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PubMed:9852310 JSONTXT

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jnlpba-st-training

Id	Subject	Object	Predicate	Lexical cue
T1	196-227	protein	denotes	host-cell transcription factors
T2	233-260	DNA	denotes	cis-regulatory DNA elements
T3	272-298	DNA	denotes	viral long terminal repeat
T4	300-303	DNA	denotes	LTR
T5	384-415	DNA	denotes	transcriptional initiation site
T6	423-432	DNA	denotes	U3 region
T7	440-443	DNA	denotes	LTR
T8	458-461	protein	denotes	Sp1
T9	466-475	protein	denotes	NF-kappaB
T10	476-489	DNA	denotes	binding sites
T11	549-578	DNA	denotes	5'-untranslated leader region
T12	580-586	DNA	denotes	5'-UTR
T13	612-636	DNA	denotes	transcriptional elements
T14	644-663	DNA	denotes	regulatory elements
T15	742-763	protein	denotes	transcription factors
T16	891-897	DNA	denotes	5'-UTR
T17	907-920	DNA	denotes	binding sites
T18	929-950	protein	denotes	transcription factors
T19	957-966	protein	denotes	NF-kappaB
T20	968-973	protein	denotes	NF-AT
T21	975-978	protein	denotes	IRF
T22	984-987	protein	denotes	Sp1
T23	1008-1021	DNA	denotes	binding sites
T24	1097-1100	DNA	denotes	LTR
T25	1151-1157	DNA	denotes	5'-UTR
T26	1189-1199	protein	denotes	nucleosome
T27	1304-1348	DNA	denotes	inducible transcription factor binding sites
T28	1356-1362	DNA	denotes	5'-UTR
T29	1374-1400	DNA	denotes	downstream enhancer domain
T30	1459-1471	DNA	denotes	LTR promoter
T31	1594-1625	protein	denotes	host-cell transcription factors
T32	1649-1655	DNA	denotes	5'-UTR

pubmed-sentences-benchmark

Id	Subject	Object	Predicate	Lexical cue
S1	0-102	Sentence	denotes	Human immunodeficiency virus type-1 transcription: role of the 5'-untranslated leader region (review).
S2	103-305	Sentence	denotes	Human immunodeficiency virus type-1 (HIV-1) transcription is dependent on the interaction of host-cell transcription factors with cis-regulatory DNA elements within the viral long terminal repeat (LTR).
S3	306-490	Sentence	denotes	Much attention has focused on the series of sequence elements upstream of the transcriptional initiation site in the U3 region of the LTR including the Sp1 and NF-kappaB binding sites.
S4	491-637	Sentence	denotes	Recent studies, however, demonstrate that the transcribed 5'-untranslated leader region (5'-UTR) also contains important transcriptional elements.
S5	638-886	Sentence	denotes	These regulatory elements situated downstream of transcription interact with constitutive and inducible transcription factors, mediate transmission of cellular activation signals, and are important for efficient HIV-1 transcription and replication.
S6	887-988	Sentence	denotes	The 5'-UTR contains binding sites for the transcription factors AP-1, NF-kappaB, NF-AT, IRF, and Sp1.
S7	989-1146	Sentence	denotes	Mutations in these binding sites can interfere with the viral response to cell activation signals, decrease LTR transcription, and inhibit viral replication.
S8	1147-1283	Sentence	denotes	The 5'-UTR also interacts with a specific nucleosome that is rapidly displaced during transcriptional activation of the latent provirus.
S9	1284-1561	Sentence	denotes	We propose that the inducible transcription factor binding sites in the 5'-UTR comprise a downstream enhancer domain that can function independent of, or in concert with, the LTR promoter to rapidly increase latent proviral transcription in response to cell activation signals.
S10	1562-1738	Sentence	denotes	In this review, we describe the host-cell transcription factors that interact with the 5'-UTR and discuss their role in the transcriptional regulation of HIV-1 gene expression.

genia-medco-coref

Id	Subject	Object	Predicate	Lexical cue
C1	0-49	NP	denotes	Human immunodeficiency virus type-1 transcription
C2	59-92	NP	denotes	the 5'-untranslated leader region
C3	103-160	NP	denotes	Human immunodeficiency virus type-1 (HIV-1) transcription
C4	196-227	NP	denotes	host-cell transcription factors
C5	268-304	NP	denotes	the viral long terminal repeat (LTR)
C6	436-443	NP	denotes	the LTR
C7	533-587	NP	denotes	the transcribed 5'-untranslated leader region (5'-UTR)
C8	602-636	NP	denotes	important transcriptional elements
C9	638-663	NP	denotes	These regulatory elements
C10	887-897	NP	denotes	The 5'-UTR
C11	907-987	NP	denotes	binding sites for the transcription factors AP-1, NF-kappaB, NF-AT, IRF, and Sp1
C12	1002-1021	NP	denotes	these binding sites
C13	1147-1157	NP	denotes	The 5'-UTR
C14	1178-1199	NP	denotes	a specific nucleosome
C15	1200-1204	NP	denotes	that
C16	1352-1362	NP	denotes	the 5'-UTR
C17	1372-1400	NP	denotes	a downstream enhancer domain
C18	1401-1405	NP	denotes	that
C20	1590-1625	NP	denotes	the host-cell transcription factors
C21	1626-1630	NP	denotes	that
C22	1645-1655	NP	denotes	the 5'-UTR
C19	1590-1655	NP	denotes	the host-cell transcription factors that interact with the 5'-UTR
C23	1668-1673	NP	denotes	their
R1	C3	C1	coref-ident	Human immunodeficiency virus type-1 (HIV-1) transcription,Human immunodeficiency virus type-1 transcription
R2	C6	C5	coref-ident	the LTR,the viral long terminal repeat (LTR)
R3	C7	C2	coref-ident	the transcribed 5'-untranslated leader region (5'-UTR),the 5'-untranslated leader region
R4	C9	C8	coref-ident	These regulatory elements,important transcriptional elements
R5	C10	C7	coref-ident	The 5'-UTR,the transcribed 5'-untranslated leader region (5'-UTR)
R6	C12	C11	coref-ident	these binding sites,"binding sites for the transcription factors AP-1, NF-kappaB, NF-AT, IRF, and Sp1"
R7	C13	C10	coref-ident	The 5'-UTR,The 5'-UTR
R8	C15	C14	coref-relat	that,a specific nucleosome
R9	C16	C13	coref-ident	the 5'-UTR,The 5'-UTR
R10	C18	C17	coref-relat	that,a downstream enhancer domain
R11	C20	C4	coref-ident	the host-cell transcription factors,host-cell transcription factors
R12	C21	C20	coref-relat	that,the host-cell transcription factors
R13	C22	C16	coref-ident	the 5'-UTR,the 5'-UTR
R14	C23	C19	coref-pron	their,the host-cell transcription factors that interact with the 5'-UTR

GENIAcorpus

Id	Subject	Object	Predicate	Lexical cue
T1	0-35	virus	denotes	Human immunodeficiency virus type-1
T2	103-138	virus	denotes	Human immunodeficiency virus type-1
T3	140-145	virus	denotes	HIV-1
T4	196-205	protein_family_or_group	denotes	host-cell
T5	206-227	protein_family_or_group	denotes	transcription factors
T6	233-260	DNA_family_or_group	denotes	cis-regulatory DNA elements
T7	272-298	DNA_domain_or_region	denotes	viral long terminal repeat
T8	300-303	DNA_domain_or_region	denotes	LTR
T9	384-415	DNA_domain_or_region	denotes	transcriptional initiation site
T10	423-432	DNA_domain_or_region	denotes	U3 region
T11	440-443	DNA_domain_or_region	denotes	LTR
T12	458-461	protein_molecule	denotes	Sp1
T13	466-475	protein_complex	denotes	NF-kappaB
T14	476-489	DNA_domain_or_region	denotes	binding sites
T15	549-578	DNA_domain_or_region	denotes	5'-untranslated leader region
T16	580-586	DNA_domain_or_region	denotes	5'-UTR
T17	612-636	DNA_family_or_group	denotes	transcriptional elements
T18	644-663	DNA_family_or_group	denotes	regulatory elements
T19	742-763	protein_family_or_group	denotes	transcription factors
T20	789-816	other_name	denotes	cellular activation signals
T21	850-855	virus	denotes	HIV-1
T22	874-885	other_name	denotes	replication
T23	891-897	DNA_domain_or_region	denotes	5'-UTR
T24	907-920	DNA_domain_or_region	denotes	binding sites
T25	929-950	protein_family_or_group	denotes	transcription factors
T26	957-966	protein_complex	denotes	NF-kappaB
T27	968-973	protein_molecule	denotes	NF-AT
T28	975-978	protein_molecule	denotes	IRF
T29	984-987	protein_molecule	denotes	Sp1
T30	1008-1021	DNA_domain_or_region	denotes	binding sites
T31	1063-1086	other_name	denotes	cell activation signals
T32	1097-1100	DNA_domain_or_region	denotes	LTR
T33	1128-1145	other_name	denotes	viral replication
T34	1151-1157	DNA_domain_or_region	denotes	5'-UTR
T35	1189-1199	protein_complex	denotes	nucleosome
T36	1233-1259	other_name	denotes	transcriptional activation
T37	1267-1282	virus	denotes	latent provirus
T38	1304-1334	DNA_domain_or_region	denotes	inducible transcription factor
T39	1335-1348	DNA_domain_or_region	denotes	binding sites
T40	1356-1362	DNA_domain_or_region	denotes	5'-UTR
T41	1374-1400	DNA_domain_or_region	denotes	downstream enhancer domain
T42	1459-1462	DNA_domain_or_region	denotes	LTR
T43	1537-1560	other_name	denotes	cell activation signals
T44	1594-1603	protein_family_or_group	denotes	host-cell
T45	1604-1625	protein_family_or_group	denotes	transcription factors
T46	1649-1655	DNA_domain_or_region	denotes	5'-UTR
T47	1686-1712	other_name	denotes	transcriptional regulation
T48	1716-1721	virus	denotes	HIV-1