> top > docs > PubMed:17003357 > annotations

PubMed:17003357 JSONTXT

Annnotations TAB JSON ListView MergeView

LitCoin-entities-OrganismTaxon-PD

Id Subject Object Predicate Lexical cue db_id
T1 1149-1154 OrganismTaxon denotes codon NCBItxid:79338

LitCoin-sentences

Id Subject Object Predicate Lexical cue
T1 0-66 Sentence denotes A haplotype-based analysis of the PTPN22 locus in type 1 diabetes.
T2 67-209 Sentence denotes A recent addition to the list of widely confirmed type 1 diabetes risk loci is the PTPN22 gene encoding a lymphoid-specific phosphatase (Lyp).
T3 210-367 Sentence denotes However, evidence supporting a role for PTPN22 in type 1 diabetes derives entirely from the study of just one coding single nucleotide polymorphism, 1858C/T.
T4 368-548 Sentence denotes In the current study, the haplotype structure of the PTPN22 region was determined, and individual haplotypes were tested for association with type 1 diabetes in family-based tests.
T5 549-676 Sentence denotes The 1858T risk allele occurred on only a single haplotype that was strongly associated with type 1 diabetes (P = 7.9 x 10(-5)).
T6 677-818 Sentence denotes After controlling for the effects of this allele, two other haplotypes were observed to be weakly associated with type 1 diabetes (P < 0.05).
T7 819-979 Sentence denotes Sequencing of the coding region of PTPN22 on these haplotypes revealed a novel variant (2250G/C) predicted to result in a nonsynonymous amino acid substitution.
T8 980-1169 Sentence denotes Analysis of PTPN22 transcripts from a subject heterozygous for this variant indicated that it interfered with normal mRNA splicing, resulting in a premature termination codon after exon 17.
T9 1170-1412 Sentence denotes These results support the conclusion that the 1858C/T allele is the major risk variant for type 1 diabetes in the PTPN22 locus, but they suggest that additional infrequent coding variants at PTPN22 may also contribute to type 1 diabetes risk.

LitCoin-entities

Id Subject Object Predicate Lexical cue db_id
3379 34-40 GeneOrGeneProduct denotes PTPN22 NCBIGene:26191
3380 50-65 DiseaseOrPhenotypicFeature denotes type 1 diabetes MESH:D003922
3381 117-132 DiseaseOrPhenotypicFeature denotes type 1 diabetes MESH:D003922
3382 150-156 GeneOrGeneProduct denotes PTPN22 NCBIGene:26191
3383 173-202 GeneOrGeneProduct denotes lymphoid-specific phosphatase NCBIGene:26191
3384 204-207 GeneOrGeneProduct denotes Lyp NCBIGene:26191
3385 250-256 GeneOrGeneProduct denotes PTPN22 NCBIGene:26191
3386 260-275 DiseaseOrPhenotypicFeature denotes type 1 diabetes MESH:D003922
3387 359-366 SequenceVariant denotes 1858C/T DBSNP:rs2476601
3388 421-427 GeneOrGeneProduct denotes PTPN22 NCBIGene:26191
3389 510-525 DiseaseOrPhenotypicFeature denotes type 1 diabetes MESH:D003922
3390 553-558 SequenceVariant denotes 1858T DBSNP:rs2476601
3391 641-656 DiseaseOrPhenotypicFeature denotes type 1 diabetes MESH:D003922
3392 791-806 DiseaseOrPhenotypicFeature denotes type 1 diabetes MESH:D003922
3393 854-860 GeneOrGeneProduct denotes PTPN22 NCBIGene:26191
3394 907-914 SequenceVariant denotes 2250G/C DBSNP:rs56048322
3395 992-998 GeneOrGeneProduct denotes PTPN22 NCBIGene:26191
3396 1216-1223 SequenceVariant denotes 1858C/T DBSNP:rs2476601
3397 1261-1276 DiseaseOrPhenotypicFeature denotes type 1 diabetes MESH:D003922
3398 1284-1290 GeneOrGeneProduct denotes PTPN22 NCBIGene:26191
3399 1361-1367 GeneOrGeneProduct denotes PTPN22 NCBIGene:26191
3400 1391-1406 DiseaseOrPhenotypicFeature denotes type 1 diabetes MESH:D003922

LitCoin-SeqVar

Id Subject Object Predicate Lexical cue
T1 359-364 SequenceVariant denotes 1858C
T2 553-558 SequenceVariant denotes 1858T
T3 907-912 SequenceVariant denotes 2250G
T4 1216-1221 SequenceVariant denotes 1858C

LitCoin-GeneOrGeneProduct-v0

Id Subject Object Predicate Lexical cue
T1 12-17 GeneOrGeneProduct denotes based
T2 34-40 GeneOrGeneProduct denotes PTPN22
T3 57-65 GeneOrGeneProduct denotes diabetes
T4 92-96 GeneOrGeneProduct denotes list
T5 124-132 GeneOrGeneProduct denotes diabetes
T6 150-156 GeneOrGeneProduct denotes PTPN22
T7 191-202 GeneOrGeneProduct denotes phosphatase
T8 250-256 GeneOrGeneProduct denotes PTPN22
T9 267-275 GeneOrGeneProduct denotes diabetes
T10 284-292 GeneOrGeneProduct denotes entirely
T11 421-427 GeneOrGeneProduct denotes PTPN22
T12 439-449 GeneOrGeneProduct denotes determined
T13 482-488 GeneOrGeneProduct denotes tested
T14 517-525 GeneOrGeneProduct denotes diabetes
T15 536-541 GeneOrGeneProduct denotes based
T16 542-547 GeneOrGeneProduct denotes tests
T17 648-656 GeneOrGeneProduct denotes diabetes
T18 731-736 GeneOrGeneProduct denotes other
T19 768-774 GeneOrGeneProduct denotes weakly
T20 798-806 GeneOrGeneProduct denotes diabetes
T21 854-860 GeneOrGeneProduct denotes PTPN22
T22 892-897 GeneOrGeneProduct denotes novel
T23 916-925 GeneOrGeneProduct denotes predicted
T24 936-940 GeneOrGeneProduct denotes in a
T25 955-965 GeneOrGeneProduct denotes amino acid
T26 992-998 GeneOrGeneProduct denotes PTPN22
T27 999-1010 GeneOrGeneProduct denotes transcripts
T28 1097-1101 GeneOrGeneProduct denotes mRNA
T29 1102-1110 GeneOrGeneProduct denotes splicing
T30 1122-1126 GeneOrGeneProduct denotes in a
T31 1238-1243 GeneOrGeneProduct denotes major
T32 1268-1276 GeneOrGeneProduct denotes diabetes
T33 1284-1290 GeneOrGeneProduct denotes PTPN22
T34 1361-1367 GeneOrGeneProduct denotes PTPN22
T35 1398-1406 GeneOrGeneProduct denotes diabetes

LitCoin-GeneOrGeneProduct-v2

Id Subject Object Predicate Lexical cue
T1 34-40 GeneOrGeneProduct denotes PTPN22
T2 57-65 GeneOrGeneProduct denotes diabetes
T3 124-132 GeneOrGeneProduct denotes diabetes
T4 150-156 GeneOrGeneProduct denotes PTPN22
T5 191-202 GeneOrGeneProduct denotes phosphatase
T6 250-256 GeneOrGeneProduct denotes PTPN22
T7 267-275 GeneOrGeneProduct denotes diabetes
T8 421-427 GeneOrGeneProduct denotes PTPN22
T9 517-525 GeneOrGeneProduct denotes diabetes
T10 648-656 GeneOrGeneProduct denotes diabetes
T11 731-736 GeneOrGeneProduct denotes other
T12 798-806 GeneOrGeneProduct denotes diabetes
T13 854-860 GeneOrGeneProduct denotes PTPN22
T14 892-897 GeneOrGeneProduct denotes novel
T15 955-965 GeneOrGeneProduct denotes amino acid
T16 992-998 GeneOrGeneProduct denotes PTPN22
T17 1097-1101 GeneOrGeneProduct denotes mRNA
T18 1238-1243 GeneOrGeneProduct denotes major
T19 1268-1276 GeneOrGeneProduct denotes diabetes
T20 1284-1290 GeneOrGeneProduct denotes PTPN22
T21 1361-1367 GeneOrGeneProduct denotes PTPN22
T22 1398-1406 GeneOrGeneProduct denotes diabetes

LitCoin-Disease-MeSH

Id Subject Object Predicate Lexical cue originalLabel
T1 50-65 DiseaseOrPhenotypicFeature denotes type 1 diabetes D003922
T2 117-132 DiseaseOrPhenotypicFeature denotes type 1 diabetes D003922
T3 260-275 DiseaseOrPhenotypicFeature denotes type 1 diabetes D003922
T4 510-525 DiseaseOrPhenotypicFeature denotes type 1 diabetes D003922
T5 641-656 DiseaseOrPhenotypicFeature denotes type 1 diabetes D003922
T6 791-806 DiseaseOrPhenotypicFeature denotes type 1 diabetes D003922
T7 1261-1276 DiseaseOrPhenotypicFeature denotes type 1 diabetes D003922
T8 1391-1406 DiseaseOrPhenotypicFeature denotes type 1 diabetes D003922

LitCoin-GeneOrGeneProduct-v3

Id Subject Object Predicate Lexical cue
T1 34-40 GeneOrGeneProduct denotes PTPN22
T2 150-156 GeneOrGeneProduct denotes PTPN22
T3 191-202 GeneOrGeneProduct denotes phosphatase
T4 250-256 GeneOrGeneProduct denotes PTPN22
T5 421-427 GeneOrGeneProduct denotes PTPN22
T6 854-860 GeneOrGeneProduct denotes PTPN22
T7 992-998 GeneOrGeneProduct denotes PTPN22
T8 1284-1290 GeneOrGeneProduct denotes PTPN22
T9 1361-1367 GeneOrGeneProduct denotes PTPN22

LitCoin_Mondo_095

Id Subject Object Predicate Lexical cue mondo_id
T1 50-65 DiseaseOrPhenotypicFeature denotes type 1 diabetes 0005147
T2 117-132 DiseaseOrPhenotypicFeature denotes type 1 diabetes 0005147
T3 204-207 DiseaseOrPhenotypicFeature denotes Lyp 0024551
T4 260-275 DiseaseOrPhenotypicFeature denotes type 1 diabetes 0005147
T5 510-525 DiseaseOrPhenotypicFeature denotes type 1 diabetes 0005147
T6 641-656 DiseaseOrPhenotypicFeature denotes type 1 diabetes 0005147
T7 791-806 DiseaseOrPhenotypicFeature denotes type 1 diabetes 0005147
T8 1261-1276 DiseaseOrPhenotypicFeature denotes type 1 diabetes 0005147
T9 1391-1406 DiseaseOrPhenotypicFeature denotes type 1 diabetes 0005147

LitCoin-MeSH-Disease-2

Id Subject Object Predicate Lexical cue ID:
T1 50-65 DiseaseOrPhenotypicFeature denotes type 1 diabetes D003922
T2 117-132 DiseaseOrPhenotypicFeature denotes type 1 diabetes D003922
T3 260-275 DiseaseOrPhenotypicFeature denotes type 1 diabetes D003922
T4 510-525 DiseaseOrPhenotypicFeature denotes type 1 diabetes D003922
T5 641-656 DiseaseOrPhenotypicFeature denotes type 1 diabetes D003922
T6 791-806 DiseaseOrPhenotypicFeature denotes type 1 diabetes D003922
T7 1261-1276 DiseaseOrPhenotypicFeature denotes type 1 diabetes D003922
T8 1391-1406 DiseaseOrPhenotypicFeature denotes type 1 diabetes D003922

LitCoin-MONDO_bioort2019

Id Subject Object Predicate Lexical cue #label
T1 50-65 DiseaseOrPhenotypicFeature denotes type 1 diabetes D003922
T2 117-132 DiseaseOrPhenotypicFeature denotes type 1 diabetes D003922
T3 260-275 DiseaseOrPhenotypicFeature denotes type 1 diabetes D003922
T4 510-525 DiseaseOrPhenotypicFeature denotes type 1 diabetes D003922
T5 641-656 DiseaseOrPhenotypicFeature denotes type 1 diabetes D003922
T6 791-806 DiseaseOrPhenotypicFeature denotes type 1 diabetes D003922
T7 1261-1276 DiseaseOrPhenotypicFeature denotes type 1 diabetes D003922
T8 1391-1406 DiseaseOrPhenotypicFeature denotes type 1 diabetes D003922

LitCoin-Chemical-MeSH-CHEBI

Id Subject Object Predicate Lexical cue ID:
T1 191-202 ChemicalEntity denotes phosphatase D010744

LitCoin-training-merged

Id Subject Object Predicate Lexical cue #label ID:
T1 191-202 ChemicalEntity denotes phosphatase D010744
T9 1361-1367 GeneOrGeneProduct denotes PTPN22
T8 1284-1290 GeneOrGeneProduct denotes PTPN22
T7 992-998 GeneOrGeneProduct denotes PTPN22
T6 854-860 GeneOrGeneProduct denotes PTPN22
T5 421-427 GeneOrGeneProduct denotes PTPN22
T4 250-256 GeneOrGeneProduct denotes PTPN22
T3 191-202 GeneOrGeneProduct denotes phosphatase
T2 150-156 GeneOrGeneProduct denotes PTPN22
T4228 34-40 GeneOrGeneProduct denotes PTPN22
T22725 1391-1406 DiseaseOrPhenotypicFeature denotes type 1 diabetes D003922
T6692 1261-1276 DiseaseOrPhenotypicFeature denotes type 1 diabetes D003922
T88422 791-806 DiseaseOrPhenotypicFeature denotes type 1 diabetes D003922
T20962 641-656 DiseaseOrPhenotypicFeature denotes type 1 diabetes D003922
T3469 510-525 DiseaseOrPhenotypicFeature denotes type 1 diabetes D003922
T61453 260-275 DiseaseOrPhenotypicFeature denotes type 1 diabetes D003922
T13626 117-132 DiseaseOrPhenotypicFeature denotes type 1 diabetes D003922
T22291 50-65 DiseaseOrPhenotypicFeature denotes type 1 diabetes D003922
T67104 1216-1221 SequenceVariant denotes 1858C
T34458 907-912 SequenceVariant denotes 2250G
T29946 553-558 SequenceVariant denotes 1858T
T22904 359-364 SequenceVariant denotes 1858C

DisGeNET

Id Subject Object Predicate Lexical cue
T0 34-40 gene:26191 denotes PTPN22
T1 50-65 disease:C0011854 denotes type 1 diabetes
T2 150-156 gene:26191 denotes PTPN22
T3 117-132 disease:C0011854 denotes type 1 diabetes
T4 250-256 gene:26191 denotes PTPN22
T5 260-275 disease:C0011854 denotes type 1 diabetes
T6 421-427 gene:26191 denotes PTPN22
T7 510-525 disease:C0011854 denotes type 1 diabetes
T8 1284-1290 gene:26191 denotes PTPN22
T9 1261-1276 disease:C0011854 denotes type 1 diabetes
T10 1284-1290 gene:26191 denotes PTPN22
T11 1391-1406 disease:C0011854 denotes type 1 diabetes
T12 1361-1367 gene:26191 denotes PTPN22
T13 1261-1276 disease:C0011854 denotes type 1 diabetes
T14 1361-1367 gene:26191 denotes PTPN22
T15 1391-1406 disease:C0011854 denotes type 1 diabetes
R1 T0 T1 associated_with PTPN22,type 1 diabetes
R2 T2 T3 associated_with PTPN22,type 1 diabetes
R3 T4 T5 associated_with PTPN22,type 1 diabetes
R4 T6 T7 associated_with PTPN22,type 1 diabetes
R5 T8 T9 associated_with PTPN22,type 1 diabetes
R6 T10 T11 associated_with PTPN22,type 1 diabetes
R7 T12 T13 associated_with PTPN22,type 1 diabetes
R8 T14 T15 associated_with PTPN22,type 1 diabetes

DisGeNET5_variant_disease

Id Subject Object Predicate Lexical cue
17003357-8#46#53#geners2476601 1216-1223 geners2476601 denotes 1858C/T
17003357-8#91#106#diseaseC0011854 1261-1276 diseaseC0011854 denotes type 1 diabetes
17003357-8#221#236#diseaseC0011854 1391-1406 diseaseC0011854 denotes type 1 diabetes
46#53#geners247660191#106#diseaseC0011854 17003357-8#46#53#geners2476601 17003357-8#91#106#diseaseC0011854 associated_with 1858C/T,type 1 diabetes
46#53#geners2476601221#236#diseaseC0011854 17003357-8#46#53#geners2476601 17003357-8#221#236#diseaseC0011854 associated_with 1858C/T,type 1 diabetes

DisGeNET5_gene_disease

Id Subject Object Predicate Lexical cue
17003357-0#34#40#gene26191 808-860 gene26191 denotes P < 0.05). Sequencing of the coding region of PTPN22
17003357-0#50#65#diseaseC0011854 970-1276 diseaseC0011854 denotes titution. Analysis of PTPN22 transcripts from a subject heterozygous for this variant indicated that it interfered with normal mRNA splicing, resulting in a premature termination codon after exon 17. These results support the conclusion that the 1858C/T allele is the major risk variant for type 1 diabetes
34#40#gene2619150#65#diseaseC0011854 17003357-0#34#40#gene26191 17003357-0#50#65#diseaseC0011854 associated_with P < 0.05). Sequencing of the coding region of PTPN22,"titution. Analysis of PTPN22 transcripts from a subject heterozygous for this variant indicated that it interfered with normal mRNA splicing, resulting in a premature termination codon after exon 17. These results support the conclusion that the 1858C/T allele is the major risk variant for type 1 diabetes"

tmVarCorpus

Id Subject Object Predicate Lexical cue
T1 359-366 DNAMutation:|SUB|C|1858|T denotes 1858C/T
T2 907-914 DNAMutation:|SUB|G|2250|C denotes 2250G/C
T3 1216-1223 DNAMutation:|SUB|C|1858|T denotes 1858C/T