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PubMed:28747658 JSONTXT

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LitCoin-entities-OrganismTaxon-PD

Id Subject Object Predicate Lexical cue db_id
T1 75-80 OrganismTaxon denotes HIV-1 NCBItxid:11676
T2 140-145 OrganismTaxon denotes HIV-1 NCBItxid:11676

LitCoin-sentences

Id Subject Object Predicate Lexical cue
T1 0-100 Sentence denotes A single amino acid substitution confers B-cell clonogenic activity to the HIV-1 matrix protein p17.
T2 101-288 Sentence denotes Recent data highlight the presence, in HIV-1-seropositive patients with lymphoma, of p17 variants (vp17s) endowed with B-cell clonogenicity, suggesting a role of vp17s in lymphomagenesis.
T3 289-427 Sentence denotes We investigated the mechanisms responsible for the functional disparity on B cells between a wild-type p17 (refp17) and a vp17 named S75X.
T4 428-942 Sentence denotes Here, we show that a single Arginine (R) to Glycine (G) mutation at position 76 in the refp17 backbone (p17R76G), as in the S75X variant, is per se sufficient to confer a B-cell clonogenic potential to the viral protein and modulate, through activation of the PTEN/PI3K/Akt signaling pathway, different molecules involved in apoptosis inhibition (CASP-9, CASP-7, DFF-45, NPM, YWHAZ, Src, PAX2, MAPK8), cell cycle promotion and cancer progression (CDK1, CDK2, CDK8, CHEK1, CHEK2, GSK-3 beta, NPM, PAK1, PP2C-alpha).
T5 943-1099 Sentence denotes Moreover, the only R to G mutation at position 76 was found to strongly impact on protein folding and oligomerization by altering the hydrogen bond network.
T6 1100-1315 Sentence denotes This generates a conformational shift in the p17 R76G mutant which enables a functional epitope(s), masked in refp17, to elicit B-cell growth-promoting signals after its interaction with a still unknown receptor(s).
T7 1316-1453 Sentence denotes Our findings offer new opportunities to understand the molecular mechanisms accounting for the B-cell growth-promoting activity of vp17s.

LitCoin-entities

Id Subject Object Predicate Lexical cue db_id
13213 75-80 OrganismTaxon denotes HIV-1 NCBITaxon:11676
13214 96-99 GeneOrGeneProduct denotes p17 NCBIGene:155348
13215 140-158 DiseaseOrPhenotypicFeature denotes HIV-1-seropositive MESH:D006679
13216 159-167 OrganismTaxon denotes patients NCBITaxon:9606
13217 173-181 DiseaseOrPhenotypicFeature denotes lymphoma MESH:D008223
13218 186-189 GeneOrGeneProduct denotes p17 NCBIGene:155348
13219 272-287 DiseaseOrPhenotypicFeature denotes lymphomagenesis MESH:D008223
13220 392-395 GeneOrGeneProduct denotes p17 NCBIGene:155348
13221 422-426 SequenceVariant denotes S75X p|SUB|S|75|X
13222 456-507 SequenceVariant denotes Arginine (R) to Glycine (G) mutation at position 76 p|SUB|R|76|G
13223 532-535 GeneOrGeneProduct denotes p17 NCBIGene:155348
13224 535-539 SequenceVariant denotes R76G p|SUB|R|76|G
13225 552-556 SequenceVariant denotes S75X p|SUB|S|75|X
13226 688-692 GeneOrGeneProduct denotes PTEN NCBIGene:5728
13227 693-697 GeneOrGeneProduct denotes PI3K NCBIGene:5291
13228 698-701 GeneOrGeneProduct denotes Akt NCBIGene:207
13229 775-781 GeneOrGeneProduct denotes CASP-9 NCBIGene:842
13230 783-789 GeneOrGeneProduct denotes CASP-7 NCBIGene:840
13231 791-797 GeneOrGeneProduct denotes DFF-45 NCBIGene:1676
13232 799-802 GeneOrGeneProduct denotes NPM NCBIGene:4869
13233 804-809 GeneOrGeneProduct denotes YWHAZ NCBIGene:7534
13234 811-814 GeneOrGeneProduct denotes Src NCBIGene:6714
13235 816-820 GeneOrGeneProduct denotes PAX2 NCBIGene:5076
13236 822-827 GeneOrGeneProduct denotes MAPK8 NCBIGene:5599
13237 855-861 DiseaseOrPhenotypicFeature denotes cancer MESH:D009369
13238 875-879 GeneOrGeneProduct denotes CDK1 NCBIGene:983
13239 881-885 GeneOrGeneProduct denotes CDK2 NCBIGene:1017
13240 887-891 GeneOrGeneProduct denotes CDK8 NCBIGene:1024
13241 893-898 GeneOrGeneProduct denotes CHEK1 NCBIGene:1111
13242 900-905 GeneOrGeneProduct denotes CHEK2 NCBIGene:11200
13243 907-917 GeneOrGeneProduct denotes GSK-3 beta NCBIGene:2932
13244 919-922 GeneOrGeneProduct denotes NPM NCBIGene:4869
13245 924-928 GeneOrGeneProduct denotes PAK1 NCBIGene:5058
13246 930-940 GeneOrGeneProduct denotes PP2C-alpha NCBIGene:5494
13247 962-992 SequenceVariant denotes R to G mutation at position 76 p|SUB|R|76|G
13248 1145-1148 GeneOrGeneProduct denotes p17 NCBIGene:155348
13249 1149-1153 SequenceVariant denotes R76G p|SUB|R|76|G

LitCoin_Mondo

Id Subject Object Predicate Lexical cue mondo_id
T1 173-181 DiseaseOrPhenotypicFeature denotes lymphoma 0005062
T2 855-861 DiseaseOrPhenotypicFeature denotes cancer 0004992

LitCoin-SeqVar

Id Subject Object Predicate Lexical cue
T1 422-426 SequenceVariant denotes S75X
T2 552-556 SequenceVariant denotes S75X
T3 1149-1153 SequenceVariant denotes R76G

LitCoin-GeneOrGeneProduct-v0

Id Subject Object Predicate Lexical cue
T1 9-19 GeneOrGeneProduct denotes amino acid
T2 43-47 GeneOrGeneProduct denotes cell
T3 59-67 GeneOrGeneProduct denotes activity
T4 81-95 GeneOrGeneProduct denotes matrix protein
T5 222-226 GeneOrGeneProduct denotes cell
T6 366-371 GeneOrGeneProduct denotes cells
T7 411-415 GeneOrGeneProduct denotes vp17
T8 484-492 GeneOrGeneProduct denotes mutation
T9 566-572 GeneOrGeneProduct denotes is per
T10 601-605 GeneOrGeneProduct denotes cell
T11 634-647 GeneOrGeneProduct denotes viral protein
T12 670-680 GeneOrGeneProduct denotes activation
T13 688-692 GeneOrGeneProduct denotes PTEN
T14 693-697 GeneOrGeneProduct denotes PI3K
T15 741-762 GeneOrGeneProduct denotes involved in apoptosis
T16 775-781 GeneOrGeneProduct denotes CASP-9
T17 783-789 GeneOrGeneProduct denotes CASP-7
T18 791-797 GeneOrGeneProduct denotes DFF-45
T19 804-809 GeneOrGeneProduct denotes YWHAZ
T20 816-820 GeneOrGeneProduct denotes PAX2
T21 822-827 GeneOrGeneProduct denotes MAPK8
T22 830-840 GeneOrGeneProduct denotes cell cycle
T23 875-879 GeneOrGeneProduct denotes CDK1
T24 881-885 GeneOrGeneProduct denotes CDK2
T25 887-891 GeneOrGeneProduct denotes CDK8
T26 893-898 GeneOrGeneProduct denotes CHEK1
T27 900-905 GeneOrGeneProduct denotes CHEK2
T28 907-917 GeneOrGeneProduct denotes GSK-3 beta
T29 924-928 GeneOrGeneProduct denotes PAK1
T30 930-940 GeneOrGeneProduct denotes PP2C-alpha
T31 969-977 GeneOrGeneProduct denotes mutation
T32 1015-1021 GeneOrGeneProduct denotes impact
T33 1025-1040 GeneOrGeneProduct denotes protein folding
T34 1086-1090 GeneOrGeneProduct denotes bond
T35 1132-1137 GeneOrGeneProduct denotes shift
T36 1154-1160 GeneOrGeneProduct denotes mutant
T37 1167-1174 GeneOrGeneProduct denotes enables
T38 1200-1206 GeneOrGeneProduct denotes masked
T39 1230-1234 GeneOrGeneProduct denotes cell
T40 1235-1241 GeneOrGeneProduct denotes growth
T41 1295-1302 GeneOrGeneProduct denotes unknown
T42 1303-1311 GeneOrGeneProduct denotes receptor
T43 1320-1328 GeneOrGeneProduct denotes findings
T44 1413-1417 GeneOrGeneProduct denotes cell
T45 1418-1424 GeneOrGeneProduct denotes growth
T46 1435-1443 GeneOrGeneProduct denotes activity

LitCoin-GeneOrGeneProduct-v2

Id Subject Object Predicate Lexical cue
T1 9-19 GeneOrGeneProduct denotes amino acid
T2 43-47 GeneOrGeneProduct denotes cell
T3 81-95 GeneOrGeneProduct denotes matrix protein
T4 222-226 GeneOrGeneProduct denotes cell
T5 601-605 GeneOrGeneProduct denotes cell
T6 634-647 GeneOrGeneProduct denotes viral protein
T7 688-692 GeneOrGeneProduct denotes PTEN
T8 693-697 GeneOrGeneProduct denotes PI3K
T9 741-762 GeneOrGeneProduct denotes involved in apoptosis
T10 775-781 GeneOrGeneProduct denotes CASP-9
T11 783-789 GeneOrGeneProduct denotes CASP-7
T12 791-797 GeneOrGeneProduct denotes DFF-45
T13 804-809 GeneOrGeneProduct denotes YWHAZ
T14 816-820 GeneOrGeneProduct denotes PAX2
T15 822-827 GeneOrGeneProduct denotes MAPK8
T16 830-840 GeneOrGeneProduct denotes cell cycle
T17 875-879 GeneOrGeneProduct denotes CDK1
T18 881-885 GeneOrGeneProduct denotes CDK2
T19 887-891 GeneOrGeneProduct denotes CDK8
T20 893-898 GeneOrGeneProduct denotes CHEK1
T21 900-905 GeneOrGeneProduct denotes CHEK2
T22 907-917 GeneOrGeneProduct denotes GSK-3 beta
T23 924-928 GeneOrGeneProduct denotes PAK1
T24 930-940 GeneOrGeneProduct denotes PP2C-alpha
T25 1015-1021 GeneOrGeneProduct denotes impact
T26 1025-1040 GeneOrGeneProduct denotes protein folding
T27 1086-1090 GeneOrGeneProduct denotes bond
T28 1154-1160 GeneOrGeneProduct denotes mutant
T29 1230-1234 GeneOrGeneProduct denotes cell
T30 1235-1241 GeneOrGeneProduct denotes growth
T31 1295-1302 GeneOrGeneProduct denotes unknown
T32 1303-1311 GeneOrGeneProduct denotes receptor
T33 1413-1417 GeneOrGeneProduct denotes cell
T34 1418-1424 GeneOrGeneProduct denotes growth

LitCoin-Disease-MeSH

Id Subject Object Predicate Lexical cue originalLabel
T1 173-181 DiseaseOrPhenotypicFeature denotes lymphoma D008223
T2 855-861 DiseaseOrPhenotypicFeature denotes cancer D009369

LitCoin-GeneOrGeneProduct-v3

Id Subject Object Predicate Lexical cue
T1 81-95 GeneOrGeneProduct denotes matrix protein
T2 634-647 GeneOrGeneProduct denotes viral protein
T3 688-692 GeneOrGeneProduct denotes PTEN
T4 693-697 GeneOrGeneProduct denotes PI3K
T5 698-701 GeneOrGeneProduct denotes Akt
T6 741-762 GeneOrGeneProduct denotes involved in apoptosis
T7 775-781 GeneOrGeneProduct denotes CASP-9
T8 783-789 GeneOrGeneProduct denotes CASP-7
T9 791-797 GeneOrGeneProduct denotes DFF-45
T10 804-809 GeneOrGeneProduct denotes YWHAZ
T11 816-820 GeneOrGeneProduct denotes PAX2
T12 822-827 GeneOrGeneProduct denotes MAPK8
T13 875-879 GeneOrGeneProduct denotes CDK1
T14 881-885 GeneOrGeneProduct denotes CDK2
T15 887-891 GeneOrGeneProduct denotes CDK8
T16 893-898 GeneOrGeneProduct denotes CHEK1
T17 900-905 GeneOrGeneProduct denotes CHEK2
T18 907-917 GeneOrGeneProduct denotes GSK-3 beta
T19 924-928 GeneOrGeneProduct denotes PAK1
T20 930-940 GeneOrGeneProduct denotes PP2C-alpha
T21 1025-1040 GeneOrGeneProduct denotes protein folding
T22 1086-1090 GeneOrGeneProduct denotes bond

LitCoin_Mondo_095

Id Subject Object Predicate Lexical cue mondo_id
T1 173-181 DiseaseOrPhenotypicFeature denotes lymphoma 0005062|0003660|0003659

LitCoin-MeSH-Disease-2

Id Subject Object Predicate Lexical cue ID:
T1 75-78 DiseaseOrPhenotypicFeature denotes HIV DISEASE
T2 140-158 DiseaseOrPhenotypicFeature denotes HIV-1-seropositive DISEASE
T3 173-181 DiseaseOrPhenotypicFeature denotes lymphoma D008223
T4 272-287 DiseaseOrPhenotypicFeature denotes lymphomagenesis DISEASE
T5 855-861 DiseaseOrPhenotypicFeature denotes cancer D009369

LitCoin-MONDO_bioort2019

Id Subject Object Predicate Lexical cue #label
T1 140-158 DiseaseOrPhenotypicFeature denotes HIV-1-seropositive DISEASE
T2 173-181 DiseaseOrPhenotypicFeature denotes lymphoma D008223
T3 272-287 DiseaseOrPhenotypicFeature denotes lymphomagenesis DISEASE
T4 855-861 DiseaseOrPhenotypicFeature denotes cancer D009369

LitCoin-NCBITaxon-2

Id Subject Object Predicate Lexical cue
T1 75-80 OrganismTaxon denotes HIV-1
T2 140-145 OrganismTaxon denotes HIV-1
T3 159-167 OrganismTaxon denotes patients

LitCoin-Chemical-MeSH-CHEBI

Id Subject Object Predicate Lexical cue ID:
T1 456-464 ChemicalEntity denotes Arginine http://purl.obolibrary.org/obo/CHEBI_29016
T2 472-479 ChemicalEntity denotes Glycine http://purl.obolibrary.org/obo/CHEBI_15428
T3 1077-1085 ChemicalEntity denotes hydrogen D006859|http://purl.obolibrary.org/obo/CHEBI_49637
T5 1188-1195 ChemicalEntity denotes epitope D000939

LitCoin-training-merged

Id Subject Object Predicate Lexical cue #label ID:
T5 1188-1195 ChemicalEntity denotes epitope D000939
T3 1077-1085 ChemicalEntity denotes hydrogen D006859|http://purl.obolibrary.org/obo/CHEBI_49637
T2 472-479 ChemicalEntity denotes Glycine http://purl.obolibrary.org/obo/CHEBI_15428
T1 456-464 ChemicalEntity denotes Arginine http://purl.obolibrary.org/obo/CHEBI_29016
T22 1086-1090 GeneOrGeneProduct denotes bond
T21 1025-1040 GeneOrGeneProduct denotes protein folding
T20 930-940 GeneOrGeneProduct denotes PP2C-alpha
T19 924-928 GeneOrGeneProduct denotes PAK1
T18 907-917 GeneOrGeneProduct denotes GSK-3 beta
T17 900-905 GeneOrGeneProduct denotes CHEK2
T16 893-898 GeneOrGeneProduct denotes CHEK1
T15 887-891 GeneOrGeneProduct denotes CDK8
T14 881-885 GeneOrGeneProduct denotes CDK2
T13 875-879 GeneOrGeneProduct denotes CDK1
T12 822-827 GeneOrGeneProduct denotes MAPK8
T11 816-820 GeneOrGeneProduct denotes PAX2
T10 804-809 GeneOrGeneProduct denotes YWHAZ
T9 791-797 GeneOrGeneProduct denotes DFF-45
T8 783-789 GeneOrGeneProduct denotes CASP-7
T7 775-781 GeneOrGeneProduct denotes CASP-9
T6 741-762 GeneOrGeneProduct denotes involved in apoptosis
T88995 698-701 GeneOrGeneProduct denotes Akt
T4 693-697 GeneOrGeneProduct denotes PI3K
T49561 688-692 GeneOrGeneProduct denotes PTEN
T33109 634-647 GeneOrGeneProduct denotes viral protein
T17656 81-95 GeneOrGeneProduct denotes matrix protein
T40648 855-861 DiseaseOrPhenotypicFeature denotes cancer D009369
T58876 272-287 DiseaseOrPhenotypicFeature denotes lymphomagenesis DISEASE
T95805 173-181 DiseaseOrPhenotypicFeature denotes lymphoma D008223
T98244 140-158 DiseaseOrPhenotypicFeature denotes HIV-1-seropositive DISEASE
T92018 159-167 OrganismTaxon denotes patients
T57228 140-145 OrganismTaxon denotes HIV-1
T50946 75-80 OrganismTaxon denotes HIV-1
T75572 1149-1153 SequenceVariant denotes R76G
T29712 552-556 SequenceVariant denotes S75X
T47249 422-426 SequenceVariant denotes S75X

mondo_disease

Id Subject Object Predicate Lexical cue mondo_id
T1 173-181 Disease denotes lymphoma http://purl.obolibrary.org/obo/MONDO_0005062
T2 855-861 Disease denotes cancer http://purl.obolibrary.org/obo/MONDO_0004992

GlyCosmos15-HP

Id Subject Object Predicate Lexical cue hp_id
T1 173-181 Phenotype denotes lymphoma HP:0002665
T2 855-861 Phenotype denotes cancer HP:0002664

NCBITAXON

Id Subject Object Predicate Lexical cue db_id
T1 472-479 OrganismTaxon denotes Glycine 3846

Anatomy-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T1 41-47 Body_part denotes B-cell http://purl.obolibrary.org/obo/CL_0000236
T2 220-226 Body_part denotes B-cell http://purl.obolibrary.org/obo/CL_0000236
T3 522-530 Body_part denotes backbone http://purl.obolibrary.org/obo/UBERON_0001130
T4 599-605 Body_part denotes B-cell http://purl.obolibrary.org/obo/CL_0000236
T5 830-840 Body_part denotes cell cycle http://purl.obolibrary.org/obo/UBERON_2000098
T6 1228-1234 Body_part denotes B-cell http://purl.obolibrary.org/obo/CL_0000236
T7 1411-1417 Body_part denotes B-cell http://purl.obolibrary.org/obo/CL_0000236

Glycosmos15-CL

Id Subject Object Predicate Lexical cue cl_id
T1 41-47 Cell denotes B-cell http://purl.obolibrary.org/obo/CL:0000236
T2 220-226 Cell denotes B-cell http://purl.obolibrary.org/obo/CL:0000236
T3 364-371 Cell denotes B cells http://purl.obolibrary.org/obo/CL:0000236
T4 597-605 Cell denotes a B-cell http://purl.obolibrary.org/obo/CL:4023097
T5 599-605 Cell denotes B-cell http://purl.obolibrary.org/obo/CL:0000236
T6 1228-1234 Cell denotes B-cell http://purl.obolibrary.org/obo/CL:0000236
T7 1411-1417 Cell denotes B-cell http://purl.obolibrary.org/obo/CL:0000236