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c_corpus

Id Subject Object Predicate Lexical cue
T2 14-18 CVCL_5552 denotes DCIS
T1 14-18 D002285 denotes DCIS
T3 14-18 D002285 denotes DCIS
T4 31-37 UBERON:0000310 denotes breast
T5 31-44 D001943 denotes breast cancer
T6 31-44 D001943 denotes breast cancer
T13 77-81 PR:Q61079 denotes SIM2
T14 77-81 PR:Q14190 denotes SIM2
T15 77-81 PR:P39742 denotes SIM2
T16 77-81 PR:Q9Y812 denotes SIM2
T17 77-81 PR:000014876 denotes SIM2
T18 77-81 CVCL_1Y14 denotes SIM2
T25 102-106 PR:Q61079 denotes SIM2
T26 102-106 PR:Q14190 denotes SIM2
T27 102-106 PR:P39742 denotes SIM2
T28 102-106 PR:Q9Y812 denotes SIM2
T29 102-106 PR:000014876 denotes SIM2
T30 102-106 CVCL_1Y14 denotes SIM2
T33 133-136 CHEBI:27565 denotes PAS
T31 133-136 PR:P33085 denotes PAS
T32 133-136 GO:0000407 denotes PAS
T34 147-160 GO:0006351 denotes transcription
T35 192-215 CL:0002327 denotes mammary epithelial cell
T37 200-231 GO:0030855 denotes epithelial cell differentiation
T45 233-237 PR:Q61079 denotes SIM2
T46 233-237 PR:Q14190 denotes SIM2
T47 233-237 PR:P39742 denotes SIM2
T48 233-237 PR:Q9Y812 denotes SIM2
T49 233-237 PR:000014876 denotes SIM2
T50 233-237 CVCL_1Y14 denotes SIM2
T51 308-313 D006801 denotes human
T52 314-320 UBERON:0000310 denotes breast
T53 314-327 D001943 denotes breast cancer
T54 314-327 D001943 denotes breast cancer
T61 337-341 PR:Q61079 denotes Sim2
T62 337-341 PR:Q14190 denotes Sim2
T63 337-341 PR:P39742 denotes Sim2
T64 337-341 PR:Q9Y812 denotes Sim2
T65 337-341 PR:000014876 denotes Sim2
T66 337-341 CVCL_1Y14 denotes Sim2
T67 359-364 10090 denotes mouse
T68 359-364 D051379 denotes mouse
T75 473-477 PR:Q61079 denotes SIM2
T76 473-477 PR:Q14190 denotes SIM2
T77 473-477 PR:P39742 denotes SIM2
T78 473-477 PR:Q9Y812 denotes SIM2
T79 473-477 PR:000014876 denotes SIM2
T80 473-477 CVCL_1Y14 denotes SIM2
T81 539-544 10090 denotes mouse
T82 539-544 D051379 denotes mouse
T89 577-581 PR:Q61079 denotes SIM2
T90 577-581 PR:Q14190 denotes SIM2
T91 577-581 PR:P39742 denotes SIM2
T92 577-581 PR:Q9Y812 denotes SIM2
T93 577-581 PR:000014876 denotes SIM2
T94 577-581 CVCL_1Y14 denotes SIM2
T95 626-639 UBERON:0001911 denotes mammary gland
T96 626-639 UBERON:0005200 denotes mammary gland
T104 685-689 PR:Q61079 denotes SIM2
T105 685-689 PR:Q14190 denotes SIM2
T106 685-689 PR:P39742 denotes SIM2
T107 685-689 PR:Q9Y812 denotes SIM2
T108 685-689 PR:000014876 denotes SIM2
T109 685-689 CVCL_1Y14 denotes SIM2
T110 701-706 D009369 denotes tumor
T111 701-706 D009369 denotes tumor
T112 701-711 CL:0001063 denotes tumor cell
T113 707-727 GO:0030154 denotes cell differentiation
T120 741-745 PR:Q61079 denotes SIM2
T121 741-745 PR:Q14190 denotes SIM2
T122 741-745 PR:P39742 denotes SIM2
T123 741-745 PR:Q9Y812 denotes SIM2
T124 741-745 PR:000014876 denotes SIM2
T125 741-745 CVCL_1Y14 denotes SIM2
T126 761-766 D006801 denotes human
T127 775-781 UBERON:0000310 denotes breast
T130 782-806 D002285 denotes ductal carcinoma in situ
T131 782-806 D002285 denotes ductal carcinoma in situ
T137 808-812 CVCL_5552 denotes DCIS
T136 808-812 D002285 denotes DCIS
T138 808-812 D002285 denotes DCIS
T145 837-841 PR:Q61079 denotes SIM2
T146 837-841 PR:Q14190 denotes SIM2
T147 837-841 PR:P39742 denotes SIM2
T148 837-841 PR:Q9Y812 denotes SIM2
T149 837-841 PR:000014876 denotes SIM2
T150 837-841 CVCL_1Y14 denotes SIM2
T152 873-877 CVCL_5552 denotes DCIS
T151 873-877 D002285 denotes DCIS
T153 873-877 D002285 denotes DCIS
T156 919-932 CVCL_5552 denotes MCF10DCIS.COM
T157 924-928 D002285 denotes DCIS
T159 924-928 D002285 denotes DCIS
T161 929-932 CHEBI:17905 denotes COM
T168 971-975 PR:Q61079 denotes SIM2
T169 971-975 PR:Q14190 denotes SIM2
T170 971-975 PR:P39742 denotes SIM2
T171 971-975 PR:Q9Y812 denotes SIM2
T172 971-975 PR:000014876 denotes SIM2
T173 971-975 CVCL_1Y14 denotes SIM2
T176 1004-1017 CVCL_5552 denotes MCF10DCIS.COM
T177 1009-1013 D002285 denotes DCIS
T179 1009-1013 D002285 denotes DCIS
T181 1014-1017 CHEBI:17905 denotes COM
T183 1038-1044 CVCL_0598 denotes MCF10A
T184 1041-1044 PR:000002396 denotes 10A
T192 1075-1079 PR:Q61079 denotes SIM2
T193 1075-1079 PR:Q14190 denotes SIM2
T194 1075-1079 PR:P39742 denotes SIM2
T195 1075-1079 PR:Q9Y812 denotes SIM2
T196 1075-1079 PR:000014876 denotes SIM2
T197 1075-1079 CVCL_1Y14 denotes SIM2
T200 1084-1097 CVCL_5552 denotes MCF10DCIS.COM
T201 1089-1093 D002285 denotes DCIS
T203 1089-1093 D002285 denotes DCIS
T205 1094-1097 CHEBI:17905 denotes COM
T212 1186-1190 PR:Q61079 denotes SIM2
T213 1186-1190 PR:Q14190 denotes SIM2
T214 1186-1190 PR:P39742 denotes SIM2
T215 1186-1190 PR:Q9Y812 denotes SIM2
T216 1186-1190 PR:000014876 denotes SIM2
T217 1186-1190 CVCL_1Y14 denotes SIM2
T220 1192-1205 CVCL_5552 denotes MCF10DCIS.com
T221 1197-1201 D002285 denotes DCIS
T223 1197-1201 D002285 denotes DCIS
T225 1202-1205 CHEBI:17905 denotes com
T226 1206-1212 D009369 denotes tumors
T227 1206-1212 D009369 denotes tumors
T234 1225-1229 PR:Q61079 denotes SIM2
T235 1225-1229 PR:Q14190 denotes SIM2
T236 1225-1229 PR:P39742 denotes SIM2
T237 1225-1229 PR:Q9Y812 denotes SIM2
T238 1225-1229 PR:000014876 denotes SIM2
T239 1225-1229 CVCL_1Y14 denotes SIM2
T240 1262-1267 D009369 denotes tumor
T241 1262-1267 D009369 denotes tumor
T242 1323-1330 D010634 denotes luminal
T243 1323-1330 D010634 denotes luminal
T244 1323-1330 CHEBI:8069 denotes luminal
T245 1340-1343 CVCL_W483 denotes CSN
T247 1340-1343 CVCL_N778 denotes CSN
T246 1340-1343 GO:0008180 denotes CSN
T248 1340-1344 PR:Q6IQT4 denotes CSN2
T249 1340-1344 PR:Q94899 denotes CSN2
T250 1340-1344 PR:P02665 denotes CSN2
T251 1340-1344 PR:P05814 denotes CSN2
T252 1340-1344 PR:Q8W207 denotes CSN2
T253 1340-1344 PR:O01422 denotes CSN2
T254 1340-1344 PR:P61202 denotes CSN2
T255 1340-1344 PR:000005941 denotes CSN2
T256 1340-1344 PR:P61203 denotes CSN2
T257 1340-1344 PR:P02666 denotes CSN2
T258 1340-1344 PR:P61201 denotes CSN2
T259 1340-1344 PR:Q9HFR0 denotes CSN2
T260 1340-1344 PR:P10598 denotes CSN2
T261 1340-1344 PR:Q54HL6 denotes CSN2
T262 1340-1344 PR:000005739 denotes CSN2
T264 1348-1354 862460 denotes casein
T263 1348-1354 CHEBI:3448 denotes casein
T265 1348-1354 D002364 denotes casein
T384 1357-1360 CHEBI:62109 denotes CDH
T403 1357-1360 CHEBI:89446 denotes CDH
T371 1357-1360 D065630 denotes CDH
T378 1357-1360 142700 denotes CDH
T414 1357-1361 PR:P12830 denotes CDH1
T415 1357-1361 PR:Q54KM3 denotes CDH1
T416 1357-1361 PR:P09803 denotes CDH1
T417 1357-1361 PR:Q06819 denotes CDH1
T418 1357-1361 PR:Q9R0T4 denotes CDH1
T419 1357-1361 PR:P53197 denotes CDH1
T420 1357-1361 PR:000001447 denotes CDH1
T421 1357-1361 PR:Q9UM11 denotes CDH1
T422 1357-1361 PR:000007725 denotes CDH1
T423 1357-1361 Q1QXE1 denotes CDH1
T424 1357-1361 PR:P08641 denotes CDH1
T431 1363-1373 D015820 denotes E-cadherin
T433 1363-1373 D015820 denotes E-cadherin
T425 1363-1373 P08641 denotes E-cadherin
T426 1363-1373 P30944 denotes E-cadherin
T427 1363-1373 Q6R8F2 denotes E-cadherin
T428 1363-1373 PR:Q24298 denotes E-cadherin
T429 1363-1373 F1PAA9 denotes E-cadherin
T430 1363-1373 P09803 denotes E-cadherin
T432 1363-1373 PR:000001447 denotes E-cadherin
T434 1363-1373 P12830 denotes E-cadherin
T435 1363-1373 Q5RAX1 denotes E-cadherin
T436 1363-1373 Q9R0T4 denotes E-cadherin
T437 1365-1373 GO:0008014 denotes cadherin
T451 1387-1397 D053538 denotes keratin-18
T442 1387-1397 O57607 denotes keratin-18
T443 1387-1397 Q5BJY9 denotes keratin-18
T444 1387-1397 Q5K2N9 denotes keratin-18
T445 1387-1397 O57611 denotes keratin-18
T446 1387-1397 Q7ZTS4 denotes keratin-18
T447 1387-1397 Q7SYF8 denotes keratin-18
T448 1387-1397 P05783 denotes keratin-18
T449 1387-1397 PR:000009458 denotes keratin-18
T450 1387-1397 Q07427 denotes keratin-18
T452 1387-1397 P05784 denotes keratin-18
T453 1387-1397 Q6P864 denotes keratin-18
T454 1437-1446 CL:0000034 denotes stem cell
T455 1482-1485 PR:P91682 denotes SMO
T456 1482-1485 PR:P97698 denotes SMO
T457 1482-1485 P56726 denotes SMO
T458 1482-1485 PR:Q9NWM0 denotes SMO
T459 1482-1485 PR:P56726 denotes SMO
T460 1482-1485 Q99835 denotes SMO
T461 1482-1485 O42224 denotes SMO
T462 1482-1485 PR:Q99K82 denotes SMO
T463 1482-1485 PR:000015288 denotes SMO
T464 1482-1485 PR:Q99835 denotes SMO
T465 1482-1485 P97698 denotes SMO
T466 1482-1485 PR:000015291 denotes SMO
T467 1487-1497 PR:000015288 denotes smoothened
T468 1500-1503 PR:000017214 denotes p63
T469 1500-1503 Q07065 denotes p63
T470 1500-1503 PR:000016567 denotes p63
T471 1500-1503 Q8BMK4 denotes p63
T472 1500-1503 Q9P2Y5 denotes p63
T473 1500-1503 PR:Q9JJP6 denotes p63
T474 1500-1503 O88898 denotes p63
T475 1500-1503 PR:Q9FL16 denotes p63
T476 1500-1503 PR:Q9H3D4 denotes p63
T477 1500-1503 Q9JJP6 denotes p63
T478 1500-1503 PR:O88898 denotes p63
T479 1500-1503 P25420 denotes p63
T480 1500-1503 PR:000005511 denotes p63
T481 1500-1503 Q9H3D4 denotes p63
T483 1505-1509 D049851 denotes SLUG
T482 1505-1509 PR:O43623 denotes SLUG
T484 1505-1509 PR:O08954 denotes SLUG
T485 1505-1509 PR:000015309 denotes SLUG
T486 1505-1509 PR:P97469 denotes SLUG
T487 1511-1516 D012908 denotes snail
T491 1528-1538 D053547 denotes keratin-14
T492 1528-1538 P02533 denotes keratin-14
T493 1528-1538 P05785 denotes keratin-14
T494 1528-1538 Q61781 denotes keratin-14
T495 1528-1538 Q6PVZ1 denotes keratin-14
T496 1528-1538 PR:000009454 denotes keratin-14
T497 1528-1538 Q6IFV1 denotes keratin-14
T498 1544-1547 PR:P31000 denotes VIM
T499 1544-1547 PR:000017298 denotes VIM
T500 1544-1547 PR:P08670 denotes VIM
T501 1544-1547 PR:P20152 denotes VIM
T508 1549-1557 D014746 denotes vimentin
T516 1549-1557 CHEBI:9982 denotes vimentin
T502 1549-1557 P48674 denotes vimentin
T503 1549-1557 Q4R4X4 denotes vimentin
T504 1549-1557 Q5R1W8 denotes vimentin
T505 1549-1557 P02544 denotes vimentin
T506 1549-1557 PR:000017298 denotes vimentin
T509 1549-1557 P84198 denotes vimentin
T511 1549-1557 P02543 denotes vimentin
T512 1549-1557 Q92155 denotes vimentin
T513 1549-1557 P31000 denotes vimentin
T514 1549-1557 P09654 denotes vimentin
T515 1549-1557 P48616 denotes vimentin
T517 1549-1557 P48670 denotes vimentin
T518 1549-1557 Q9MZA9 denotes vimentin
T519 1549-1557 P20152 denotes vimentin
T520 1549-1557 P08670 denotes vimentin
T507 1549-1557 GO:0045099 denotes vimentin
T510 1549-1557 GO:0045098 denotes vimentin
T527 1582-1586 PR:Q61079 denotes SIM2
T528 1582-1586 PR:Q14190 denotes SIM2
T529 1582-1586 PR:P39742 denotes SIM2
T530 1582-1586 PR:Q9Y812 denotes SIM2
T531 1582-1586 PR:000014876 denotes SIM2
T532 1582-1586 CVCL_1Y14 denotes SIM2
T535 1602-1615 CVCL_5552 denotes MCF10DCIS.COM
T536 1607-1611 D002285 denotes DCIS
T538 1607-1611 D002285 denotes DCIS
T540 1612-1615 CHEBI:17905 denotes COM
T541 1679-1683 UBERON:0002048 denotes lung
T542 1684-1694 D009362 denotes metastasis
T543 1684-1694 D009362 denotes metastasis
T544 1724-1732 D006364 denotes Hedgehog
T545 1733-1742 GO:0023052 denotes signaling
T546 1747-1753 UBERON:0027368 denotes matrix
T553 1837-1841 PR:Q61079 denotes SIM2
T554 1837-1841 PR:Q14190 denotes SIM2
T555 1837-1841 PR:P39742 denotes SIM2
T556 1837-1841 PR:Q9Y812 denotes SIM2
T557 1837-1841 PR:000014876 denotes SIM2
T558 1837-1841 CVCL_1Y14 denotes SIM2
T559 1856-1861 D006801 denotes human
T560 1862-1868 UBERON:0000310 denotes breast
T561 1862-1874 D001943 denotes breast tumor
T562 1862-1874 D001943 denotes breast tumor

PubmedHPO

Id Subject Object Predicate Lexical cue
T1 314-327 HP_0003002 denotes breast cancer
T2 314-327 HP_0100013 denotes breast cancer
T3 321-327 HP_0002664 denotes cancer
T4 701-706 HP_0002664 denotes tumor
T5 897-903 HP_0002664 denotes cancer
T6 1206-1212 HP_0002664 denotes tumors
T7 1262-1267 HP_0002664 denotes tumor
T8 1862-1874 HP_0003002 denotes breast tumor
T9 1862-1874 HP_0100013 denotes breast tumor
T10 1869-1874 HP_0002664 denotes tumor

Allie

Id Subject Object Predicate Lexical cue
SS1_22777354_0_0 60-75 expanded denotes Singleminded-2s
SS2_22777354_0_0 77-82 abbr denotes SIM2s
SS1_22777354_1_0 85-100 expanded denotes Singleminded-2s
SS2_22777354_1_0 102-107 abbr denotes SIM2s
SS1_22777354_4_0 782-806 expanded denotes ductal carcinoma in situ
SS2_22777354_4_0 808-812 abbr denotes DCIS
SS1_22777354_4_1 881-903 expanded denotes invasive ductal cancer
SS2_22777354_4_1 905-908 abbr denotes IDC
SS1_22777354_6_0 1387-1397 expanded denotes keratin-18
SS2_22777354_6_0 1380-1385 abbr denotes KER18
SS1_22777354_6_1 1528-1538 expanded denotes keratin-14
SS2_22777354_6_1 1521-1526 abbr denotes KER14
AE1_22777354_0_0 SS1_22777354_0_0 SS2_22777354_0_0 abbreviatedTo Singleminded-2s,SIM2s
AE1_22777354_1_0 SS1_22777354_1_0 SS2_22777354_1_0 abbreviatedTo Singleminded-2s,SIM2s
AE1_22777354_4_0 SS1_22777354_4_0 SS2_22777354_4_0 abbreviatedTo ductal carcinoma in situ,DCIS
AE1_22777354_4_1 SS1_22777354_4_1 SS2_22777354_4_1 abbreviatedTo invasive ductal cancer,IDC
AE1_22777354_6_0 SS1_22777354_6_0 SS2_22777354_6_0 abbreviatedTo keratin-18,KER18
AE1_22777354_6_1 SS1_22777354_6_1 SS2_22777354_6_1 abbreviatedTo keratin-14,KER14

UseCases_ArguminSci_Discourse

Id Subject Object Predicate Lexical cue
T1 0-84 DRI_Background denotes Regulation of DCIS to invasive breast cancer progression by Singleminded-2s (SIM2s).
T2 85-232 DRI_Background denotes Singleminded-2s (SIM2s) is a member of the bHLH/PAS family of transcription factors and a key regulator of mammary epithelial cell differentiation.
T3 233-328 DRI_Background denotes SIM2s is highly expressed in mammary epithelial cells and downregulated in human breast cancer.
T4 329-656 DRI_Challenge denotes Loss of Sim2s causes aberrant mouse mammary ductal development, with features suggestive of malignant transformation, whereas overexpression of SIM2s promotes precocious alveolar differentiation in nulliparous mouse mammary glands, suggesting that SIM2s is required for establishing and enhancing mammary gland differentiation.
T5 657-910 DRI_Outcome denotes To test the hypothesis that SIM2s regulates tumor cell differentiation, we analyzed SIM2s expression in human primary breast ductal carcinoma in situ (DCIS) samples and found that SIM2s is lost with progression from DCIS to invasive ductal cancer (IDC).
T6 911-1173 DRI_Outcome denotes Using a MCF10DCIS.COM progression model, we have shown that SIM2s expression is decreased in MCF10DCIS.COM cells compared with MCF10A cells, and reestablishment of SIM2s in MCF10DCIS.COM cells significantly inhibits growth and invasion both in vitro and in vivo.
T7 1174-1560 DRI_Background denotes Analysis of SIM2s-MCF10DCIS.com tumors showed that SIM2s promoted a more differentiated tumor phenotype including the expression of a broad range of luminal markers (CSN2 (β-casein), CDH1 (E-cadherin), and KER18 (keratin-18)) and suppressed genes associated with stem cell maintenance and a basal phenotype (SMO (smoothened), p63, SLUG (snail-2), KER14 (keratin-14) and VIM (vimentin)).
T8 1561-1783 DRI_Background denotes Furthermore, loss of SIM2s expression in MCF10DCIS.COM xenografts resulted in a more invasive phenotype and increased lung metastasis likely due to an increase in Hedgehog signaling and matrix metalloproteinase expression.
T9 1784-1928 DRI_Outcome denotes Together, these exciting new data support a role for SIM2s in promoting human breast tumor differentiation and maintaining epithelial integrity.

PubMed_ArguminSci

Id Subject Object Predicate Lexical cue
T1 85-232 DRI_Background denotes Singleminded-2s (SIM2s) is a member of the bHLH/PAS family of transcription factors and a key regulator of mammary epithelial cell differentiation.
T2 233-328 DRI_Background denotes SIM2s is highly expressed in mammary epithelial cells and downregulated in human breast cancer.
T3 329-656 DRI_Challenge denotes Loss of Sim2s causes aberrant mouse mammary ductal development, with features suggestive of malignant transformation, whereas overexpression of SIM2s promotes precocious alveolar differentiation in nulliparous mouse mammary glands, suggesting that SIM2s is required for establishing and enhancing mammary gland differentiation.
T4 657-910 DRI_Outcome denotes To test the hypothesis that SIM2s regulates tumor cell differentiation, we analyzed SIM2s expression in human primary breast ductal carcinoma in situ (DCIS) samples and found that SIM2s is lost with progression from DCIS to invasive ductal cancer (IDC).
T5 911-1173 DRI_Outcome denotes Using a MCF10DCIS.COM progression model, we have shown that SIM2s expression is decreased in MCF10DCIS.COM cells compared with MCF10A cells, and reestablishment of SIM2s in MCF10DCIS.COM cells significantly inhibits growth and invasion both in vitro and in vivo.
T6 1174-1560 DRI_Background denotes Analysis of SIM2s-MCF10DCIS.com tumors showed that SIM2s promoted a more differentiated tumor phenotype including the expression of a broad range of luminal markers (CSN2 (β-casein), CDH1 (E-cadherin), and KER18 (keratin-18)) and suppressed genes associated with stem cell maintenance and a basal phenotype (SMO (smoothened), p63, SLUG (snail-2), KER14 (keratin-14) and VIM (vimentin)).
T7 1561-1783 DRI_Background denotes Furthermore, loss of SIM2s expression in MCF10DCIS.COM xenografts resulted in a more invasive phenotype and increased lung metastasis likely due to an increase in Hedgehog signaling and matrix metalloproteinase expression.
T8 1784-1928 DRI_Outcome denotes Together, these exciting new data support a role for SIM2s in promoting human breast tumor differentiation and maintaining epithelial integrity.

DisGeNET5_gene_disease

Id Subject Object Predicate Lexical cue
22777354-0#77#81#gene6493 77-81 gene6493 denotes SIM2
22777354-0#14#18#diseaseC0007124 14-18 diseaseC0007124 denotes DCIS
22777354-0#22#44#diseaseC0853879 22-44 diseaseC0853879 denotes invasive breast cancer
22777354-7#21#25#gene6493 1582-1586 gene6493 denotes SIM2
22777354-7#118#133#diseaseC0153676 1679-1694 diseaseC0153676 denotes lung metastasis
22777354-8#53#57#gene6493 1837-1841 gene6493 denotes SIM2
22777354-8#78#90#diseaseC1458155 1862-1874 diseaseC1458155 denotes breast tumor
77#81#gene649314#18#diseaseC0007124 22777354-0#77#81#gene6493 22777354-0#14#18#diseaseC0007124 associated_with SIM2,DCIS
77#81#gene649322#44#diseaseC0853879 22777354-0#77#81#gene6493 22777354-0#22#44#diseaseC0853879 associated_with SIM2,invasive breast cancer
21#25#gene6493118#133#diseaseC0153676 22777354-7#21#25#gene6493 22777354-7#118#133#diseaseC0153676 associated_with SIM2,lung metastasis
53#57#gene649378#90#diseaseC1458155 22777354-8#53#57#gene6493 22777354-8#78#90#diseaseC1458155 associated_with SIM2,breast tumor