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jnlpba-st-training

Id Subject Object Predicate Lexical cue
T1 4-37 DNA denotes evolutionarily conserved sequence
T2 54-91 protein denotes human Ig heavy chain S gamma 3 region
T3 98-116 DNA denotes inducible promoter
T4 144-155 protein denotes CD40 ligand
T5 160-164 protein denotes IL-4
T6 181-216 DNA denotes NF-kappa B and STAT-6 binding sites
T7 330-333 protein denotes IgG
T8 434-456 cell_type denotes germinal center B cell
T9 474-495 cell_line denotes IgM+ IgD+ CL-01 cells
T10 523-532 protein denotes I gamma 3
T11 533-566 DNA denotes evolutionarily conserved sequence
T12 568-571 DNA denotes ECS
T13 580-588 DNA denotes germline
T14 623-643 DNA denotes human C gamma 3 gene
T15 649-658 protein denotes I gamma 3
T16 659-662 DNA denotes ECS
T17 684-729 DNA denotes major I gamma 3 transcription initiation site
T18 789-804 DNA denotes human I gamma 1
T19 806-815 DNA denotes I gamma 2
T20 821-830 DNA denotes I gamma 4
T21 840-872 DNA denotes Reporter luciferase gene vectors
T22 888-905 DNA denotes human gamma 3 ECS
T23 929-940 cell_line denotes CL-01 cells
T24 1029-1033 protein denotes CD40
T25 1037-1048 protein denotes CD40 ligand
T26 1050-1055 protein denotes CD40L
T27 1073-1077 protein denotes IL-4
T28 1100-1111 cell_line denotes CL-01 cells
T29 1118-1123 protein denotes CD40L
T30 1151-1155 protein denotes IL-4
T31 1202-1226 DNA denotes luciferase reporter gene
T32 1295-1323 DNA denotes NF-kappa B/Rel binding motif
T33 1344-1355 DNA denotes gamma 3 ECS
T34 1379-1384 protein denotes CD40L
T35 1389-1393 protein denotes IL-4
T36 1403-1422 DNA denotes STAT-6-binding site
T37 1452-1456 protein denotes IL-4
T38 1521-1534 protein denotes p50/p65/c-Rel
T39 1539-1545 protein denotes STAT-6
T40 1573-1578 protein denotes CD40L
T41 1583-1587 protein denotes IL-4
T42 1624-1634 DNA denotes DNA motifs
T43 1646-1649 DNA denotes ECS
T44 1679-1713 DNA denotes CD40L and IL-4 responsive elements
T45 1828-1839 DNA denotes gamma 3 ECS
T46 1876-1888 DNA denotes cis elements
T47 1913-1918 protein denotes CD40L
T48 1923-1927 protein denotes IL-4
T49 1972-1992 DNA denotes human C gamma 3 gene

pubmed-sentences-benchmark

Id Subject Object Predicate Lexical cue
S1 0-217 Sentence denotes The evolutionarily conserved sequence upstream of the human Ig heavy chain S gamma 3 region is an inducible promoter: synergistic activation by CD40 ligand and IL-4 via cooperative NF-kappa B and STAT-6 binding sites.
S2 218-388 Sentence denotes Germline C gamma gene transcription is a crucial event in the process that leads to switch DNA recombination to IgG, but its regulation in the human is poorly understood.
S3 389-644 Sentence denotes We took advantage of our monoclonal model of germinal center B cell differentiation, IgM+ IgD+ CL-01 cells, to define the role of the I gamma 3 evolutionarily conserved sequence (ECS) in the germline transcriptional activation of the human C gamma 3 gene.
S4 645-839 Sentence denotes The I gamma 3 ECS lies upstream of the major I gamma 3 transcription initiation site and displays more than 90% identity with the corresponding human I gamma 1, I gamma 2, and I gamma 4 regions.
S5 840-1078 Sentence denotes Reporter luciferase gene vectors containing the human gamma 3 ECS were used to transfect CL-01 cells, which have been shown to undergo Smu-->S gamma 3 DNA recombination, upon engagement of CD40 by CD40 ligand (CD40L) and exposure to IL-4.
S6 1079-1238 Sentence denotes In these transfected CL-01 cells, CD40:CD40L engagement and exposure to IL-4 synergistically induced gamma 3 ECS-dependent luciferase reporter gene activation.
S7 1239-1470 Sentence denotes Targeted mutational analysis demonstrated that a tandem NF-kappa B/Rel binding motif is critical for the gamma 3 ECS responsiveness to both CD40L and IL-4, while a STAT-6-binding site is additionally required for IL-4 inducibility.
S8 1471-1650 Sentence denotes Electrophoretic mobility shift assays showed that p50/p65/c-Rel and STAT-6 are effectively induced by CD40L and IL-4, respectively, and bind to specific DNA motifs within the ECS.
S9 1651-1817 Sentence denotes These partially overlapping CD40L and IL-4 responsive elements are functionally cooperative as the disruption of one of them prevents synergistic promoter activation.
S10 1818-1993 Sentence denotes Thus, the gamma 3 ECS is an inducible promoter containing cis elements that critically mediate CD40L and IL-4-triggered transcriptional activation of the human C gamma 3 gene.

genia-medco-coref

Id Subject Object Predicate Lexical cue
C2 144-155 NP denotes CD40 ligand
C3 160-164 NP denotes IL-4
C1 144-164 NP denotes CD40 ligand and IL-4
C4 218-253 NP denotes Germline C gamma gene transcription
C5 257-287 NP denotes a crucial event in the process
C6 288-292 NP denotes that
C7 339-342 NP denotes its
C8 410-472 NP denotes our monoclonal model of germinal center B cell differentiation
C9 474-495 NP denotes IgM+ IgD+ CL-01 cells
C10 519-572 NP denotes the I gamma 3 evolutionarily conserved sequence (ECS)
C11 619-643 NP denotes the human C gamma 3 gene
C12 645-662 NP denotes The I gamma 3 ECS
C13 884-905 NP denotes the human gamma 3 ECS
C14 929-940 NP denotes CL-01 cells
C15 942-947 NP denotes which
C16 1037-1056 NP denotes CD40 ligand (CD40L)
C18 1073-1077 NP denotes IL-4
C17 1061-1077 NP denotes exposure to IL-4
C20 1151-1155 NP denotes IL-4
C19 1139-1155 NP denotes exposure to IL-4
C21 1374-1393 NP denotes both CD40L and IL-4
C23 1573-1578 NP denotes CD40L
C24 1583-1587 NP denotes IL-4
C22 1573-1587 NP denotes CD40L and IL-4
C25 1679-1713 NP denotes CD40L and IL-4 responsive elements
C26 1771-1775 NP denotes them
C27 1824-1839 NP denotes the gamma 3 ECS
C28 1876-1888 NP denotes cis elements
C29 1889-1893 NP denotes that
C30 1968-1992 NP denotes the human C gamma 3 gene
R1 C6 C5 coref-relat that,a crucial event in the process
R2 C7 C4 coref-pron its,Germline C gamma gene transcription
R3 C9 C8 coref-appos IgM+ IgD+ CL-01 cells,our monoclonal model of germinal center B cell differentiation
R4 C12 C10 coref-ident The I gamma 3 ECS,the I gamma 3 evolutionarily conserved sequence (ECS)
R5 C15 C14 coref-relat which,CL-01 cells
R6 C16 C2 coref-ident CD40 ligand (CD40L),CD40 ligand
R7 C18 C3 coref-ident IL-4,IL-4
R8 C20 C18 coref-ident IL-4,IL-4
R9 C19 C17 coref-ident exposure to IL-4,exposure to IL-4
R10 C21 C1 coref-ident both CD40L and IL-4,CD40 ligand and IL-4
R11 C23 C16 coref-ident CD40L,CD40 ligand (CD40L)
R12 C24 C20 coref-ident IL-4,IL-4
R13 C22 C21 coref-ident CD40L and IL-4,both CD40L and IL-4
R14 C26 C25 coref-pron them,CD40L and IL-4 responsive elements
R15 C27 C13 coref-ident the gamma 3 ECS,the human gamma 3 ECS
R16 C29 C28 coref-relat that,cis elements
R17 C30 C11 coref-ident the human C gamma 3 gene,the human C gamma 3 gene

GENIAcorpus

Id Subject Object Predicate Lexical cue
T1 4-37 DNA_domain_or_region denotes evolutionarily conserved sequence
T2 54-91 protein_domain_or_region denotes human Ig heavy chain S gamma 3 region
T3 98-116 DNA_domain_or_region denotes inducible promoter
T4 144-155 protein_molecule denotes CD40 ligand
T5 160-164 protein_molecule denotes IL-4
T6 218-253 other_name denotes Germline C gamma gene transcription
T7 330-333 protein_family_or_group denotes IgG
T8 361-366 multi_cell denotes human
T9 434-456 cell_type denotes germinal center B cell
T10 474-495 cell_line denotes IgM+ IgD+ CL-01 cells
T11 523-532 protein_molecule denotes I gamma 3
T12 533-566 DNA_domain_or_region denotes evolutionarily conserved sequence
T13 568-571 DNA_domain_or_region denotes ECS
T14 580-588 DNA_domain_or_region denotes germline
T15 623-643 DNA_domain_or_region denotes human C gamma 3 gene
T16 649-658 protein_molecule denotes I gamma 3
T17 659-662 DNA_domain_or_region denotes ECS
T18 684-689 DNA_domain_or_region denotes major
T19 690-699 protein_molecule denotes I gamma 3
T20 789-804 DNA_domain_or_region denotes human I gamma 1
T21 806-815 DNA_domain_or_region denotes I gamma 2
T22 821-830 DNA_domain_or_region denotes I gamma 4
T23 840-872 DNA_family_or_group denotes Reporter luciferase gene vectors
T24 888-901 DNA_domain_or_region denotes human gamma 3
T25 902-905 DNA_domain_or_region denotes ECS
T26 929-940 cell_line denotes CL-01 cells
T27 991-1008 other_name denotes DNA recombination
T28 1029-1033 protein_molecule denotes CD40
T29 1037-1048 protein_molecule denotes CD40 ligand
T30 1050-1055 protein_molecule denotes CD40L
T31 1073-1077 protein_molecule denotes IL-4
T32 1100-1111 cell_line denotes CL-01 cells
T33 1113-1118 other_name denotes CD40:
T34 1118-1123 protein_molecule denotes CD40L
T35 1151-1155 protein_molecule denotes IL-4
T36 1180-1201 other_name denotes gamma 3 ECS-dependent
T37 1202-1226 DNA_domain_or_region denotes luciferase reporter gene
T38 1295-1305 protein_complex denotes NF-kappa B
T39 1344-1355 DNA_domain_or_region denotes gamma 3 ECS
T40 1379-1384 protein_molecule denotes CD40L
T41 1389-1393 protein_molecule denotes IL-4
T42 1403-1422 DNA_domain_or_region denotes STAT-6-binding site
T43 1452-1456 protein_molecule denotes IL-4
T44 1471-1508 other_name denotes Electrophoretic mobility shift assays
T45 1521-1534 protein_molecule denotes p50/p65/c-Rel
T46 1539-1545 protein_molecule denotes STAT-6
T47 1573-1578 protein_molecule denotes CD40L
T48 1583-1587 protein_molecule denotes IL-4
T49 1624-1634 DNA_domain_or_region denotes DNA motifs
T50 1646-1649 DNA_domain_or_region denotes ECS
T51 1785-1816 other_name denotes synergistic promoter activation
T52 1828-1839 DNA_domain_or_region denotes gamma 3 ECS
T53 1876-1888 DNA_family_or_group denotes cis elements
T54 1913-1918 protein_molecule denotes CD40L
T55 1923-1927 protein_molecule denotes IL-4
T56 1972-1992 DNA_domain_or_region denotes human C gamma 3 gene