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PubMed:28068934 JSONTXT

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PubTator4TogoVar

Id Subject Object Predicate Lexical cue proteinmutation
28068934_0 491-497 ProteinMutation denotes H1047R rs121913279
28068934_1 503-509 ProteinMutation denotes H1047L rs121913279

LitCoin-sentences

Id Subject Object Predicate Lexical cue
T1 0-130 Sentence denotes Concordance between PIK3CA mutations in endoscopic biopsy and surgically resected specimens of esophageal squamous cell carcinoma.
T2 131-255 Sentence denotes BACKGROUND: PIK3CA mutations are expected to be potential therapeutic targets for esophageal squamous cell carcinoma (ESCC).
T3 256-405 Sentence denotes We aimed to clarify the concordance between PIK3CA mutations detected in endoscopic biopsy specimens and corresponding surgically resected specimens.
T4 406-414 Sentence denotes METHODS:
T5 415-779 Sentence denotes We examined five hotspot mutations in the PIK3CA gene (E542K, E545K, E546K, H1047R, and H1047L) in formalin-fixed and paraffin-embedded tissue sections of paired endoscopic biopsy and surgically resected specimens from 181 patients undergoing curative resection for ESCC between 2000 and 2011 using a Luminex technology-based multiplex gene mutation detection kit.
T6 780-788 Sentence denotes RESULTS:
T7 789-913 Sentence denotes Mutation analyses were successfully performed for both endoscopic biopsy and surgically resected specimens in all the cases.
T8 914-1015 Sentence denotes A PIK3CA mutation was detected in either type of specimen in 13 cases (7.2%, 95% confidence interval:
T9 1016-1026 Sentence denotes 3.9-12.0).
T10 1027-1185 Sentence denotes The overall concordance rate, positive predictive value, and negative predictive value were 98.3% (178/181), 90.9% (10/11), and 98.8% (168/170), respectively.
T11 1186-1320 Sentence denotes Among patients with a PIK3CA mutation detected in both types of specimens, the concordance between PIK3CA mutation genotypes was 100%.
T12 1321-1621 Sentence denotes There were three cases with a discordant mutation status between the types of specimens (PIK3CA mutation in surgically resected specimen and wild-type in biopsy specimen in two cases, and the opposite pattern in one case), suggesting possible intratumoral heterogeneity in the PIK3CA mutation status.
T13 1622-1634 Sentence denotes CONCLUSIONS:
T14 1635-1883 Sentence denotes The PIK3CA mutation status was highly concordant between endoscopic biopsy and surgically resected specimens from the same patient, suggesting that endoscopic biopsy specimens can be clinically used to detect PIK3CA mutations in patients with ESCC.

LitCoin-entities

Id Subject Object Predicate Lexical cue db_id
12037 20-26 GeneOrGeneProduct denotes PIK3CA NCBIGene:5290
12038 95-129 DiseaseOrPhenotypicFeature denotes esophageal squamous cell carcinoma MESH:D000077277
12039 143-149 GeneOrGeneProduct denotes PIK3CA NCBIGene:5290
12040 213-247 DiseaseOrPhenotypicFeature denotes esophageal squamous cell carcinoma MESH:D000077277
12041 249-253 DiseaseOrPhenotypicFeature denotes ESCC MESH:D000077277
12042 300-306 GeneOrGeneProduct denotes PIK3CA NCBIGene:5290
12043 457-463 GeneOrGeneProduct denotes PIK3CA NCBIGene:5290
12044 470-475 SequenceVariant denotes E542K DBSNP:rs121913273
12045 477-482 SequenceVariant denotes E545K DBSNP:rs104886003
12046 484-489 SequenceVariant denotes E546K p|SUB|E|546|K
12047 491-497 SequenceVariant denotes H1047R DBSNP:rs121913279
12048 503-509 SequenceVariant denotes H1047L DBSNP:rs121913279
12049 514-522 ChemicalEntity denotes formalin MESH:D005557
12050 533-541 ChemicalEntity denotes paraffin MESH:D010232
12051 638-646 OrganismTaxon denotes patients NCBITaxon:9606
12052 681-685 DiseaseOrPhenotypicFeature denotes ESCC MESH:D000077277
12053 916-922 GeneOrGeneProduct denotes PIK3CA NCBIGene:5290
12054 1192-1200 OrganismTaxon denotes patients NCBITaxon:9606
12055 1208-1214 GeneOrGeneProduct denotes PIK3CA NCBIGene:5290
12056 1285-1291 GeneOrGeneProduct denotes PIK3CA NCBIGene:5290
12057 1410-1416 GeneOrGeneProduct denotes PIK3CA NCBIGene:5290
12058 1598-1604 GeneOrGeneProduct denotes PIK3CA NCBIGene:5290
12059 1639-1645 GeneOrGeneProduct denotes PIK3CA NCBIGene:5290
12060 1758-1765 OrganismTaxon denotes patient NCBITaxon:9606
12061 1844-1850 GeneOrGeneProduct denotes PIK3CA NCBIGene:5290
12062 1864-1872 OrganismTaxon denotes patients NCBITaxon:9606
12063 1878-1882 DiseaseOrPhenotypicFeature denotes ESCC MESH:D000077277

LitCoin_Mondo

Id Subject Object Predicate Lexical cue mondo_id
T1 95-129 DiseaseOrPhenotypicFeature denotes esophageal squamous cell carcinoma 0005580
T2 106-129 DiseaseOrPhenotypicFeature denotes squamous cell carcinoma 0005096
T3 120-129 DiseaseOrPhenotypicFeature denotes carcinoma 0004993
T4 213-247 DiseaseOrPhenotypicFeature denotes esophageal squamous cell carcinoma 0005580
T5 224-247 DiseaseOrPhenotypicFeature denotes squamous cell carcinoma 0005096
T6 238-247 DiseaseOrPhenotypicFeature denotes carcinoma 0004993

LitCoin-SeqVar

Id Subject Object Predicate Lexical cue
T1 470-475 SequenceVariant denotes E542K
T2 477-482 SequenceVariant denotes E545K
T3 484-489 SequenceVariant denotes E546K
T4 491-497 SequenceVariant denotes H1047R
T5 503-509 SequenceVariant denotes H1047L

LitCoin-GeneOrGeneProduct-v0

Id Subject Object Predicate Lexical cue
T1 20-26 GeneOrGeneProduct denotes PIK3CA
T2 27-36 GeneOrGeneProduct denotes mutations
T3 115-119 GeneOrGeneProduct denotes cell
T4 143-149 GeneOrGeneProduct denotes PIK3CA
T5 150-159 GeneOrGeneProduct denotes mutations
T6 233-237 GeneOrGeneProduct denotes cell
T7 249-253 GeneOrGeneProduct denotes ESCC
T8 300-306 GeneOrGeneProduct denotes PIK3CA
T9 307-316 GeneOrGeneProduct denotes mutations
T10 406-413 GeneOrGeneProduct denotes METHODS
T11 440-449 GeneOrGeneProduct denotes mutations
T12 457-463 GeneOrGeneProduct denotes PIK3CA
T13 570-576 GeneOrGeneProduct denotes paired
T14 681-685 GeneOrGeneProduct denotes ESCC
T15 735-740 GeneOrGeneProduct denotes based
T16 756-764 GeneOrGeneProduct denotes mutation
T17 789-797 GeneOrGeneProduct denotes Mutation
T18 899-902 GeneOrGeneProduct denotes all
T19 903-912 GeneOrGeneProduct denotes the cases
T20 916-922 GeneOrGeneProduct denotes PIK3CA
T21 923-931 GeneOrGeneProduct denotes mutation
T22 972-977 GeneOrGeneProduct denotes in 13
T23 978-983 GeneOrGeneProduct denotes cases
T24 1066-1076 GeneOrGeneProduct denotes predictive
T25 1077-1082 GeneOrGeneProduct denotes value
T26 1097-1107 GeneOrGeneProduct denotes predictive
T27 1108-1113 GeneOrGeneProduct denotes value
T28 1208-1214 GeneOrGeneProduct denotes PIK3CA
T29 1215-1223 GeneOrGeneProduct denotes mutation
T30 1285-1291 GeneOrGeneProduct denotes PIK3CA
T31 1292-1300 GeneOrGeneProduct denotes mutation
T32 1338-1343 GeneOrGeneProduct denotes cases
T33 1362-1370 GeneOrGeneProduct denotes mutation
T34 1410-1416 GeneOrGeneProduct denotes PIK3CA
T35 1417-1425 GeneOrGeneProduct denotes mutation
T36 1498-1503 GeneOrGeneProduct denotes cases
T37 1537-1541 GeneOrGeneProduct denotes case
T38 1598-1604 GeneOrGeneProduct denotes PIK3CA
T39 1605-1613 GeneOrGeneProduct denotes mutation
T40 1639-1645 GeneOrGeneProduct denotes PIK3CA
T41 1646-1654 GeneOrGeneProduct denotes mutation
T42 1666-1672 GeneOrGeneProduct denotes highly
T43 1844-1850 GeneOrGeneProduct denotes PIK3CA
T44 1851-1860 GeneOrGeneProduct denotes mutations
T45 1878-1882 GeneOrGeneProduct denotes ESCC

LitCoin-GeneOrGeneProduct-v2

Id Subject Object Predicate Lexical cue
T1 20-26 GeneOrGeneProduct denotes PIK3CA
T2 115-119 GeneOrGeneProduct denotes cell
T3 143-149 GeneOrGeneProduct denotes PIK3CA
T4 233-237 GeneOrGeneProduct denotes cell
T5 300-306 GeneOrGeneProduct denotes PIK3CA
T6 457-463 GeneOrGeneProduct denotes PIK3CA
T7 570-576 GeneOrGeneProduct denotes paired
T8 916-922 GeneOrGeneProduct denotes PIK3CA
T9 1208-1214 GeneOrGeneProduct denotes PIK3CA
T10 1285-1291 GeneOrGeneProduct denotes PIK3CA
T11 1410-1416 GeneOrGeneProduct denotes PIK3CA
T12 1598-1604 GeneOrGeneProduct denotes PIK3CA
T13 1639-1645 GeneOrGeneProduct denotes PIK3CA
T14 1844-1850 GeneOrGeneProduct denotes PIK3CA

LitCoin-Disease-MeSH

Id Subject Object Predicate Lexical cue originalLabel
T1 95-129 DiseaseOrPhenotypicFeature denotes esophageal squamous cell carcinoma D000077277
T2 213-247 DiseaseOrPhenotypicFeature denotes esophageal squamous cell carcinoma D000077277
T3 249-253 DiseaseOrPhenotypicFeature denotes ESCC D000077277
T4 681-685 DiseaseOrPhenotypicFeature denotes ESCC D000077277
T5 1878-1882 DiseaseOrPhenotypicFeature denotes ESCC D000077277

LitCoin-GeneOrGeneProduct-v3

Id Subject Object Predicate Lexical cue
T1 20-26 GeneOrGeneProduct denotes PIK3CA
T2 143-149 GeneOrGeneProduct denotes PIK3CA
T3 300-306 GeneOrGeneProduct denotes PIK3CA
T4 457-463 GeneOrGeneProduct denotes PIK3CA
T5 916-922 GeneOrGeneProduct denotes PIK3CA
T6 1208-1214 GeneOrGeneProduct denotes PIK3CA
T7 1285-1291 GeneOrGeneProduct denotes PIK3CA
T8 1410-1416 GeneOrGeneProduct denotes PIK3CA
T9 1598-1604 GeneOrGeneProduct denotes PIK3CA
T10 1639-1645 GeneOrGeneProduct denotes PIK3CA
T11 1844-1850 GeneOrGeneProduct denotes PIK3CA

LitCoin_Mondo_095

Id Subject Object Predicate Lexical cue mondo_id
T1 95-129 DiseaseOrPhenotypicFeature denotes esophageal squamous cell carcinoma 0005580
T2 213-247 DiseaseOrPhenotypicFeature denotes esophageal squamous cell carcinoma 0005580
T3 249-253 DiseaseOrPhenotypicFeature denotes ESCC 0005580
T4 681-685 DiseaseOrPhenotypicFeature denotes ESCC 0005580
T5 1811-1814 DiseaseOrPhenotypicFeature denotes can 0012833
T6 1878-1882 DiseaseOrPhenotypicFeature denotes ESCC 0005580

LitCoin-MeSH-Disease-2

Id Subject Object Predicate Lexical cue ID:
T1 95-129 DiseaseOrPhenotypicFeature denotes esophageal squamous cell carcinoma D000077277
T2 213-247 DiseaseOrPhenotypicFeature denotes esophageal squamous cell carcinoma D000077277
T3 249-253 DiseaseOrPhenotypicFeature denotes ESCC D000077277
T4 681-685 DiseaseOrPhenotypicFeature denotes ESCC D000077277
T5 1878-1882 DiseaseOrPhenotypicFeature denotes ESCC D000077277

LitCoin-NCBITaxon-2

Id Subject Object Predicate Lexical cue
T1 638-646 OrganismTaxon denotes patients
T2 1192-1200 OrganismTaxon denotes patients
T3 1758-1765 OrganismTaxon denotes patient
T4 1864-1872 OrganismTaxon denotes patients

LitCoin-MONDO_bioort2019

Id Subject Object Predicate Lexical cue #label
T1 95-129 DiseaseOrPhenotypicFeature denotes esophageal squamous cell carcinoma D000077277
T2 213-247 DiseaseOrPhenotypicFeature denotes esophageal squamous cell carcinoma D000077277
T3 249-253 DiseaseOrPhenotypicFeature denotes ESCC D000077277
T4 681-685 DiseaseOrPhenotypicFeature denotes ESCC D000077277
T5 1878-1882 DiseaseOrPhenotypicFeature denotes ESCC D000077277

LitCoin-Chemical-MeSH-CHEBI

Id Subject Object Predicate Lexical cue ID:
T1 514-522 ChemicalEntity denotes formalin D005557
T2 533-541 ChemicalEntity denotes paraffin D010232|ChemicalEntity

LitCoin-training-merged

Id Subject Object Predicate Lexical cue #label ID:
T2 533-541 ChemicalEntity denotes paraffin ChemicalEntity|D010232
T1 514-522 ChemicalEntity denotes formalin D005557
T11 1844-1850 GeneOrGeneProduct denotes PIK3CA
T10 1639-1645 GeneOrGeneProduct denotes PIK3CA
T9 1598-1604 GeneOrGeneProduct denotes PIK3CA
T8 1410-1416 GeneOrGeneProduct denotes PIK3CA
T7 1285-1291 GeneOrGeneProduct denotes PIK3CA
T6 1208-1214 GeneOrGeneProduct denotes PIK3CA
T5 916-922 GeneOrGeneProduct denotes PIK3CA
T4 457-463 GeneOrGeneProduct denotes PIK3CA
T3 300-306 GeneOrGeneProduct denotes PIK3CA
T47772 143-149 GeneOrGeneProduct denotes PIK3CA
T55038 20-26 GeneOrGeneProduct denotes PIK3CA
T31313 1878-1882 DiseaseOrPhenotypicFeature denotes ESCC D000077277
T76861 681-685 DiseaseOrPhenotypicFeature denotes ESCC D000077277
T79411 249-253 DiseaseOrPhenotypicFeature denotes ESCC D000077277
T15688 213-247 DiseaseOrPhenotypicFeature denotes esophageal squamous cell carcinoma D000077277
T92720 95-129 DiseaseOrPhenotypicFeature denotes esophageal squamous cell carcinoma D000077277
T95960 1864-1872 OrganismTaxon denotes patients
T25540 1758-1765 OrganismTaxon denotes patient
T63662 1192-1200 OrganismTaxon denotes patients
T58424 638-646 OrganismTaxon denotes patients
T74027 503-509 SequenceVariant denotes H1047L
T42809 491-497 SequenceVariant denotes H1047R
T3154 484-489 SequenceVariant denotes E546K
T72399 477-482 SequenceVariant denotes E545K
T23816 470-475 SequenceVariant denotes E542K