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PubMed:17910065 JSONTXT

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LitCoin-entities

Id Subject Object Predicate Lexical cue db_id
4412 50-55 OrganismTaxon denotes human NCBITaxon:9606
4413 56-60 GeneOrGeneProduct denotes PAX9 NCBIGene:5083
4414 68-79 DiseaseOrPhenotypicFeature denotes oligodontia MESH:C538049
4415 81-85 GeneOrGeneProduct denotes PAX9 NCBIGene:5083
4416 90-94 GeneOrGeneProduct denotes MSX1 NCBIGene:4487
4417 188-194 OrganismTaxon denotes humans NCBITaxon:9606
4418 240-278 DiseaseOrPhenotypicFeature denotes nonsyndromic and syndromic oligodontia MESH:C538049
4419 322-346 DiseaseOrPhenotypicFeature denotes nonsyndromic oligodontia MESH:C538049
4420 364-368 GeneOrGeneProduct denotes PAX9 NCBIGene:5083
4421 373-377 GeneOrGeneProduct denotes MSX1 NCBIGene:4487
4422 484-489 SequenceVariant denotes C139T DBSNP:rs121917720
4423 504-508 GeneOrGeneProduct denotes PAX9 NCBIGene:5083
4424 614-618 GeneOrGeneProduct denotes MSX1 NCBIGene:4487
4425 624-629 SequenceVariant denotes C139T DBSNP:rs121917720
4426 686-710 SequenceVariant denotes arginine by a tryptophan DBSNP:rs121917720
4427 712-716 SequenceVariant denotes R47W DBSNP:rs121917720
4428 782-786 GeneOrGeneProduct denotes PAX9 NCBIGene:5083
4429 850-871 DiseaseOrPhenotypicFeature denotes oligodontia phenotype MESH:C538049
4430 945-949 GeneOrGeneProduct denotes PAX9 NCBIGene:5083
4431 1008-1012 SequenceVariant denotes R47W DBSNP:rs121917720

LitCoin-sentences

Id Subject Object Predicate Lexical cue
T1 0-80 Sentence denotes A novel missense mutation in the paired domain of human PAX9 causes oligodontia.
T2 81-184 Sentence denotes PAX9 and MSX1 are transcription factors that play essential roles in craniofacial and limb development.
T3 185-293 Sentence denotes In humans, mutations in both genes are associated with nonsyndromic and syndromic oligodontia, respectively.
T4 294-378 Sentence denotes We screened one family with nonsyndromic oligodontia for mutations in PAX9 and MSX1.
T5 379-547 Sentence denotes Single stranded conformational polymorphism (SSCP) analysis and sequencing revealed a novel heterozygous C139T transition in PAX9 in the affected members of the family.
T6 548-619 Sentence denotes There were no mutations detected in the entire coding sequence of MSX1.
T7 620-801 Sentence denotes The C139T mutation, predicted to result in the substitution of an arginine by a tryptophan (R47W) in the N-terminal subdomain, affected conserved residues in the PAX9 paired domain.
T8 802-1003 Sentence denotes To elucidate the pathogenic mechanism producing oligodontia phenotype caused by this mutation, we analyzed the binding of wild-type and mutant PAX9 paired domain protein to double-stranded DNA targets.
T9 1004-1157 Sentence denotes The R47W mutation dramatically reduced DNA binding suggesting that the mutant protein with consequent haploinsufficiency results in a clinical phenotype.

LitCoin-entities-OrganismTaxon-PD

Id Subject Object Predicate Lexical cue db_id
T1 50-55 OrganismTaxon denotes human NCBItxid:9606
T2 188-194 OrganismTaxon denotes humans NCBItxid:9605

LitCoin-SeqVar

Id Subject Object Predicate Lexical cue
T1 484-489 SequenceVariant denotes C139T
T2 624-629 SequenceVariant denotes C139T
T3 712-716 SequenceVariant denotes R47W
T4 1008-1012 SequenceVariant denotes R47W

LitCoin-GeneOrGeneProduct-v0

Id Subject Object Predicate Lexical cue
T1 2-7 GeneOrGeneProduct denotes novel
T2 8-16 GeneOrGeneProduct denotes missense
T3 17-25 GeneOrGeneProduct denotes mutation
T4 33-39 GeneOrGeneProduct denotes paired
T5 56-60 GeneOrGeneProduct denotes PAX9
T6 81-85 GeneOrGeneProduct denotes PAX9
T7 90-94 GeneOrGeneProduct denotes MSX1
T8 99-120 GeneOrGeneProduct denotes transcription factors
T9 167-171 GeneOrGeneProduct denotes limb
T10 196-205 GeneOrGeneProduct denotes mutations
T11 257-266 GeneOrGeneProduct denotes syndromic
T12 351-360 GeneOrGeneProduct denotes mutations
T13 364-368 GeneOrGeneProduct denotes PAX9
T14 373-377 GeneOrGeneProduct denotes MSX1
T15 386-394 GeneOrGeneProduct denotes stranded
T16 465-470 GeneOrGeneProduct denotes novel
T17 504-508 GeneOrGeneProduct denotes PAX9
T18 559-571 GeneOrGeneProduct denotes no mutations
T19 588-594 GeneOrGeneProduct denotes entire
T20 614-618 GeneOrGeneProduct denotes MSX1
T21 630-638 GeneOrGeneProduct denotes mutation
T22 640-649 GeneOrGeneProduct denotes predicted
T23 725-735 GeneOrGeneProduct denotes N-terminal
T24 756-765 GeneOrGeneProduct denotes conserved
T25 782-786 GeneOrGeneProduct denotes PAX9
T26 787-793 GeneOrGeneProduct denotes paired
T27 887-895 GeneOrGeneProduct denotes mutation
T28 913-920 GeneOrGeneProduct denotes binding
T29 938-944 GeneOrGeneProduct denotes mutant
T30 945-949 GeneOrGeneProduct denotes PAX9
T31 950-956 GeneOrGeneProduct denotes paired
T32 964-971 GeneOrGeneProduct denotes protein
T33 975-981 GeneOrGeneProduct denotes double
T34 982-990 GeneOrGeneProduct denotes stranded
T35 1013-1021 GeneOrGeneProduct denotes mutation
T36 1035-1042 GeneOrGeneProduct denotes reduced
T37 1043-1054 GeneOrGeneProduct denotes DNA binding
T38 1075-1081 GeneOrGeneProduct denotes mutant
T39 1082-1089 GeneOrGeneProduct denotes protein
T40 1106-1124 GeneOrGeneProduct denotes haploinsufficiency
T41 1133-1137 GeneOrGeneProduct denotes in a

LitCoin-GeneOrGeneProduct-v2

Id Subject Object Predicate Lexical cue
T1 2-7 GeneOrGeneProduct denotes novel
T2 33-39 GeneOrGeneProduct denotes paired
T3 56-60 GeneOrGeneProduct denotes PAX9
T4 81-85 GeneOrGeneProduct denotes PAX9
T5 90-94 GeneOrGeneProduct denotes MSX1
T6 99-120 GeneOrGeneProduct denotes transcription factors
T7 364-368 GeneOrGeneProduct denotes PAX9
T8 373-377 GeneOrGeneProduct denotes MSX1
T9 386-394 GeneOrGeneProduct denotes stranded
T10 465-470 GeneOrGeneProduct denotes novel
T11 504-508 GeneOrGeneProduct denotes PAX9
T12 614-618 GeneOrGeneProduct denotes MSX1
T13 725-735 GeneOrGeneProduct denotes N-terminal
T14 756-765 GeneOrGeneProduct denotes conserved
T15 782-786 GeneOrGeneProduct denotes PAX9
T16 787-793 GeneOrGeneProduct denotes paired
T17 913-920 GeneOrGeneProduct denotes binding
T18 938-944 GeneOrGeneProduct denotes mutant
T19 945-949 GeneOrGeneProduct denotes PAX9
T20 950-956 GeneOrGeneProduct denotes paired
T21 964-971 GeneOrGeneProduct denotes protein
T22 975-981 GeneOrGeneProduct denotes double
T23 982-990 GeneOrGeneProduct denotes stranded
T24 1035-1042 GeneOrGeneProduct denotes reduced
T25 1043-1054 GeneOrGeneProduct denotes DNA binding
T26 1075-1081 GeneOrGeneProduct denotes mutant
T27 1082-1089 GeneOrGeneProduct denotes protein

LitCoin-Disease-MeSH

Id Subject Object Predicate Lexical cue originalLabel
T1 257-266 DiseaseOrPhenotypicFeature denotes syndromic D013577

LitCoin-GeneOrGeneProduct-v3

Id Subject Object Predicate Lexical cue
T1 56-60 GeneOrGeneProduct denotes PAX9
T2 81-85 GeneOrGeneProduct denotes PAX9
T3 90-94 GeneOrGeneProduct denotes MSX1
T4 364-368 GeneOrGeneProduct denotes PAX9
T5 373-377 GeneOrGeneProduct denotes MSX1
T6 386-394 GeneOrGeneProduct denotes stranded
T7 504-508 GeneOrGeneProduct denotes PAX9
T8 614-618 GeneOrGeneProduct denotes MSX1
T9 725-735 GeneOrGeneProduct denotes N-terminal
T10 782-786 GeneOrGeneProduct denotes PAX9
T11 945-949 GeneOrGeneProduct denotes PAX9
T12 982-990 GeneOrGeneProduct denotes stranded

LitCoin_Mondo_095

Id Subject Object Predicate Lexical cue mondo_id
T1 68-79 DiseaseOrPhenotypicFeature denotes oligodontia 0005486
T2 267-278 DiseaseOrPhenotypicFeature denotes oligodontia 0005486
T3 335-346 DiseaseOrPhenotypicFeature denotes oligodontia 0005486
T4 850-861 DiseaseOrPhenotypicFeature denotes oligodontia 0005486

LitCoin-MeSH-Disease-2

Id Subject Object Predicate Lexical cue ID:
T1 68-79 DiseaseOrPhenotypicFeature denotes oligodontia DISEASE
T2 267-278 DiseaseOrPhenotypicFeature denotes oligodontia DISEASE
T3 322-346 DiseaseOrPhenotypicFeature denotes nonsyndromic oligodontia DISEASE
T4 850-871 DiseaseOrPhenotypicFeature denotes oligodontia phenotype DISEASE

LitCoin-MONDO_bioort2019

Id Subject Object Predicate Lexical cue #label
T1 68-79 DiseaseOrPhenotypicFeature denotes oligodontia DISEASE
T2 267-278 DiseaseOrPhenotypicFeature denotes oligodontia DISEASE
T3 322-346 DiseaseOrPhenotypicFeature denotes nonsyndromic oligodontia DISEASE
T4 850-871 DiseaseOrPhenotypicFeature denotes oligodontia phenotype DISEASE

LitCoin-Chemical-MeSH-CHEBI

Id Subject Object Predicate Lexical cue ID:
T1 686-694 ChemicalEntity denotes arginine http://purl.obolibrary.org/obo/CHEBI_32696|http://purl.obolibrary.org/obo/CHEBI_29016|http://purl.obolibrary.org/obo/CHEBI_16467
T4 700-710 ChemicalEntity denotes tryptophan http://purl.obolibrary.org/obo/CHEBI_57912|http://purl.obolibrary.org/obo/CHEBI_57719|http://purl.obolibrary.org/obo/CHEBI_27897|http://purl.obolibrary.org/obo/CHEBI_16828

LitCoin-NCBITaxon-2

Id Subject Object Predicate Lexical cue
T1 50-55 OrganismTaxon denotes human
T2 188-194 OrganismTaxon denotes humans

LitCoin-training-merged

Id Subject Object Predicate Lexical cue #label ID:
T4 700-710 ChemicalEntity denotes tryptophan http://purl.obolibrary.org/obo/CHEBI_16828|http://purl.obolibrary.org/obo/CHEBI_27897|http://purl.obolibrary.org/obo/CHEBI_57719|http://purl.obolibrary.org/obo/CHEBI_57912
T1 686-694 ChemicalEntity denotes arginine http://purl.obolibrary.org/obo/CHEBI_16467|http://purl.obolibrary.org/obo/CHEBI_29016|http://purl.obolibrary.org/obo/CHEBI_32696
T12 982-990 GeneOrGeneProduct denotes stranded
T11 945-949 GeneOrGeneProduct denotes PAX9
T10 782-786 GeneOrGeneProduct denotes PAX9
T9 725-735 GeneOrGeneProduct denotes N-terminal
T8 614-618 GeneOrGeneProduct denotes MSX1
T7 504-508 GeneOrGeneProduct denotes PAX9
T6 386-394 GeneOrGeneProduct denotes stranded
T5 373-377 GeneOrGeneProduct denotes MSX1
T73288 364-368 GeneOrGeneProduct denotes PAX9
T3 90-94 GeneOrGeneProduct denotes MSX1
T2 81-85 GeneOrGeneProduct denotes PAX9
T75352 56-60 GeneOrGeneProduct denotes PAX9
T13516 850-871 DiseaseOrPhenotypicFeature denotes oligodontia phenotype DISEASE
T80589 322-346 DiseaseOrPhenotypicFeature denotes nonsyndromic oligodontia DISEASE
T78294 267-278 DiseaseOrPhenotypicFeature denotes oligodontia DISEASE
T19660 68-79 DiseaseOrPhenotypicFeature denotes oligodontia DISEASE
T12058 188-194 OrganismTaxon denotes humans
T1932 50-55 OrganismTaxon denotes human
T74008 1008-1012 SequenceVariant denotes R47W
T98955 712-716 SequenceVariant denotes R47W
T4189 624-629 SequenceVariant denotes C139T
T53318 484-489 SequenceVariant denotes C139T

sentences

Id Subject Object Predicate Lexical cue
TextSentencer_T1 0-80 Sentence denotes A novel missense mutation in the paired domain of human PAX9 causes oligodontia.
TextSentencer_T2 81-184 Sentence denotes PAX9 and MSX1 are transcription factors that play essential roles in craniofacial and limb development.
TextSentencer_T3 185-293 Sentence denotes In humans, mutations in both genes are associated with nonsyndromic and syndromic oligodontia, respectively.
TextSentencer_T4 294-378 Sentence denotes We screened one family with nonsyndromic oligodontia for mutations in PAX9 and MSX1.
TextSentencer_T5 379-547 Sentence denotes Single stranded conformational polymorphism (SSCP) analysis and sequencing revealed a novel heterozygous C139T transition in PAX9 in the affected members of the family.
TextSentencer_T6 548-619 Sentence denotes There were no mutations detected in the entire coding sequence of MSX1.
TextSentencer_T7 620-801 Sentence denotes The C139T mutation, predicted to result in the substitution of an arginine by a tryptophan (R47W) in the N-terminal subdomain, affected conserved residues in the PAX9 paired domain.
TextSentencer_T8 802-1003 Sentence denotes To elucidate the pathogenic mechanism producing oligodontia phenotype caused by this mutation, we analyzed the binding of wild-type and mutant PAX9 paired domain protein to double-stranded DNA targets.
TextSentencer_T9 1004-1157 Sentence denotes The R47W mutation dramatically reduced DNA binding suggesting that the mutant protein with consequent haploinsufficiency results in a clinical phenotype.
T1 0-80 Sentence denotes A novel missense mutation in the paired domain of human PAX9 causes oligodontia.
T2 81-184 Sentence denotes PAX9 and MSX1 are transcription factors that play essential roles in craniofacial and limb development.
T3 185-293 Sentence denotes In humans, mutations in both genes are associated with nonsyndromic and syndromic oligodontia, respectively.
T4 294-378 Sentence denotes We screened one family with nonsyndromic oligodontia for mutations in PAX9 and MSX1.
T5 379-547 Sentence denotes Single stranded conformational polymorphism (SSCP) analysis and sequencing revealed a novel heterozygous C139T transition in PAX9 in the affected members of the family.
T6 548-619 Sentence denotes There were no mutations detected in the entire coding sequence of MSX1.
T7 620-801 Sentence denotes The C139T mutation, predicted to result in the substitution of an arginine by a tryptophan (R47W) in the N-terminal subdomain, affected conserved residues in the PAX9 paired domain.
T8 802-1003 Sentence denotes To elucidate the pathogenic mechanism producing oligodontia phenotype caused by this mutation, we analyzed the binding of wild-type and mutant PAX9 paired domain protein to double-stranded DNA targets.
T9 1004-1157 Sentence denotes The R47W mutation dramatically reduced DNA binding suggesting that the mutant protein with consequent haploinsufficiency results in a clinical phenotype.

DisGeNET

Id Subject Object Predicate Lexical cue
T0 56-60 gene:5083 denotes PAX9
T1 68-79 disease:C0020608 denotes oligodontia
R1 T0 T1 associated_with PAX9,oligodontia

PubmedHPO

Id Subject Object Predicate Lexical cue
T1 267-278 HP_0000677 denotes oligodontia
T2 335-346 HP_0000677 denotes oligodontia
T3 850-861 HP_0000677 denotes oligodontia
T1 267-278 HP_0000677 denotes oligodontia
T2 335-346 HP_0000677 denotes oligodontia
T3 850-861 HP_0000677 denotes oligodontia

DisGeNET5_gene_disease

Id Subject Object Predicate Lexical cue
17910065-0#56#60#gene5083 56-60 gene5083 denotes PAX9
17910065-0#68#79#diseaseC0020608 68-79 diseaseC0020608 denotes oligodontia
17910065-0#68#79#diseaseC4082304 68-79 diseaseC4082304 denotes oligodontia
17910065-3#79#83#gene4487 373-377 gene4487 denotes MSX1
17910065-3#41#52#diseaseC0020608 335-346 diseaseC0020608 denotes oligodontia
17910065-3#41#52#diseaseC4082304 335-346 diseaseC4082304 denotes oligodontia
56#60#gene508368#79#diseaseC0020608 17910065-0#56#60#gene5083 17910065-0#68#79#diseaseC0020608 associated_with PAX9,oligodontia
56#60#gene508368#79#diseaseC4082304 17910065-0#56#60#gene5083 17910065-0#68#79#diseaseC4082304 associated_with PAX9,oligodontia
79#83#gene448741#52#diseaseC0020608 17910065-3#79#83#gene4487 17910065-3#41#52#diseaseC0020608 associated_with MSX1,oligodontia
79#83#gene448741#52#diseaseC4082304 17910065-3#79#83#gene4487 17910065-3#41#52#diseaseC4082304 associated_with MSX1,oligodontia

PubCasesHPO

Id Subject Object Predicate Lexical cue
TI1 68-79 HP:0000677 denotes oligodontia
AB1 267-278 HP:0000677 denotes oligodontia
AB2 335-346 HP:0000677 denotes oligodontia
AB3 850-861 HP:0000677 denotes oligodontia

PubCasesORDO

Id Subject Object Predicate Lexical cue
TI1 68-79 ORDO:99798 denotes oligodontia
AB1 267-278 ORDO:99798 denotes oligodontia
AB2 335-346 ORDO:99798 denotes oligodontia
AB3 850-861 ORDO:99798 denotes oligodontia

performance-test

Id Subject Object Predicate Lexical cue
PD-UBERON-AE-B_T1 167-171 http://purl.obolibrary.org/obo/UBERON_0002101 denotes limb

tmVarCorpus

Id Subject Object Predicate Lexical cue
T1 484-489 DNAMutation:c|SUB|C|139|T denotes C139T
T2 624-629 DNAMutation:c|SUB|C|139|T denotes C139T
T3 712-716 ProteinMutation:p|SUB|R|47|W denotes R47W
T4 1008-1012 ProteinMutation:p|SUB|R|47|W denotes R47W