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PubMed:1502171 JSONTXT

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jnlpba-st-training

Id Subject Object Predicate Lexical cue
T1 34-55 DNA denotes HLA-DRA gene promoter
T2 90-102 DNA denotes octamer site
T3 141-157 protein denotes interferon gamma
T4 175-230 DNA denotes major histocompatibility complex class II gene promoter
T5 231-234 DNA denotes DRA
T6 275-293 DNA denotes cis-acting regions
T7 348-360 DNA denotes DRA promoter
T8 397-408 cell_type denotes intact cell
T9 521-533 cell_line denotes B-cell lines
T10 541-553 DNA denotes octamer site
T11 562-581 DNA denotes Y, X1, and X2 boxes
T12 583-623 cell_line denotes Class II antigen expressing T-cell lines
T13 657-669 cell_line denotes B-cell lines
T14 677-707 cell_line denotes class II-negative T-cell lines
T15 738-757 cell_line denotes lymphoid cell lines
T16 763-775 DNA denotes octamer site
T17 872-902 protein denotes lymphoid-specific OTF-2 factor
T18 921-973 cell_line denotes class II-positive nonlymphoid glioblastoma cell line
T19 1011-1023 DNA denotes octamer site
T20 1052-1075 protein denotes ubiquitous OTF-1 factor
T21 1083-1100 DNA denotes open binding site
T22 1112-1124 DNA denotes DRA promoter
T23 1147-1152 protein denotes OTF-1
T24 1199-1216 cell_line denotes glioblastoma line
T25 1218-1234 protein denotes Interferon gamma
T26 1271-1293 cell_line denotes glioblastoma cell line
T27 1439-1455 protein denotes interferon gamma
T28 1471-1486 DNA denotes poised promoter
T29 1539-1546 DNA denotes X boxes
T30 1661-1663 DNA denotes X1
T31 1668-1670 DNA denotes X2
T32 1719-1735 protein denotes interferon gamma

DisGeNET5_gene_disease

Id Subject Object Predicate Lexical cue
1502171-8#10#13#gene1811 1112-1115 gene1811 denotes DRA
1502171-8#45#50#gene5451 1147-1152 gene5451 denotes OTF-1
1502171-8#97#109#diseaseC0017636 1199-1211 diseaseC0017636 denotes glioblastoma
1502171-9#0#16#gene3458 1218-1234 gene3458 denotes Interferon gamma
1502171-9#53#65#diseaseC0017636 1271-1283 diseaseC0017636 denotes glioblastoma
10#13#gene181197#109#diseaseC0017636 1502171-8#10#13#gene1811 1502171-8#97#109#diseaseC0017636 associated_with DRA,glioblastoma
45#50#gene545197#109#diseaseC0017636 1502171-8#45#50#gene5451 1502171-8#97#109#diseaseC0017636 associated_with OTF-1,glioblastoma
0#16#gene345853#65#diseaseC0017636 1502171-9#0#16#gene3458 1502171-9#53#65#diseaseC0017636 associated_with Interferon gamma,glioblastoma

genia-medco-coref

Id Subject Object Predicate Lexical cue
C1 30-55 NP denotes the HLA-DRA gene promoter
C2 86-102 NP denotes the octamer site
C3 141-157 NP denotes interferon gamma
C4 171-234 NP denotes the major histocompatibility complex class II gene promoter DRA
C5 344-360 NP denotes the DRA promoter
C6 365-408 NP denotes protein-DNA interactions in the intact cell
C7 410-415 NP denotes which
C8 505-517 NP denotes interactions
C9 521-533 NP denotes B-cell lines
C10 537-553 NP denotes the octamer site
C11 565-581 NP denotes X1, and X2 boxes
C12 657-669 NP denotes B-cell lines
C13 721-733 NP denotes interactions
C14 759-775 NP denotes the octamer site
C15 917-973 NP denotes the class II-positive nonlymphoid glioblastoma cell line
C16 991-1003 NP denotes interactions
C17 1007-1023 NP denotes the octamer site
C18 1048-1075 NP denotes the ubiquitous OTF-1 factor
C19 1108-1124 NP denotes the DRA promoter
C20 1147-1152 NP denotes OTF-1
C21 1195-1216 NP denotes the glioblastoma line
C22 1218-1234 NP denotes Interferon gamma
C23 1266-1293 NP denotes this glioblastoma cell line
C24 1325-1363 NP denotes X1 and X2 box protein-DNA interactions
C25 1439-1455 NP denotes interferon gamma
C26 1535-1546 NP denotes the X boxes
C27 1661-1683 NP denotes X1 and X2 interactions
C28 1719-1735 NP denotes interferon gamma
R1 C4 C1 coref-other the major histocompatibility complex class II gene promoter DRA,the HLA-DRA gene promoter
R2 C5 C4 coref-ident the DRA promoter,the major histocompatibility complex class II gene promoter DRA
R3 C7 C6 coref-relat which,protein-DNA interactions in the intact cell
R4 C8 C6 coref-other interactions,protein-DNA interactions in the intact cell
R5 C10 C2 coref-ident the octamer site,the octamer site
R6 C12 C9 coref-ident B-cell lines,B-cell lines
R7 C13 C6 coref-other interactions,protein-DNA interactions in the intact cell
R8 C14 C10 coref-ident the octamer site,the octamer site
R9 C16 C6 coref-other interactions,protein-DNA interactions in the intact cell
R10 C17 C14 coref-ident the octamer site,the octamer site
R11 C19 C5 coref-ident the DRA promoter,the DRA promoter
R12 C20 C18 coref-ident OTF-1,the ubiquitous OTF-1 factor
R13 C21 C15 coref-ident the glioblastoma line,the class II-positive nonlymphoid glioblastoma cell line
R14 C22 C3 coref-other Interferon gamma,interferon gamma
R15 C23 C21 coref-ident this glioblastoma cell line,the glioblastoma line
R16 C24 C6 coref-other X1 and X2 box protein-DNA interactions,protein-DNA interactions in the intact cell
R17 C25 C22 coref-ident interferon gamma,Interferon gamma
R18 C26 C11 coref-other the X boxes,"X1, and X2 boxes"
R19 C27 C24 coref-ident X1 and X2 interactions,X1 and X2 box protein-DNA interactions
R20 C28 C25 coref-ident interferon gamma,interferon gamma

pubmed-sentences-benchmark

Id Subject Object Predicate Lexical cue
S1 0-158 Sentence denotes In vivo footprint analysis of the HLA-DRA gene promoter: cell-specific interaction at the octamer site and up-regulation of X box binding by interferon gamma.
S2 159-326 Sentence denotes Analysis of the major histocompatibility complex class II gene promoter DRA has previously identified at least five cis-acting regions required for maximal expression.
S3 327-455 Sentence denotes We have examined the DRA promoter for protein-DNA interactions in the intact cell, which may mediate transcriptional activation.
S4 456-582 Sentence denotes Using in vivo genomic footprinting we identified interactions in B-cell lines at the octamer site and the Y, X1, and X2 boxes.
S5 583-734 Sentence denotes Class II antigen expressing T-cell lines maintained contacts identical to B-cell lines, while class II-negative T-cell lines exhibited no interactions.
S6 735-824 Sentence denotes In lymphoid cell lines, the octamer site is occupied and required for maximal expression.
S7 825-903 Sentence denotes This is most likely due to the presence of the lymphoid-specific OTF-2 factor.
S8 904-1101 Sentence denotes In contrast, the class II-positive nonlymphoid glioblastoma cell line does not exhibit interactions at the octamer site despite the presence of the ubiquitous OTF-1 factor and an open binding site.
S9 1102-1217 Sentence denotes Thus, the DRA promoter discriminates against OTF-1 activation at the level of DNA binding in the glioblastoma line.
S10 1218-1411 Sentence denotes Interferon gamma induces class II expression in this glioblastoma cell line and, in parallel, up-regulates X1 and X2 box protein-DNA interactions, while all other interactions remain unchanged.
S11 1412-1570 Sentence denotes These results suggest that interferon gamma functions on a poised promoter by altering weak, nonproductive interactions at the X boxes to strong interactions.
S12 1571-1754 Sentence denotes These findings provide direct in vivo evidence to strongly suggest that the modulation of X1 and X2 interactions is an important constituent of the interferon gamma induction pathway.

GENIAcorpus

Id Subject Object Predicate Lexical cue
T1 0-26 other_name denotes In vivo footprint analysis
T2 34-55 DNA_domain_or_region denotes HLA-DRA gene promoter
T3 90-102 DNA_domain_or_region denotes octamer site
T4 124-137 other_name denotes X box binding
T5 141-157 protein_molecule denotes interferon gamma
T6 175-216 protein_complex denotes major histocompatibility complex class II
T7 231-234 DNA_domain_or_region denotes DRA
T8 275-293 DNA_domain_or_region denotes cis-acting regions
T9 348-360 DNA_domain_or_region denotes DRA promoter
T10 365-389 other_name denotes protein-DNA interactions
T11 397-408 cell_type denotes intact cell
T12 428-454 other_name denotes transcriptional activation
T13 462-490 other_name denotes in vivo genomic footprinting
T14 521-533 cell_line denotes B-cell lines
T15 541-553 DNA_domain_or_region denotes octamer site
T16 583-623 cell_line denotes Class II antigen expressing T-cell lines
T17 657-669 cell_line denotes B-cell lines
T18 677-707 cell_line denotes class II-negative T-cell lines
T19 738-757 cell_line denotes lymphoid cell lines
T20 763-775 DNA_domain_or_region denotes octamer site
T21 872-902 protein_molecule denotes lymphoid-specific OTF-2 factor
T22 921-973 cell_line denotes class II-positive nonlymphoid glioblastoma cell line
T23 1011-1023 DNA_domain_or_region denotes octamer site
T24 1052-1075 protein_molecule denotes ubiquitous OTF-1 factor
T25 1083-1100 DNA_domain_or_region denotes open binding site
T26 1112-1124 DNA_domain_or_region denotes DRA promoter
T27 1147-1152 protein_molecule denotes OTF-1
T28 1199-1216 cell_line denotes glioblastoma line
T29 1218-1234 protein_molecule denotes Interferon gamma
T30 1243-1262 other_name denotes class II expression
T31 1271-1293 cell_line denotes glioblastoma cell line
T32 1439-1455 protein_molecule denotes interferon gamma
T33 1471-1486 DNA_domain_or_region denotes poised promoter
T34 1539-1546 DNA_family_or_group denotes X boxes
T35 1661-1663 DNA_domain_or_region denotes X1
T36 1668-1670 DNA_domain_or_region denotes X2
T37 1719-1735 protein_molecule denotes interferon gamma

DisGeNET

Id Subject Object Predicate Lexical cue
T0 1147-1152 gene:5451 denotes OTF-1
T1 1199-1211 disease:C0017636 denotes glioblastoma
T2 1112-1115 gene:1811 denotes DRA
T3 1199-1211 disease:C0017636 denotes glioblastoma
T4 1218-1234 gene:3458 denotes Interferon gamma
T5 1271-1283 disease:C0017636 denotes glioblastoma
R1 T0 T1 associated_with OTF-1,glioblastoma
R2 T2 T3 associated_with DRA,glioblastoma
R3 T4 T5 associated_with Interferon gamma,glioblastoma