1712 T2777 T2776 compound testing,correction
R1713 T2778 T2773 auxpass was,used
R1714 T2779 T2773 prep in,used
R1715 T2780 T2779 pobj addition,in
R1716 T2781 T2782 aux to,obtain
R1717 T2782 T2773 advcl obtain,used
R1718 T2783 T2784 npadvmod cadmium,responsive
R1719 T2784 T2786 amod responsive,genes
R1720 T2785 T2784 punct -,responsive
R1722 T2787 T2786 punct ", ",genes
R1723 T2788 T2789 npadvmod MTF,independent
R1724 T2789 T2786 amod independent,genes
R1725 T2790 T2788 punct -,MTF
R1726 T2791 T2788 nummod 1,MTF
R1727 T2792 T2789 punct -,independent
R1728 T2793 T2773 punct .,used
R1729 T2795 T2796 nsubjpass Genes,considered
R1730 T2797 T2796 auxpass were,considered
R1731 T2798 T2799 aux to,expressed
R1732 T2799 T2796 xcomp expressed,considered
R1733 T2800 T2799 auxpass be,expressed
R1734 T2801 T2799 advmod differentially,expressed
R1735 T2802 T2803 mark if,was
R1736 T2803 T2799 advcl was,expressed
R1737 T2804 T2803 expl there,was
R1738 T2805 T2806 advmod at,least
R1739 T2806 T2807 advmod least,2-fold
R1740 T2807 T2809 nummod 2-fold,difference
R1741 T2808 T2807 quantmod a,2-fold
R1742 T2809 T2803 attr difference,was
R1743 T2810 T2809 prep in,difference
R1744 T2811 T2812 compound expression,levels
R1745 T2812 T2810 pobj levels,in
R1746 T2813 T2812 prep of,levels
R1747 T2814 T2815 det the,groups
R1748 T2815 T2813 pobj groups,of
R1749 T2816 T2815 amod compared,groups
R1750 T2817 T2815 amod experimental,groups
R1751 T2818 T2819 punct (,genotype
R1752 T2819 T2803 parataxis genotype,was
R1753 T2820 T2819 cc and,genotype
R1754 T2821 T2822 amod respective,treatment
R1755 T2822 T2819 conj treatment,genotype
R1756 T2823 T2819 punct ),genotype
R1757 T2824 T2796 punct .,considered
R1758 T2826 T2827 det The,result
R1759 T2827 T2828 nsubjpass result,considered
R1760 T2829 T2828 auxpass was,considered
R1761 T2830 T2828 oprd reliable,considered
R1762 T2831 T2832 mark if,scored
R1763 T2832 T2828 advcl scored,considered
R1764 T2833 T2834 compound signal,values
R1765 T2834 T2832 nsubjpass values,scored
R1766 T2835 T2834 prep for,values
R1767 T2836 T2837 det the,gene
R1768 T2837 T2835 pobj gene,for
R1769 T2838 T2837 amod respective,gene
R1770 T2839 T2832 auxpass were,scored
R1771 T2840 T2841 punct ‘,present
R1772 T2841 T2832 oprd present,scored
R1773 T2842 T2832 punct ’,scored
R1774 T2843 T2844 advmod at,least
R1775 T2844 T2845 advmod least,for
R1776 T2845 T2828 prep for,considered
R1777 T2846 T2847 det all,mice
R1778 T2847 T2845 pobj mice,for
R1779 T2848 T2847 prep in,mice
R1780 T2849 T2850 nummod one,group
R1781 T2850 T2848 pobj group,in
R1782 T2851 T2850 amod experimental,group
R1783 T2852 T2845 cc or,for
R1784 T2853 T2845 conj for,for
R1785 T2854 T2855 nummod two,mice
R1786 T2855 T2853 pobj mice,for
R1787 T2856 T2855 prep in,mice
R1788 T2857 T2856 pobj each,in
R1789 T2858 T2857 prep of,each
R1790 T2859 T2860 nummod two,groups
R1791 T2860 T2858 pobj groups,of
R1792 T2861 T2828 punct .,considered
R1793 T2863 T2864 aux To,screen
R1794 T2864 T2865 advcl screen,obtained
R1795 T2866 T2864 prep for,screen
R1796 T2867 T2868 det the,presence
R1797 T2868 T2866 pobj presence,for
R1798 T2869 T2868 prep of,presence
R1799 T2870 T2871 det the,sequence
R1800 T2871 T2869 pobj sequence,of
R1801 T2872 T2871 compound MRE,sequence
R1802 T2873 T2871 compound core,sequence
R1803 T2874 T2871 compound consensus,sequence
R1804 T2875 T2871 appos TGCRCNC,sequence
R1805 T2876 T2868 prep in,presence
R1806 T2877 T2878 det the,region
R1807 T2878 T2876 pobj region,in
R1808 T2879 T2878 compound promoter,region
R1809 T2880 T2865 punct ", ",obtained
R1810 T2881 T2882 det the,sequences
R1811 T2882 T2865 nsubjpass sequences,obtained
R1812 T2883 T2882 amod upstream,sequences
R1813 T2884 T2882 prep of,sequences
R1814 T2885 T2886 det the,genes
R1815 T2886 T2884 pobj genes,of
R1816 T2887 T2886 amod respective,genes
R1817 T2888 T2865 auxpass were,obtained
R1818 T2889 T2865 prep from,obtained
R1819 T2890 T2891 det the,Database
R1820 T2891 T2889 pobj Database,from
R1821 T2892 T2891 nmod University,Database
R1822 T2893 T2892 prep of,University
R1823 T2894 T2895 compound California,Cruz
R1824 T2895 T2893 pobj Cruz,of
R1825 T2896 T2895 compound Santa,Cruz
R1826 T2897 T2892 punct (,University
R1827 T2898 T2892 appos UCSC,University
R1828 T2899 T2891 punct ),Database
R1829 T2900 T2891 compound Genome,Database
R1830 T2901 T2891 compound Browser,Database
R1831 T2902 T2903 punct (,November
R1832 T2903 T2891 parataxis November,Database
R1833 T2904 T2903 punct ;,November
R1834 T2905 T2903 nmod October,November
R1835 T2906 T2903 punct /,November
R1836 T2907 T2903 nummod 2004,November
R1837 T2908 T2903 punct ),November
R1838 T2909 T2910 punct (,28
R1839 T2910 T2891 parataxis 28,Database
R1840 T2911 T2910 punct ),28
R1841 T2912 T2865 punct .,obtained
R1577 T2628 T2626 pobj Kit,with
R1721 T2786 T2782 dobj genes,obtain

2_test

Id Subject Object Predicate Lexical cue
16221973-2440339-77403413 261-263 2440339 denotes 27
16221973-12519945-77403414 1955-1957 12519945 denotes 28

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
T2458 68-73 UBERON:0002107 denotes liver
T2459 74-80 UBERON:0000479 denotes tissue
T2460 84-86 CHEBI:76777 denotes pI
T2461 124-128 PR:000010717 denotes Mtf1
T2462 128-130 PR:000010788 denotes Mx
T2463 139-143 PR:000010717 denotes Mtf1
T2464 143-147 SO:0000346 denotes loxP
T2465 148-152 NCBITaxon:10088 denotes mice
T2466 266-270 SO:0000704 denotes Gene
T2467 266-281 GO:0010467 denotes Gene expression
T2468 362-367 NCBITaxon:10088 denotes Mouse
T2469 368-374 SO:0001026 denotes Genome
T2470 466-474 CHEBI:33893 denotes reagents
T2471 530-545 SO:0000985 denotes Double-Stranded
T2472 670-680 SO:0000673 denotes Transcript
T2473 1298-1303 PR:000010717 denotes MTF-1
T2474 1316-1321 SO:0000704 denotes genes
T2475 1323-1328 SO:0000704 denotes Genes
T2476 1366-1375 GO:0010467 denotes expressed
T2477 1421-1431 GO:0010467 denotes expression
T2478 1583-1587 SO:0000704 denotes gene
T2479 1627-1631 NCBITaxon:10088 denotes mice
T2480 1669-1673 NCBITaxon:10088 denotes mice
T2481 1740-1749 SO:0000993 denotes consensus
T2482 1774-1782 SO:0000167 denotes promoter
T2483 1832-1837 SO:0000704 denotes genes
T2484 1904-1910 SO:0001026 denotes Genome

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
T2485 46-49 CHEBI_SO_EXT:RNA denotes RNA
T2486 68-73 UBERON:0002107 denotes liver
T2487 74-80 UBERON:0000479 denotes tissue
T2488 84-86 CHEBI:76777 denotes pI
T2489 87-89 CHEBI_EXT:polyC_acid denotes pC
T2490 108-115 CHEBI_EXT:cadmium denotes cadmium
T2491 124-128 PR_EXT:000010717 denotes Mtf1
T2492 128-130 PR_EXT:000010788 denotes Mx
T2493 139-143 PR_EXT:000010717 denotes Mtf1
T2494 143-147 SO_EXT:0000346 denotes loxP
T2495 148-152 NCBITaxon:10088 denotes mice
T2496 164-172 SO_EXT:genotype_or_entity_with_genotype denotes genotype
T2497 203-207 PATO_UBERON_EXT:male_or_bearer_of_maleness denotes male
T2498 266-270 SO_EXT:0000704 denotes Gene
T2499 266-281 GO:0010467 denotes Gene expression
T2500 362-367 NCBITaxon:10088 denotes Mouse
T2501 368-374 SO_EXT:0001026 denotes Genome
T2502 466-474 CHEBI_EXT:33893 denotes reagents
T2503 491-495 SO_EXT:cDNA denotes cDNA
T2504 530-550 SO_EXT:double_stranded_complementary_DNA denotes Double-Stranded cDNA
T2505 597-600 CHEBI_SO_EXT:RNA denotes RNA
T2506 611-624 GO_EXT:transcription denotes transcription
T2507 666-669 CHEBI_SO_EXT:RNA denotes RNA
T2508 670-680 SO_EXT:0000673 denotes Transcript
T2509 681-689 CHEBI_SO_EXT:molecular_label_or_mark_or_tag_process denotes Labeling
T2510 725-729 SO_EXT:cDNA denotes cDNA
T2511 748-752 SO_EXT:cDNA denotes cDNA
T2512 954-959 CHEBI_SO_EXT:molecular_probe denotes probe
T2513 1155-1163 OBI_SO_EXT:gene_or_genetic_investigation_or_genetic_process denotes Genetics
T2514 1278-1285 CHEBI_EXT:cadmium denotes cadmium
T2515 1298-1303 PR_EXT:000010717 denotes MTF-1
T2516 1316-1321 SO_EXT:0000704 denotes genes
T2517 1323-1328 SO_EXT:0000704 denotes Genes
T2518 1366-1375 GO:0010467 denotes expressed
T2519 1421-1431 GO:0010467 denotes expression
T2520 1476-1484 SO_EXT:genotype_or_entity_with_genotype denotes genotype
T2521 1583-1587 SO_EXT:0000704 denotes gene
T2522 1627-1631 NCBITaxon:10088 denotes mice
T2523 1669-1673 NCBITaxon:10088 denotes mice
T2524 1740-1749 SO:0000993 denotes consensus
T2525 1750-1758 SO_EXT:biological_sequence denotes sequence
T2526 1774-1782 SO_EXT:0000167 denotes promoter
T2527 1795-1803 SO_EXT:sequence_upstreamness denotes upstream
T2528 1804-1813 SO_EXT:biological_sequence denotes sequences
T2529 1832-1837 SO_EXT:0000704 denotes genes
T2530 1904-1910 SO_EXT:0001026 denotes Genome