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PubMed:17634480 JSONTXT

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LitCoin-sentences

Id Subject Object Predicate Lexical cue
T1 0-109 Sentence denotes Common germline genetic variation in antioxidant defense genes and survival after diagnosis of breast cancer.
T2 110-118 Sentence denotes PURPOSE:
T3 119-253 Sentence denotes The prognosis of breast cancer varies considerably among individuals, and inherited genetic factors may help explain this variability.
T4 254-434 Sentence denotes Of particular interest are genes involved in defense against reactive oxygen species (ROS) because ROS are thought to cause DNA damage and contribute to the pathogenesis of cancer.
T5 435-456 Sentence denotes PATIENTS AND METHODS:
T6 457-735 Sentence denotes We examined associations between 54 polymorphisms that tag the known common variants (minor allele frequency > 0.05) in 10 genes involved in oxidative damage repair (CAT, SOD1, SOD2, GPX1, GPX4, GSR, TXN, TXN2, TXNRD1, and TXNRD2) and survival in 4,470 women with breast cancer.
T7 736-744 Sentence denotes RESULTS:
T8 745-949 Sentence denotes Two single nucleotide polymorphisms (SNPs) in GPX4 (rs713041 and rs757229) were associated with all-cause mortality even after adjusting for multiple hypothesis testing (adjusted P = .0041 and P = .0035).
T9 950-1004 Sentence denotes These SNPs are correlated with each other (r2 = 0.61).
T10 1005-1272 Sentence denotes GPX4 rs713041 is located near the selenocysteine insertion sequence element in the GPX4 3' untranslated region, and the rare allele of this SNP is associated with an increased risk of death, with a hazard ratio of 1.27 per rare allele carried (95% CI, 1.13 to 11.43).
T11 1273-1372 Sentence denotes This effect was not attenuated after adjusting for tumor stage, grade, or estrogen receptor status.
T12 1373-1596 Sentence denotes We found that the common allele is preferentially expressed in normal lymphocytes, normal breast, and breast tumors compared with the rare allele, but there were no differences in total levels of GPX4 mRNA across genotypes.
T13 1597-1608 Sentence denotes CONCLUSION:
T14 1609-1756 Sentence denotes These data provide strong support for the hypothesis that common variation in GPX4 is associated with prognosis after a diagnosis of breast cancer.

LitCoin-entities-OrganismTaxon-PD

Id Subject Object Predicate Lexical cue db_id
T1 1054-1072 OrganismTaxon denotes insertion sequence NCBItxid:45328

LitCoin-entities

Id Subject Object Predicate Lexical cue db_id
4256 95-108 DiseaseOrPhenotypicFeature denotes breast cancer MESH:D001943
4257 136-149 DiseaseOrPhenotypicFeature denotes breast cancer MESH:D001943
4258 315-338 ChemicalEntity denotes reactive oxygen species MESH:D017382
4259 340-343 ChemicalEntity denotes ROS MESH:D017382
4260 353-356 ChemicalEntity denotes ROS MESH:D017382
4261 427-433 DiseaseOrPhenotypicFeature denotes cancer MESH:D009369
4262 435-443 OrganismTaxon denotes PATIENTS NCBITaxon:9606
4263 623-626 GeneOrGeneProduct denotes CAT NCBIGene:847
4264 628-632 GeneOrGeneProduct denotes SOD1 NCBIGene:6647
4265 634-638 GeneOrGeneProduct denotes SOD2 NCBIGene:6648
4266 640-644 GeneOrGeneProduct denotes GPX1 NCBIGene:2876
4267 646-650 GeneOrGeneProduct denotes GPX4 NCBIGene:2879
4268 652-655 GeneOrGeneProduct denotes GSR NCBIGene:2936
4269 657-660 GeneOrGeneProduct denotes TXN NCBIGene:7295
4270 662-666 GeneOrGeneProduct denotes TXN2 NCBIGene:25828
4271 668-674 GeneOrGeneProduct denotes TXNRD1 NCBIGene:7296
4272 680-686 GeneOrGeneProduct denotes TXNRD2 NCBIGene:10587
4273 710-715 OrganismTaxon denotes women NCBITaxon:9606
4274 721-734 DiseaseOrPhenotypicFeature denotes breast cancer MESH:D001943
4275 791-795 GeneOrGeneProduct denotes GPX4 NCBIGene:2879
4276 797-805 SequenceVariant denotes rs713041 DBSNP:rs713041
4277 810-818 SequenceVariant denotes rs757229 DBSNP:rs757229
4278 1005-1009 GeneOrGeneProduct denotes GPX4 NCBIGene:2879
4279 1010-1018 SequenceVariant denotes rs713041 DBSNP:rs713041
4280 1039-1053 ChemicalEntity denotes selenocysteine MESH:D017279
4281 1088-1092 GeneOrGeneProduct denotes GPX4 NCBIGene:2879
4282 1189-1194 DiseaseOrPhenotypicFeature denotes death MESH:D003643
4283 1324-1329 DiseaseOrPhenotypicFeature denotes tumor MESH:D009369
4284 1347-1364 GeneOrGeneProduct denotes estrogen receptor NCBIGene:2099
4285 1475-1488 DiseaseOrPhenotypicFeature denotes breast tumors MESH:D001943
4286 1569-1573 GeneOrGeneProduct denotes GPX4 NCBIGene:2879
4287 1687-1691 GeneOrGeneProduct denotes GPX4 NCBIGene:2879
4288 1742-1755 DiseaseOrPhenotypicFeature denotes breast cancer MESH:D001943

LitCoin_Mondo

Id Subject Object Predicate Lexical cue mondo_id
T1 95-108 DiseaseOrPhenotypicFeature denotes breast cancer 0007254
T2 102-108 DiseaseOrPhenotypicFeature denotes cancer 0004992
T3 136-149 DiseaseOrPhenotypicFeature denotes breast cancer 0007254
T4 143-149 DiseaseOrPhenotypicFeature denotes cancer 0004992
T5 193-202 DiseaseOrPhenotypicFeature denotes inherited 0021152
T6 427-433 DiseaseOrPhenotypicFeature denotes cancer 0004992
T7 721-734 DiseaseOrPhenotypicFeature denotes breast cancer 0007254
T8 728-734 DiseaseOrPhenotypicFeature denotes cancer 0004992
T9 1125-1129 DiseaseOrPhenotypicFeature denotes rare 0021136
T10 1228-1232 DiseaseOrPhenotypicFeature denotes rare 0021136
T11 1507-1511 DiseaseOrPhenotypicFeature denotes rare 0021136
T12 1742-1755 DiseaseOrPhenotypicFeature denotes breast cancer 0007254
T13 1749-1755 DiseaseOrPhenotypicFeature denotes cancer 0004992

LitCoin-SeqVar

Id Subject Object Predicate Lexical cue
T1 797-805 SequenceVariant denotes rs713041
T2 810-818 SequenceVariant denotes rs757229
T3 1010-1018 SequenceVariant denotes rs713041

LitCoin-GeneOrGeneProduct-v0

Id Subject Object Predicate Lexical cue
T1 49-56 GeneOrGeneProduct denotes defense
T2 150-156 GeneOrGeneProduct denotes varies
T3 211-218 GeneOrGeneProduct denotes factors
T4 223-227 GeneOrGeneProduct denotes help
T5 299-306 GeneOrGeneProduct denotes defense
T6 382-388 GeneOrGeneProduct denotes damage
T7 444-455 GeneOrGeneProduct denotes AND METHODS
T8 543-548 GeneOrGeneProduct denotes minor
T9 556-565 GeneOrGeneProduct denotes frequency
T10 574-579 GeneOrGeneProduct denotes in 10
T11 608-614 GeneOrGeneProduct denotes damage
T12 623-626 GeneOrGeneProduct denotes CAT
T13 628-632 GeneOrGeneProduct denotes SOD1
T14 634-638 GeneOrGeneProduct denotes SOD2
T15 640-644 GeneOrGeneProduct denotes GPX1
T16 646-650 GeneOrGeneProduct denotes GPX4
T17 662-666 GeneOrGeneProduct denotes TXN2
T18 668-674 GeneOrGeneProduct denotes TXNRD1
T19 680-686 GeneOrGeneProduct denotes TXNRD2
T20 791-795 GeneOrGeneProduct denotes GPX4
T21 841-844 GeneOrGeneProduct denotes all
T22 861-865 GeneOrGeneProduct denotes even
T23 886-894 GeneOrGeneProduct denotes multiple
T24 906-913 GeneOrGeneProduct denotes testing
T25 986-991 GeneOrGeneProduct denotes other
T26 1005-1009 GeneOrGeneProduct denotes GPX4
T27 1088-1092 GeneOrGeneProduct denotes GPX4
T28 1125-1129 GeneOrGeneProduct denotes rare
T29 1224-1227 GeneOrGeneProduct denotes per
T30 1228-1232 GeneOrGeneProduct denotes rare
T31 1293-1303 GeneOrGeneProduct denotes attenuated
T32 1324-1329 GeneOrGeneProduct denotes tumor
T33 1347-1364 GeneOrGeneProduct denotes estrogen receptor
T34 1443-1454 GeneOrGeneProduct denotes lymphocytes
T35 1482-1488 GeneOrGeneProduct denotes tumors
T36 1507-1511 GeneOrGeneProduct denotes rare
T37 1553-1558 GeneOrGeneProduct denotes total
T38 1569-1573 GeneOrGeneProduct denotes GPX4
T39 1574-1578 GeneOrGeneProduct denotes mRNA
T40 1687-1691 GeneOrGeneProduct denotes GPX4

LitCoin-GeneOrGeneProduct-v2

Id Subject Object Predicate Lexical cue
T1 543-548 GeneOrGeneProduct denotes minor
T2 556-565 GeneOrGeneProduct denotes frequency
T3 628-632 GeneOrGeneProduct denotes SOD1
T4 634-638 GeneOrGeneProduct denotes SOD2
T5 640-644 GeneOrGeneProduct denotes GPX1
T6 646-650 GeneOrGeneProduct denotes GPX4
T7 662-666 GeneOrGeneProduct denotes TXN2
T8 668-674 GeneOrGeneProduct denotes TXNRD1
T9 680-686 GeneOrGeneProduct denotes TXNRD2
T10 791-795 GeneOrGeneProduct denotes GPX4
T11 861-865 GeneOrGeneProduct denotes even
T12 886-894 GeneOrGeneProduct denotes multiple
T13 986-991 GeneOrGeneProduct denotes other
T14 1005-1009 GeneOrGeneProduct denotes GPX4
T15 1088-1092 GeneOrGeneProduct denotes GPX4
T16 1125-1129 GeneOrGeneProduct denotes rare
T17 1228-1232 GeneOrGeneProduct denotes rare
T18 1293-1303 GeneOrGeneProduct denotes attenuated
T19 1347-1364 GeneOrGeneProduct denotes estrogen receptor
T20 1443-1454 GeneOrGeneProduct denotes lymphocytes
T21 1507-1511 GeneOrGeneProduct denotes rare
T22 1569-1573 GeneOrGeneProduct denotes GPX4
T23 1574-1578 GeneOrGeneProduct denotes mRNA
T24 1687-1691 GeneOrGeneProduct denotes GPX4

LitCoin-Disease-MeSH

Id Subject Object Predicate Lexical cue originalLabel
T1 95-108 DiseaseOrPhenotypicFeature denotes breast cancer D001943
T2 136-149 DiseaseOrPhenotypicFeature denotes breast cancer D001943
T3 427-433 DiseaseOrPhenotypicFeature denotes cancer D009369
T4 721-734 DiseaseOrPhenotypicFeature denotes breast cancer D001943
T5 1189-1194 DiseaseOrPhenotypicFeature denotes death D003643
T6 1324-1329 DiseaseOrPhenotypicFeature denotes tumor D009369
T7 1475-1488 DiseaseOrPhenotypicFeature denotes breast tumors D001943
T8 1742-1755 DiseaseOrPhenotypicFeature denotes breast cancer D001943

LitCoin-GeneOrGeneProduct-v3

Id Subject Object Predicate Lexical cue
T1 628-632 GeneOrGeneProduct denotes SOD1
T2 634-638 GeneOrGeneProduct denotes SOD2
T3 640-644 GeneOrGeneProduct denotes GPX1
T4 646-650 GeneOrGeneProduct denotes GPX4
T5 662-666 GeneOrGeneProduct denotes TXN2
T6 668-674 GeneOrGeneProduct denotes TXNRD1
T7 680-686 GeneOrGeneProduct denotes TXNRD2
T8 791-795 GeneOrGeneProduct denotes GPX4
T9 1005-1009 GeneOrGeneProduct denotes GPX4
T10 1088-1092 GeneOrGeneProduct denotes GPX4
T11 1347-1364 GeneOrGeneProduct denotes estrogen receptor
T12 1569-1573 GeneOrGeneProduct denotes GPX4
T13 1687-1691 GeneOrGeneProduct denotes GPX4

LitCoin_Mondo_095

Id Subject Object Predicate Lexical cue mondo_id
T1 95-108 DiseaseOrPhenotypicFeature denotes breast cancer 0007254|0004989
T3 136-149 DiseaseOrPhenotypicFeature denotes breast cancer 0007254|0004989
T5 721-734 DiseaseOrPhenotypicFeature denotes breast cancer 0007254|0004989
T7 1324-1329 DiseaseOrPhenotypicFeature denotes tumor 0005070
T8 1742-1755 DiseaseOrPhenotypicFeature denotes breast cancer 0007254|0004989

LitCoin-MeSH-Disease-2

Id Subject Object Predicate Lexical cue ID:
T1 95-108 DiseaseOrPhenotypicFeature denotes breast cancer D001943
T2 136-149 DiseaseOrPhenotypicFeature denotes breast cancer D001943
T3 427-433 DiseaseOrPhenotypicFeature denotes cancer D009369
T4 721-734 DiseaseOrPhenotypicFeature denotes breast cancer D001943
T5 1189-1194 DiseaseOrPhenotypicFeature denotes death D003643
T6 1324-1329 DiseaseOrPhenotypicFeature denotes tumor D009369
T7 1475-1488 DiseaseOrPhenotypicFeature denotes breast tumors D001943
T8 1742-1755 DiseaseOrPhenotypicFeature denotes breast cancer D001943

LitCoin-MONDO_bioort2019

Id Subject Object Predicate Lexical cue #label
T1 95-108 DiseaseOrPhenotypicFeature denotes breast cancer D001943
T2 136-149 DiseaseOrPhenotypicFeature denotes breast cancer D001943
T3 427-433 DiseaseOrPhenotypicFeature denotes cancer D009369
T4 721-734 DiseaseOrPhenotypicFeature denotes breast cancer D001943
T5 1324-1329 DiseaseOrPhenotypicFeature denotes tumor D009369
T6 1475-1488 DiseaseOrPhenotypicFeature denotes breast tumors D001943
T7 1742-1755 DiseaseOrPhenotypicFeature denotes breast cancer D001943

LitCoin-NCBITaxon-2

Id Subject Object Predicate Lexical cue
T1 623-626 OrganismTaxon denotes CAT
T2 710-715 OrganismTaxon denotes women

LitCoin-Chemical-MeSH-CHEBI

Id Subject Object Predicate Lexical cue ID:
T1 37-48 ChemicalEntity denotes antioxidant ChemicalEntity
T2 315-338 ChemicalEntity denotes reactive oxygen species D017382|http://purl.obolibrary.org/obo/CHEBI_26523
T4 340-343 ChemicalEntity denotes ROS http://purl.obolibrary.org/obo/CHEBI_26523
T5 353-356 ChemicalEntity denotes ROS http://purl.obolibrary.org/obo/CHEBI_26523
T6 1039-1053 ChemicalEntity denotes selenocysteine http://purl.obolibrary.org/obo/CHEBI_9093
T7 1347-1355 ChemicalEntity denotes estrogen ChemicalEntity

LitCoin-training-merged

Id Subject Object Predicate Lexical cue #label ID:
T7 1347-1355 ChemicalEntity denotes estrogen ChemicalEntity
T6 1039-1053 ChemicalEntity denotes selenocysteine http://purl.obolibrary.org/obo/CHEBI_9093
T5 353-356 ChemicalEntity denotes ROS http://purl.obolibrary.org/obo/CHEBI_26523
T4 340-343 ChemicalEntity denotes ROS http://purl.obolibrary.org/obo/CHEBI_26523
T2 315-338 ChemicalEntity denotes reactive oxygen species http://purl.obolibrary.org/obo/CHEBI_26523|D017382
T1 37-48 ChemicalEntity denotes antioxidant ChemicalEntity
T13 1687-1691 GeneOrGeneProduct denotes GPX4
T12 1569-1573 GeneOrGeneProduct denotes GPX4
T11 1347-1364 GeneOrGeneProduct denotes estrogen receptor
T10 1088-1092 GeneOrGeneProduct denotes GPX4
T9 1005-1009 GeneOrGeneProduct denotes GPX4
T8 791-795 GeneOrGeneProduct denotes GPX4
T33362 680-686 GeneOrGeneProduct denotes TXNRD2
T76933 668-674 GeneOrGeneProduct denotes TXNRD1
T87379 662-666 GeneOrGeneProduct denotes TXN2
T80136 646-650 GeneOrGeneProduct denotes GPX4
T3 640-644 GeneOrGeneProduct denotes GPX1
T38059 634-638 GeneOrGeneProduct denotes SOD2
T57624 628-632 GeneOrGeneProduct denotes SOD1
T44267 1742-1755 DiseaseOrPhenotypicFeature denotes breast cancer D001943
T42065 1475-1488 DiseaseOrPhenotypicFeature denotes breast tumors D001943
T58251 1324-1329 DiseaseOrPhenotypicFeature denotes tumor D009369
T69392 721-734 DiseaseOrPhenotypicFeature denotes breast cancer D001943
T13886 427-433 DiseaseOrPhenotypicFeature denotes cancer D009369
T46941 136-149 DiseaseOrPhenotypicFeature denotes breast cancer D001943
T55677 95-108 DiseaseOrPhenotypicFeature denotes breast cancer D001943
T48876 710-715 OrganismTaxon denotes women
T2074 623-626 OrganismTaxon denotes CAT
T77946 1010-1018 SequenceVariant denotes rs713041
T18217 810-818 SequenceVariant denotes rs757229
T28836 797-805 SequenceVariant denotes rs713041

DisGeNET

Id Subject Object Predicate Lexical cue
T0 668-674 gene:7296 denotes TXNRD1
T1 721-734 disease:C0006142 denotes breast cancer
T2 668-674 gene:7296 denotes TXNRD1
T3 721-734 disease:C0678222 denotes breast cancer
T4 680-686 gene:10587 denotes TXNRD2
T5 721-734 disease:C0006142 denotes breast cancer
T6 680-686 gene:10587 denotes TXNRD2
T7 721-734 disease:C0678222 denotes breast cancer
T8 1569-1573 gene:2879 denotes GPX4
T9 1475-1488 disease:C1458155 denotes breast tumors
T10 1687-1691 gene:2879 denotes GPX4
T11 1742-1755 disease:C0006142 denotes breast cancer
T12 1687-1691 gene:2879 denotes GPX4
T13 1742-1755 disease:C0678222 denotes breast cancer
R1 T0 T1 associated_with TXNRD1,breast cancer
R2 T2 T3 associated_with TXNRD1,breast cancer
R3 T4 T5 associated_with TXNRD2,breast cancer
R4 T6 T7 associated_with TXNRD2,breast cancer
R5 T8 T9 associated_with GPX4,breast tumors
R6 T10 T11 associated_with GPX4,breast cancer
R7 T12 T13 associated_with GPX4,breast cancer

PubmedHPO

Id Subject Object Predicate Lexical cue
T1 136-149 HP_0003002 denotes breast cancer
T2 136-149 HP_0100013 denotes breast cancer
T3 143-149 HP_0002664 denotes cancer
T4 427-433 HP_0002664 denotes cancer

DisGeNET5_gene_disease

Id Subject Object Predicate Lexical cue
17634480-3#223#229#gene10587 680-686 gene10587 denotes TXNRD2
17634480-3#264#277#diseaseC0006142 721-734 diseaseC0006142 denotes breast cancer
17634480-3#264#277#diseaseC0678222 721-734 diseaseC0678222 denotes breast cancer
17634480-8#196#200#gene2879 1569-1573 gene2879 denotes GPX4
17634480-8#102#115#diseaseC1458155 1475-1488 diseaseC1458155 denotes breast tumors
17634480-9#78#82#gene2879 1687-1691 gene2879 denotes GPX4
17634480-9#133#146#diseaseC0006142 1742-1755 diseaseC0006142 denotes breast cancer
17634480-9#133#146#diseaseC0678222 1742-1755 diseaseC0678222 denotes breast cancer
223#229#gene10587264#277#diseaseC0006142 17634480-3#223#229#gene10587 17634480-3#264#277#diseaseC0006142 associated_with TXNRD2,breast cancer
223#229#gene10587264#277#diseaseC0678222 17634480-3#223#229#gene10587 17634480-3#264#277#diseaseC0678222 associated_with TXNRD2,breast cancer
196#200#gene2879102#115#diseaseC1458155 17634480-8#196#200#gene2879 17634480-8#102#115#diseaseC1458155 associated_with GPX4,breast tumors
78#82#gene2879133#146#diseaseC0006142 17634480-9#78#82#gene2879 17634480-9#133#146#diseaseC0006142 associated_with GPX4,breast cancer
78#82#gene2879133#146#diseaseC0678222 17634480-9#78#82#gene2879 17634480-9#133#146#diseaseC0678222 associated_with GPX4,breast cancer

tmVarCorpus

Id Subject Object Predicate Lexical cue
T1 797-805 SNP:rs713041 denotes rs713041
T2 810-818 SNP:rs757229 denotes rs757229
T3 1010-1018 SNP:rs713041 denotes rs713041