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PubMed:2056282 JSONTXT

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jnlpba-st-training

Id Subject Object Predicate Lexical cue
T1 6-33 protein denotes tumor necrosis factor alpha
T2 67-96 cell_line denotes stimulated T and B cell lines
T3 124-183 DNA denotes human tumor necrosis factor alpha (TNF-alpha) gene promoter
T4 255-290 cell_line denotes human T and B lymphocyte cell lines
T5 318-341 DNA denotes -52 and +89 nucleotides
T6 370-396 DNA denotes transcriptional start site
T7 691-709 DNA denotes TNF-alpha promoter
T8 764-784 protein denotes transcription factor
T9 785-795 protein denotes NF-kappa B
T10 826-840 RNA denotes TNF-alpha mRNA
T11 882-892 protein denotes NF-kappa B
T12 935-953 cell_line denotes T and B cell lines
T13 965-980 DNA denotes kappa 1-kappa 3
T14 1010-1028 DNA denotes TNF-alpha promoter
T15 1094-1108 RNA denotes TNF-alpha mRNA
T16 1193-1203 protein denotes NF-kappa B
T17 1256-1271 protein denotes protein factors
T18 1349-1370 DNA denotes heterologous promoter
T19 1376-1415 cell_line denotes B (Raji), but not a T (HUT78) cell line
T20 1464-1482 DNA denotes TNF-alpha promoter
T21 1589-1613 DNA denotes NF-kappa B binding sites

PubmedHPO

Id Subject Object Predicate Lexical cue
T1 130-135 HP_0002664 denotes tumor

pubmed-sentences-benchmark

Id Subject Object Predicate Lexical cue
S1 0-97 Sentence denotes Human tumor necrosis factor alpha gene regulation in phorbol ester stimulated T and B cell lines.
S2 98-397 Sentence denotes The minimal region of the human tumor necrosis factor alpha (TNF-alpha) gene promoter necessary for its transcriptional induction by phorbol esters (PMA) in human T and B lymphocyte cell lines has been localized between -52 and +89 nucleotides (nt) relative to the gene's transcriptional start site.
S3 398-662 Sentence denotes Comparison of these sequences to those required to mediate virus or lipopolysaccharide (LPS) induction of the gene reveal significant differences, and thus, the sequence requirements for PMA induction are distinct from those that mediate induction by virus or LPS.
S4 663-954 Sentence denotes Although three sites in the TNF-alpha promoter (kappa 1, kappa 2, and kappa 3) specifically bind the transcription factor NF-kappa B in lymphoid nuclear extracts, TNF-alpha mRNA induction by PMA does not correlate with NF-kappa B binding activities displayed by different T and B cell lines.
S5 955-1082 Sentence denotes Moreover, kappa 1-kappa 3 can each be deleted from the TNF-alpha promoter with little effect on the gene's inducibility by PMA.
S6 1083-1272 Sentence denotes Therefore, TNF-alpha mRNA induction by PMA, like its induction by virus and LPS, is not primarily mediated by NF-kappa B, but rather is mediated through other sequences and protein factors.
S7 1273-1416 Sentence denotes Surprisingly, multimers of kappa 1-kappa 3 can confer PMA inducibility on a heterologous promoter in a B (Raji), but not a T (HUT78) cell line.
S8 1417-1614 Sentence denotes However they are not functional on a truncated TNF-alpha promoter, indicating that promoter context and cell type specificity influence the PMA inducible function of these NF-kappa B binding sites.

genia-medco-coref

Id Subject Object Predicate Lexical cue
C1 0-38 NP denotes Human tumor necrosis factor alpha gene
C2 53-66 NP denotes phorbol ester
C3 78-96 NP denotes T and B cell lines
C5 120-174 NP denotes the human tumor necrosis factor alpha (TNF-alpha) gene
C4 120-183 NP denotes the human tumor necrosis factor alpha (TNF-alpha) gene promoter
C6 198-201 NP denotes its
C7 231-251 NP denotes phorbol esters (PMA)
C8 255-290 NP denotes human T and B lymphocyte cell lines
C9 457-490 NP denotes virus or lipopolysaccharide (LPS)
C10 555-580 NP denotes the sequence requirements
C11 585-598 NP denotes PMA induction
C12 617-622 NP denotes those
C13 623-627 NP denotes that
C14 649-661 NP denotes virus or LPS
C15 672-683 NP denotes three sites
C17 687-700 NP denotes the TNF-alpha
C16 687-709 NP denotes the TNF-alpha promoter
C18 710-741 NP denotes (kappa 1, kappa 2, and kappa 3)
C19 760-795 NP denotes the transcription factor NF-kappa B
C21 826-835 NP denotes TNF-alpha
C20 826-850 NP denotes TNF-alpha mRNA induction
C22 854-857 NP denotes PMA
C23 882-911 NP denotes NF-kappa B binding activities
C24 935-953 NP denotes T and B cell lines
C25 965-980 NP denotes kappa 1-kappa 3
C27 1010-1019 NP denotes TNF-alpha
C26 1006-1028 NP denotes the TNF-alpha promoter
C28 1078-1081 NP denotes PMA
C30 1094-1103 NP denotes TNF-alpha
C29 1094-1118 NP denotes TNF-alpha mRNA induction
C31 1122-1125 NP denotes PMA
C32 1132-1135 NP denotes its
C33 1149-1162 NP denotes virus and LPS
C34 1193-1203 NP denotes NF-kappa B
C35 1287-1315 NP denotes multimers of kappa 1-kappa 3
C37 1464-1473 NP denotes TNF-alpha
C36 1464-1482 NP denotes TNF-alpha promoter
C39 1589-1599 NP denotes NF-kappa B
C38 1583-1613 NP denotes these NF-kappa B binding sites
R1 C5 C1 coref-ident the human tumor necrosis factor alpha (TNF-alpha) gene,Human tumor necrosis factor alpha gene
R2 C6 C4 coref-pron its,the human tumor necrosis factor alpha (TNF-alpha) gene promoter
R3 C7 C2 coref-ident phorbol esters (PMA),phorbol ester
R4 C8 C3 coref-ident human T and B lymphocyte cell lines,T and B cell lines
R5 C11 C7 coref-other PMA induction,phorbol esters (PMA)
R6 C12 C10 coref-pron those,the sequence requirements
R7 C13 C12 coref-relat that,those
R8 C14 C9 coref-ident virus or LPS,virus or lipopolysaccharide (LPS)
R9 C17 C5 coref-ident the TNF-alpha,the human tumor necrosis factor alpha (TNF-alpha) gene
R10 C16 C4 coref-ident the TNF-alpha promoter,the human tumor necrosis factor alpha (TNF-alpha) gene promoter
R11 C18 C15 coref-ident "(kappa 1, kappa 2, and kappa 3)",three sites
R12 C21 C17 coref-ident TNF-alpha,the TNF-alpha
R13 C22 C7 coref-ident PMA,phorbol esters (PMA)
R14 C23 C19 coref-other NF-kappa B binding activities,the transcription factor NF-kappa B
R15 C24 C8 coref-ident T and B cell lines,human T and B lymphocyte cell lines
R16 C25 C18 coref-ident kappa 1-kappa 3,"(kappa 1, kappa 2, and kappa 3)"
R17 C27 C21 coref-ident TNF-alpha,TNF-alpha
R18 C26 C16 coref-ident the TNF-alpha promoter,the TNF-alpha promoter
R19 C28 C22 coref-ident PMA,PMA
R20 C30 C27 coref-ident TNF-alpha,TNF-alpha
R21 C29 C20 coref-ident TNF-alpha mRNA induction,TNF-alpha mRNA induction
R22 C31 C28 coref-ident PMA,PMA
R23 C32 C29 coref-pron its,TNF-alpha mRNA induction
R24 C33 C14 coref-ident virus and LPS,virus or LPS
R25 C34 C19 coref-ident NF-kappa B,the transcription factor NF-kappa B
R26 C35 C25 coref-ident multimers of kappa 1-kappa 3,kappa 1-kappa 3
R27 C37 C30 coref-ident TNF-alpha,TNF-alpha
R28 C36 C26 coref-ident TNF-alpha promoter,the TNF-alpha promoter
R29 C39 C34 coref-ident NF-kappa B,NF-kappa B
R30 C38 C34 coref-other these NF-kappa B binding sites,NF-kappa B

GENIAcorpus

Id Subject Object Predicate Lexical cue
T1 0-5 other_name denotes Human
T2 6-33 protein_molecule denotes tumor necrosis factor alpha
T3 53-66 other_organic_compound denotes phorbol ester
T4 124-157 protein_molecule denotes human tumor necrosis factor alpha
T5 159-168 protein_molecule denotes TNF-alpha
T6 231-245 other_organic_compound denotes phorbol esters
T7 247-250 other_organic_compound denotes PMA
T8 255-262 cell_line denotes human T
T9 267-290 cell_line denotes B lymphocyte cell lines
T10 318-341 DNA_domain_or_region denotes -52 and +89 nucleotides
T11 370-396 DNA_domain_or_region denotes transcriptional start site
T12 466-484 lipid denotes lipopolysaccharide
T13 486-489 lipid denotes LPS
T14 585-588 other_organic_compound denotes PMA
T15 649-654 virus denotes virus
T16 658-661 lipid denotes LPS
T17 691-700 protein_molecule denotes TNF-alpha
T18 764-784 protein_family_or_group denotes transcription factor
T19 785-795 protein_molecule denotes NF-kappa B
T20 808-824 cell_component denotes nuclear extracts
T21 826-835 protein_molecule denotes TNF-alpha
T22 854-857 other_organic_compound denotes PMA
T23 882-892 protein_molecule denotes NF-kappa B
T24 965-980 DNA_domain_or_region denotes kappa 1-kappa 3
T25 1010-1019 protein_molecule denotes TNF-alpha
T26 1062-1074 other_name denotes inducibility
T27 1078-1081 other_organic_compound denotes PMA
T28 1094-1103 protein_molecule denotes TNF-alpha
T29 1122-1125 other_organic_compound denotes PMA
T30 1149-1154 virus denotes virus
T31 1159-1162 lipid denotes LPS
T32 1193-1203 protein_molecule denotes NF-kappa B
T33 1256-1271 protein_family_or_group denotes protein factors
T34 1327-1330 other_organic_compound denotes PMA
T35 1349-1370 DNA_domain_or_region denotes heterologous promoter
T36 1379-1383 cell_line denotes Raji
T37 1399-1404 cell_line denotes HUT78
T38 1464-1473 protein_molecule denotes TNF-alpha
T39 1500-1516 other_name denotes promoter context
T40 1557-1560 other_organic_compound denotes PMA
T41 1589-1599 protein_molecule denotes NF-kappa B