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PubMed:18507837 JSONTXT

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LitCoin-sentences

Id Subject Object Predicate Lexical cue
T1 0-139 Sentence denotes Effects of common germline genetic variation in cell cycle control genes on breast cancer survival: results from a population-based cohort.
T2 140-153 Sentence denotes INTRODUCTION:
T3 154-320 Sentence denotes Somatic alterations have been shown to correlate with breast cancer prognosis and survival, but less is known about the effects of common inherited genetic variation.
T4 321-416 Sentence denotes Of particular interest are genes involved in cell cycle pathways, which regulate cell division.
T5 417-425 Sentence denotes METHODS:
T6 426-862 Sentence denotes We examined associations between common germline genetic variation in 13 genes involved in cell cycle control (CCND1, CCND2, CCND3, CCNE1, CDK2 [p33], CDK4, CDK6, CDKN1A [p21, Cip1], CDKN1B [p27, Kip1], CDKN2A [p16], CDKN2B [p15], CDKN2C [p18], and CDKN2D [p19]) and survival among women diagnosed with invasive breast cancer participating in the SEARCH (Studies of Epidemiology and Risk factors in Cancer Heredity) breast cancer study.
T7 863-1010 Sentence denotes DNA from up to 4,470 women was genotyped for 85 polymorphisms that tag the known common polymorphisms (minor allele frequency > 0.05) in the genes.
T8 1011-1118 Sentence denotes The genotypes of each polymorphism were tested for association with survival using Cox regression analysis.
T9 1119-1127 Sentence denotes RESULTS:
T10 1128-1322 Sentence denotes The rare allele of the tagging single nucleotide polymorphism (SNP) rs2479717 is associated with an increased risk of death (hazard ratio = 1.26 per rare allele carried, 95% confidence interval:
T11 1323-1430 Sentence denotes 1.12 to 1.42; P = 0.0001), which was not attenuated after adjusting for tumour stage, grade, and treatment.
T12 1431-1553 Sentence denotes This SNP is part of a large linkage disequilibrium block, which contains CCND3, BYSL, TRFP, USP49, C6ofr49, FRS3, and PGC.
T14 1715-1847 Sentence denotes Elevated expression of the C6orf49 transcript was associated with breast cancer survival, adding biological interest to the finding.
T13 1554-1714 Sentence denotes We evaluated the association of survival and somatic expression of these genes in breast tumours using expression microarray data from seven published datasets.
T15 1848-1859 Sentence denotes CONCLUSION:
T16 1860-1989 Sentence denotes It is possible that CCND3 rs2479717, or another variant it tags, is associated with prognosis after a diagnosis of breast cancer.
T17 1990-2041 Sentence denotes Further study is required to validate this finding.

LitCoin-entities

Id Subject Object Predicate Lexical cue db_id
5166 76-89 DiseaseOrPhenotypicFeature denotes breast cancer MESH:D001943
5167 208-221 DiseaseOrPhenotypicFeature denotes breast cancer MESH:D001943
5168 537-542 GeneOrGeneProduct denotes CCND1 NCBIGene:595
5169 544-549 GeneOrGeneProduct denotes CCND2 NCBIGene:894
5170 551-556 GeneOrGeneProduct denotes CCND3 NCBIGene:896
5171 558-563 GeneOrGeneProduct denotes CCNE1 NCBIGene:898
5172 565-575 GeneOrGeneProduct denotes CDK2 [p33] NCBIGene:1017
5173 577-581 GeneOrGeneProduct denotes CDK4 NCBIGene:1019
5174 583-587 GeneOrGeneProduct denotes CDK6 NCBIGene:1021
5175 589-595 GeneOrGeneProduct denotes CDKN1A NCBIGene:1026
5176 597-600 GeneOrGeneProduct denotes p21 NCBIGene:1026
5177 602-606 GeneOrGeneProduct denotes Cip1 NCBIGene:1026
5178 609-615 GeneOrGeneProduct denotes CDKN1B NCBIGene:1027
5179 617-626 GeneOrGeneProduct denotes p27, Kip1 NCBIGene:1027
5180 629-635 GeneOrGeneProduct denotes CDKN2A NCBIGene:1029
5181 637-640 GeneOrGeneProduct denotes p16 NCBIGene:1029
5182 643-649 GeneOrGeneProduct denotes CDKN2B NCBIGene:1030
5183 651-654 GeneOrGeneProduct denotes p15 NCBIGene:1030
5184 657-663 GeneOrGeneProduct denotes CDKN2C NCBIGene:1031
5185 665-668 GeneOrGeneProduct denotes p18 NCBIGene:1031
5186 675-681 GeneOrGeneProduct denotes CDKN2D NCBIGene:1032
5187 683-686 GeneOrGeneProduct denotes p19 NCBIGene:1029
5188 708-713 OrganismTaxon denotes women NCBITaxon:9606
5189 729-751 DiseaseOrPhenotypicFeature denotes invasive breast cancer MESH:D001943
5190 842-855 DiseaseOrPhenotypicFeature denotes breast cancer MESH:D001943
5191 884-889 OrganismTaxon denotes women NCBITaxon:9606
5192 1196-1205 SequenceVariant denotes rs2479717 DBSNP:rs2479717
5193 1246-1251 DiseaseOrPhenotypicFeature denotes death MESH:D003643
5194 1395-1401 DiseaseOrPhenotypicFeature denotes tumour MESH:D009369
5195 1504-1509 GeneOrGeneProduct denotes CCND3 NCBIGene:896
5196 1511-1515 GeneOrGeneProduct denotes BYSL NCBIGene:705
5197 1517-1521 GeneOrGeneProduct denotes TRFP NCBIGene:55031
5198 1523-1528 GeneOrGeneProduct denotes USP49 NCBIGene:25862
5199 1530-1537 GeneOrGeneProduct denotes C6ofr49 NCBIGene:29964
5200 1539-1543 GeneOrGeneProduct denotes FRS3 NCBIGene:10817
5201 1549-1552 GeneOrGeneProduct denotes PGC NCBIGene:5225
5202 1636-1650 DiseaseOrPhenotypicFeature denotes breast tumours MESH:D001943
5203 1742-1749 GeneOrGeneProduct denotes C6orf49 NCBIGene:29964
5204 1781-1794 DiseaseOrPhenotypicFeature denotes breast cancer MESH:D001943
5205 1880-1885 GeneOrGeneProduct denotes CCND3 NCBIGene:896
5206 1886-1895 SequenceVariant denotes rs2479717 DBSNP:rs2479717
5207 1975-1988 DiseaseOrPhenotypicFeature denotes breast cancer MESH:D001943

LitCoin_Mondo

Id Subject Object Predicate Lexical cue mondo_id
T1 76-89 DiseaseOrPhenotypicFeature denotes breast cancer 0007254
T2 83-89 DiseaseOrPhenotypicFeature denotes cancer 0004992
T3 208-221 DiseaseOrPhenotypicFeature denotes breast cancer 0007254
T4 215-221 DiseaseOrPhenotypicFeature denotes cancer 0004992
T5 292-301 DiseaseOrPhenotypicFeature denotes inherited 0021152
T6 738-751 DiseaseOrPhenotypicFeature denotes breast cancer 0007254
T7 745-751 DiseaseOrPhenotypicFeature denotes cancer 0004992
T8 825-831 DiseaseOrPhenotypicFeature denotes Cancer 0004992
T9 842-855 DiseaseOrPhenotypicFeature denotes breast cancer 0007254
T10 849-855 DiseaseOrPhenotypicFeature denotes cancer 0004992
T11 1132-1136 DiseaseOrPhenotypicFeature denotes rare 0021136
T12 1277-1281 DiseaseOrPhenotypicFeature denotes rare 0021136
T13 1781-1794 DiseaseOrPhenotypicFeature denotes breast cancer 0007254
T14 1788-1794 DiseaseOrPhenotypicFeature denotes cancer 0004992
T15 1975-1988 DiseaseOrPhenotypicFeature denotes breast cancer 0007254
T16 1982-1988 DiseaseOrPhenotypicFeature denotes cancer 0004992

LitCoin-SeqVar

Id Subject Object Predicate Lexical cue
T1 1196-1205 SequenceVariant denotes rs2479717
T2 1886-1895 SequenceVariant denotes rs2479717

LitCoin-GeneOrGeneProduct-v0

Id Subject Object Predicate Lexical cue
T1 48-66 GeneOrGeneProduct denotes cell cycle control
T2 126-131 GeneOrGeneProduct denotes based
T3 366-376 GeneOrGeneProduct denotes cell cycle
T4 402-406 GeneOrGeneProduct denotes cell
T5 417-424 GeneOrGeneProduct denotes METHODS
T6 493-498 GeneOrGeneProduct denotes in 13
T7 517-535 GeneOrGeneProduct denotes cell cycle control
T8 537-542 GeneOrGeneProduct denotes CCND1
T9 544-549 GeneOrGeneProduct denotes CCND2
T10 551-556 GeneOrGeneProduct denotes CCND3
T11 558-563 GeneOrGeneProduct denotes CCNE1
T12 565-569 GeneOrGeneProduct denotes CDK2
T13 577-581 GeneOrGeneProduct denotes CDK4
T14 583-587 GeneOrGeneProduct denotes CDK6
T15 589-595 GeneOrGeneProduct denotes CDKN1A
T16 602-606 GeneOrGeneProduct denotes Cip1
T17 609-615 GeneOrGeneProduct denotes CDKN1B
T18 622-626 GeneOrGeneProduct denotes Kip1
T19 629-635 GeneOrGeneProduct denotes CDKN2A
T20 643-649 GeneOrGeneProduct denotes CDKN2B
T21 657-663 GeneOrGeneProduct denotes CDKN2C
T22 675-681 GeneOrGeneProduct denotes CDKN2D
T23 683-686 GeneOrGeneProduct denotes p19
T24 814-821 GeneOrGeneProduct denotes factors
T25 904-910 GeneOrGeneProduct denotes for 85
T26 966-971 GeneOrGeneProduct denotes minor
T27 979-988 GeneOrGeneProduct denotes frequency
T28 1051-1057 GeneOrGeneProduct denotes tested
T29 1132-1136 GeneOrGeneProduct denotes rare
T30 1273-1276 GeneOrGeneProduct denotes per
T31 1277-1281 GeneOrGeneProduct denotes rare
T32 1364-1374 GeneOrGeneProduct denotes attenuated
T33 1443-1447 GeneOrGeneProduct denotes part
T34 1453-1458 GeneOrGeneProduct denotes large
T35 1482-1487 GeneOrGeneProduct denotes block
T36 1504-1509 GeneOrGeneProduct denotes CCND3
T37 1511-1515 GeneOrGeneProduct denotes BYSL
T38 1517-1521 GeneOrGeneProduct denotes TRFP
T39 1523-1528 GeneOrGeneProduct denotes USP49
T40 1539-1543 GeneOrGeneProduct denotes FRS3
T41 1742-1749 GeneOrGeneProduct denotes C6orf49
T42 1750-1760 GeneOrGeneProduct denotes transcript
T43 1839-1846 GeneOrGeneProduct denotes finding
T44 1880-1885 GeneOrGeneProduct denotes CCND3
T45 2033-2040 GeneOrGeneProduct denotes finding

LitCoin-GeneOrGeneProduct-v2

Id Subject Object Predicate Lexical cue
T1 48-66 GeneOrGeneProduct denotes cell cycle control
T2 366-376 GeneOrGeneProduct denotes cell cycle
T3 402-406 GeneOrGeneProduct denotes cell
T4 517-535 GeneOrGeneProduct denotes cell cycle control
T5 537-542 GeneOrGeneProduct denotes CCND1
T6 544-549 GeneOrGeneProduct denotes CCND2
T7 551-556 GeneOrGeneProduct denotes CCND3
T8 558-563 GeneOrGeneProduct denotes CCNE1
T9 565-569 GeneOrGeneProduct denotes CDK2
T10 577-581 GeneOrGeneProduct denotes CDK4
T11 583-587 GeneOrGeneProduct denotes CDK6
T12 589-595 GeneOrGeneProduct denotes CDKN1A
T13 602-606 GeneOrGeneProduct denotes Cip1
T14 609-615 GeneOrGeneProduct denotes CDKN1B
T15 622-626 GeneOrGeneProduct denotes Kip1
T16 629-635 GeneOrGeneProduct denotes CDKN2A
T17 643-649 GeneOrGeneProduct denotes CDKN2B
T18 657-663 GeneOrGeneProduct denotes CDKN2C
T19 675-681 GeneOrGeneProduct denotes CDKN2D
T20 966-971 GeneOrGeneProduct denotes minor
T21 979-988 GeneOrGeneProduct denotes frequency
T22 1132-1136 GeneOrGeneProduct denotes rare
T23 1277-1281 GeneOrGeneProduct denotes rare
T24 1364-1374 GeneOrGeneProduct denotes attenuated
T25 1453-1458 GeneOrGeneProduct denotes large
T26 1504-1509 GeneOrGeneProduct denotes CCND3
T27 1511-1515 GeneOrGeneProduct denotes BYSL
T28 1517-1521 GeneOrGeneProduct denotes TRFP
T29 1523-1528 GeneOrGeneProduct denotes USP49
T30 1539-1543 GeneOrGeneProduct denotes FRS3
T31 1742-1749 GeneOrGeneProduct denotes C6orf49
T32 1750-1760 GeneOrGeneProduct denotes transcript
T33 1880-1885 GeneOrGeneProduct denotes CCND3

LitCoin-Disease-MeSH

Id Subject Object Predicate Lexical cue originalLabel
T1 76-89 DiseaseOrPhenotypicFeature denotes breast cancer D001943
T2 208-221 DiseaseOrPhenotypicFeature denotes breast cancer D001943
T3 738-751 DiseaseOrPhenotypicFeature denotes breast cancer D001943
T4 825-831 DiseaseOrPhenotypicFeature denotes Cancer D009369
T5 842-855 DiseaseOrPhenotypicFeature denotes breast cancer D001943
T6 1246-1251 DiseaseOrPhenotypicFeature denotes death D003643
T7 1395-1401 DiseaseOrPhenotypicFeature denotes tumour DISEASE
T8 1643-1650 DiseaseOrPhenotypicFeature denotes tumours DISEASE
T9 1781-1794 DiseaseOrPhenotypicFeature denotes breast cancer D001943
T10 1975-1988 DiseaseOrPhenotypicFeature denotes breast cancer D001943

PMID_GLOBAL

Id Subject Object Predicate Lexical cue mondo_id
T1 76-89 DiseaseOrPhenotypicFeature denotes breast cancer 0004989|0007254
T3 208-221 DiseaseOrPhenotypicFeature denotes breast cancer 0004989|0007254
T5 729-751 DiseaseOrPhenotypicFeature denotes invasive breast cancer 0006256
T6 842-855 DiseaseOrPhenotypicFeature denotes breast cancer 0004989|0007254
T8 1781-1794 DiseaseOrPhenotypicFeature denotes breast cancer 0004989|0007254
T10 1975-1988 DiseaseOrPhenotypicFeature denotes breast cancer 0004989|0007254

LitCoin-GeneOrGeneProduct-v3

Id Subject Object Predicate Lexical cue
T1 393-415 GeneOrGeneProduct denotes regulate cell division
T2 537-542 GeneOrGeneProduct denotes CCND1
T3 544-549 GeneOrGeneProduct denotes CCND2
T4 551-556 GeneOrGeneProduct denotes CCND3
T5 558-563 GeneOrGeneProduct denotes CCNE1
T6 565-569 GeneOrGeneProduct denotes CDK2
T7 577-581 GeneOrGeneProduct denotes CDK4
T8 583-587 GeneOrGeneProduct denotes CDK6
T9 589-595 GeneOrGeneProduct denotes CDKN1A
T10 602-606 GeneOrGeneProduct denotes Cip1
T11 609-615 GeneOrGeneProduct denotes CDKN1B
T12 622-626 GeneOrGeneProduct denotes Kip1
T13 629-635 GeneOrGeneProduct denotes CDKN2A
T14 643-649 GeneOrGeneProduct denotes CDKN2B
T15 657-663 GeneOrGeneProduct denotes CDKN2C
T16 675-681 GeneOrGeneProduct denotes CDKN2D
T17 1504-1509 GeneOrGeneProduct denotes CCND3
T18 1511-1515 GeneOrGeneProduct denotes BYSL
T19 1517-1521 GeneOrGeneProduct denotes TRFP
T20 1523-1528 GeneOrGeneProduct denotes USP49
T21 1539-1543 GeneOrGeneProduct denotes FRS3
T22 1742-1749 GeneOrGeneProduct denotes C6orf49
T23 1880-1885 GeneOrGeneProduct denotes CCND3

LitCoin_Mondo_095

Id Subject Object Predicate Lexical cue mondo_id
T1 76-89 DiseaseOrPhenotypicFeature denotes breast cancer 0007254|0004989
T3 208-221 DiseaseOrPhenotypicFeature denotes breast cancer 0007254|0004989
T5 729-751 DiseaseOrPhenotypicFeature denotes invasive breast cancer 0006256
T6 842-855 DiseaseOrPhenotypicFeature denotes breast cancer 0007254|0004989
T8 1781-1794 DiseaseOrPhenotypicFeature denotes breast cancer 0007254|0004989
T10 1975-1988 DiseaseOrPhenotypicFeature denotes breast cancer 0007254|0004989

LitCoin-MeSH-Disease-2

Id Subject Object Predicate Lexical cue ID:
T1 76-89 DiseaseOrPhenotypicFeature denotes breast cancer D001943
T2 208-221 DiseaseOrPhenotypicFeature denotes breast cancer D001943
T3 738-751 DiseaseOrPhenotypicFeature denotes breast cancer D001943
T4 825-831 DiseaseOrPhenotypicFeature denotes Cancer D009369
T5 842-855 DiseaseOrPhenotypicFeature denotes breast cancer D001943
T6 1246-1251 DiseaseOrPhenotypicFeature denotes death D003643
T7 1395-1401 DiseaseOrPhenotypicFeature denotes tumour DISEASE
T8 1636-1650 DiseaseOrPhenotypicFeature denotes breast tumours DISEASE
T9 1781-1794 DiseaseOrPhenotypicFeature denotes breast cancer D001943
T10 1975-1988 DiseaseOrPhenotypicFeature denotes breast cancer D001943

LitCoin-MONDO_bioort2019

Id Subject Object Predicate Lexical cue #label
T1 76-89 DiseaseOrPhenotypicFeature denotes breast cancer D001943
T2 208-221 DiseaseOrPhenotypicFeature denotes breast cancer D001943
T3 738-751 DiseaseOrPhenotypicFeature denotes breast cancer D001943
T4 825-831 DiseaseOrPhenotypicFeature denotes Cancer D009369
T5 842-855 DiseaseOrPhenotypicFeature denotes breast cancer D001943
T6 1395-1401 DiseaseOrPhenotypicFeature denotes tumour DISEASE
T7 1636-1650 DiseaseOrPhenotypicFeature denotes breast tumours DISEASE
T8 1781-1794 DiseaseOrPhenotypicFeature denotes breast cancer D001943
T9 1975-1988 DiseaseOrPhenotypicFeature denotes breast cancer D001943

LitCoin-Chemical-MeSH-CHEBI

Id Subject Object Predicate Lexical cue ID:
T1 1549-1552 ChemicalEntity denotes PGC http://purl.obolibrary.org/obo/CHEBI_26336

LitCoin-NCBITaxon-2

Id Subject Object Predicate Lexical cue
T1 708-713 OrganismTaxon denotes women
T2 884-889 OrganismTaxon denotes women

LitCoin-training-merged

Id Subject Object Predicate Lexical cue #label ID:
T1 1549-1552 ChemicalEntity denotes PGC http://purl.obolibrary.org/obo/CHEBI_26336
T23 1880-1885 GeneOrGeneProduct denotes CCND3
T22 1742-1749 GeneOrGeneProduct denotes C6orf49
T21 1539-1543 GeneOrGeneProduct denotes FRS3
T20 1523-1528 GeneOrGeneProduct denotes USP49
T19 1517-1521 GeneOrGeneProduct denotes TRFP
T18 1511-1515 GeneOrGeneProduct denotes BYSL
T17 1504-1509 GeneOrGeneProduct denotes CCND3
T16 675-681 GeneOrGeneProduct denotes CDKN2D
T15 657-663 GeneOrGeneProduct denotes CDKN2C
T14 643-649 GeneOrGeneProduct denotes CDKN2B
T13 629-635 GeneOrGeneProduct denotes CDKN2A
T12 622-626 GeneOrGeneProduct denotes Kip1
T11 609-615 GeneOrGeneProduct denotes CDKN1B
T10 602-606 GeneOrGeneProduct denotes Cip1
T9 589-595 GeneOrGeneProduct denotes CDKN1A
T8 583-587 GeneOrGeneProduct denotes CDK6
T7 577-581 GeneOrGeneProduct denotes CDK4
T6 565-569 GeneOrGeneProduct denotes CDK2
T5 558-563 GeneOrGeneProduct denotes CCNE1
T4 551-556 GeneOrGeneProduct denotes CCND3
T3 544-549 GeneOrGeneProduct denotes CCND2
T2 537-542 GeneOrGeneProduct denotes CCND1
T8480 393-415 GeneOrGeneProduct denotes regulate cell division
T62634 1975-1988 DiseaseOrPhenotypicFeature denotes breast cancer D001943
T19796 1781-1794 DiseaseOrPhenotypicFeature denotes breast cancer D001943
T43039 1636-1650 DiseaseOrPhenotypicFeature denotes breast tumours DISEASE
T16682 1395-1401 DiseaseOrPhenotypicFeature denotes tumour DISEASE
T88411 842-855 DiseaseOrPhenotypicFeature denotes breast cancer D001943
T67153 825-831 DiseaseOrPhenotypicFeature denotes Cancer D009369
T37765 738-751 DiseaseOrPhenotypicFeature denotes breast cancer D001943
T7739 208-221 DiseaseOrPhenotypicFeature denotes breast cancer D001943
T76452 76-89 DiseaseOrPhenotypicFeature denotes breast cancer D001943
T1377 884-889 OrganismTaxon denotes women
T42870 708-713 OrganismTaxon denotes women
T48466 1886-1895 SequenceVariant denotes rs2479717
T87232 1196-1205 SequenceVariant denotes rs2479717

DisGeNET

Id Subject Object Predicate Lexical cue
T0 1742-1749 gene:29964 denotes C6orf49
T1 1781-1794 disease:C0006142 denotes breast cancer
T2 1742-1749 gene:29964 denotes C6orf49
T3 1781-1794 disease:C0678222 denotes breast cancer
R1 T0 T1 associated_with C6orf49,breast cancer
R2 T2 T3 associated_with C6orf49,breast cancer

DisGeNET5_variant_disease

Id Subject Object Predicate Lexical cue
18507837-10#26#35#geners2479717 1886-1895 geners2479717 denotes rs2479717
18507837-10#115#128#diseaseC0006142 1975-1988 diseaseC0006142 denotes breast cancer
18507837-10#115#128#diseaseC0678222 1975-1988 diseaseC0678222 denotes breast cancer
26#35#geners2479717115#128#diseaseC0006142 18507837-10#26#35#geners2479717 18507837-10#115#128#diseaseC0006142 associated_with rs2479717,breast cancer
26#35#geners2479717115#128#diseaseC0678222 18507837-10#26#35#geners2479717 18507837-10#115#128#diseaseC0678222 associated_with rs2479717,breast cancer