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PubMed:20949073 JSONTXT

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LitCoin-entities

Id Subject Object Predicate Lexical cue db_id
8148 531-546 DiseaseOrPhenotypicFeature denotes cystic fibrosis MESH:D003550
8149 547-555 OrganismTaxon denotes patients NCBITaxon:9606
8150 575-580 SequenceVariant denotes E831X DBSNP:rs397508387
8151 591-598 SequenceVariant denotes 2623G>T DBSNP:rs397508387
8152 607-611 GeneOrGeneProduct denotes CFTR NCBIGene:1080

LitCoin-sentences

Id Subject Object Predicate Lexical cue
T9 1108-1252 Sentence denotes This molecular study reveals a naturally occurring mechanism where the effect of either modifier genes or epigenetic factors could be suspected.
T1 0-77 Sentence denotes Alternative splicing at a NAGNAG acceptor site as a novel phenotype modifier.
T2 78-231 Sentence denotes Approximately 30% of alleles causing genetic disorders generate premature termination codons (PTCs), which are usually associated with severe phenotypes.
T3 232-313 Sentence denotes However, bypassing the deleterious stop codon can lead to a mild disease outcome.
T4 314-435 Sentence denotes Splicing at NAGNAG tandem splice sites has been reported to result in insertion or deletion (indel) of three nucleotides.
T5 436-617 Sentence denotes We identified such a mechanism as the origin of the mild to asymptomatic phenotype observed in cystic fibrosis patients homozygous for the E831X mutation (2623G>T) in the CFTR gene.
T6 618-790 Sentence denotes Analyses performed on nasal epithelial cell mRNA detected three distinct isoforms, a considerably more complex situation than expected for a single nucleotide substitution.
T7 791-960 Sentence denotes Structure-function studies and in silico analyses provided the first experimental evidence of an indel of a stop codon by alternative splicing at a NAGNAG acceptor site.
T8 961-1107 Sentence denotes In addition to contributing to proteome plasticity, alternative splicing at a NAGNAG tandem site can thus remove a disease-causing UAG stop codon.
T10 1253-1365 Sentence denotes This finding is of importance for genetic counseling as well as for deciding appropriate therapeutic strategies.

LitCoin-entities-OrganismTaxon-PD

Id Subject Object Predicate Lexical cue db_id
T1 272-277 OrganismTaxon denotes codon NCBItxid:79338
T2 904-909 OrganismTaxon denotes codon NCBItxid:79338
T3 1101-1106 OrganismTaxon denotes codon NCBItxid:79338

LitCoin_Mondo

Id Subject Object Predicate Lexical cue mondo_id
T1 531-546 DiseaseOrPhenotypicFeature denotes cystic fibrosis 0009061

LitCoin-SeqVar

Id Subject Object Predicate Lexical cue
T1 575-580 SequenceVariant denotes E831X
T2 591-596 SequenceVariant denotes 2623G

LitCoin-GeneOrGeneProduct-v0

Id Subject Object Predicate Lexical cue
T1 12-20 GeneOrGeneProduct denotes splicing
T2 52-57 GeneOrGeneProduct denotes novel
T3 78-91 GeneOrGeneProduct denotes Approximately
T4 241-250 GeneOrGeneProduct denotes bypassing
T5 267-271 GeneOrGeneProduct denotes stop
T6 314-322 GeneOrGeneProduct denotes Splicing
T7 340-346 GeneOrGeneProduct denotes splice
T8 531-537 GeneOrGeneProduct denotes cystic
T9 581-589 GeneOrGeneProduct denotes mutation
T10 607-611 GeneOrGeneProduct denotes CFTR
T11 657-661 GeneOrGeneProduct denotes cell
T12 662-666 GeneOrGeneProduct denotes mRNA
T13 899-903 GeneOrGeneProduct denotes stop
T14 925-933 GeneOrGeneProduct denotes splicing
T15 1025-1033 GeneOrGeneProduct denotes splicing
T16 1096-1100 GeneOrGeneProduct denotes stop
T17 1225-1232 GeneOrGeneProduct denotes factors
T18 1258-1265 GeneOrGeneProduct denotes finding

LitCoin-GeneOrGeneProduct-v2

Id Subject Object Predicate Lexical cue
T1 52-57 GeneOrGeneProduct denotes novel
T2 267-271 GeneOrGeneProduct denotes stop
T3 531-537 GeneOrGeneProduct denotes cystic
T4 607-611 GeneOrGeneProduct denotes CFTR
T5 657-661 GeneOrGeneProduct denotes cell
T6 662-666 GeneOrGeneProduct denotes mRNA
T7 899-903 GeneOrGeneProduct denotes stop
T8 1096-1100 GeneOrGeneProduct denotes stop

LitCoin-Disease-MeSH

Id Subject Object Predicate Lexical cue originalLabel
T1 115-132 DiseaseOrPhenotypicFeature denotes genetic disorders D030342
T2 297-304 DiseaseOrPhenotypicFeature denotes disease D004194
T3 531-546 DiseaseOrPhenotypicFeature denotes cystic fibrosis D003550
T4 1076-1083 DiseaseOrPhenotypicFeature denotes disease D004194

LitCoin_Mondo_095

Id Subject Object Predicate Lexical cue mondo_id
T1 115-132 DiseaseOrPhenotypicFeature denotes genetic disorders 0003847
T2 278-281 DiseaseOrPhenotypicFeature denotes can 0012833
T3 531-546 DiseaseOrPhenotypicFeature denotes cystic fibrosis 0009061
T4 1058-1061 DiseaseOrPhenotypicFeature denotes can 0012833

LitCoin-GeneOrGeneProduct-v3

Id Subject Object Predicate Lexical cue
T1 607-611 GeneOrGeneProduct denotes CFTR

LitCoin-MeSH-Disease-2

Id Subject Object Predicate Lexical cue ID:
T1 115-132 DiseaseOrPhenotypicFeature denotes genetic disorders D030342
T2 297-304 DiseaseOrPhenotypicFeature denotes disease D004194
T3 531-546 DiseaseOrPhenotypicFeature denotes cystic fibrosis D003550
T4 1076-1083 DiseaseOrPhenotypicFeature denotes disease D004194

LitCoin-MONDO_bioort2019

Id Subject Object Predicate Lexical cue #label
T1 531-546 DiseaseOrPhenotypicFeature denotes cystic fibrosis D003550

LitCoin-Chemical-MeSH-CHEBI

Id Subject Object Predicate Lexical cue ID:
T1 282-286 ChemicalEntity denotes lead D007854

LitCoin-NCBITaxon-2

Id Subject Object Predicate Lexical cue
T1 547-555 OrganismTaxon denotes patients

LitCoin-training-merged

Id Subject Object Predicate Lexical cue #label ID:
T1 282-286 ChemicalEntity denotes lead D007854
T2819 607-611 GeneOrGeneProduct denotes CFTR
T19009 531-546 DiseaseOrPhenotypicFeature denotes cystic fibrosis D003550
T33933 547-555 OrganismTaxon denotes patients
T2 591-596 SequenceVariant denotes 2623G
T19178 575-580 SequenceVariant denotes E831X

DisGeNET

Id Subject Object Predicate Lexical cue
T0 607-611 gene:1080 denotes CFTR
T1 531-546 disease:C0010674 denotes cystic fibrosis
R1 T0 T1 associated_with CFTR,cystic fibrosis

Allie

Id Subject Object Predicate Lexical cue
SS1_20949073_1_0 142-170 expanded denotes premature termination codons
SS2_20949073_1_0 172-176 abbr denotes PTCs
AE1_20949073_1_0 SS1_20949073_1_0 SS2_20949073_1_0 abbreviatedTo premature termination codons,PTCs

DisGeNET5_gene_disease

Id Subject Object Predicate Lexical cue
20949073-4#171#175#gene1080 607-611 gene1080 denotes CFTR
20949073-4#95#110#diseaseC0010674 531-546 diseaseC0010674 denotes cystic fibrosis
171#175#gene108095#110#diseaseC0010674 20949073-4#171#175#gene1080 20949073-4#95#110#diseaseC0010674 associated_with CFTR,cystic fibrosis

tmVarCorpus

Id Subject Object Predicate Lexical cue
T1 575-580 ProteinMutation:p|SUB|E|831|X denotes E831X
T2 591-598 DNAMutation:|SUB|G|2623|T denotes 2623G>T