Optimal Threshold Determination for Interpreting Semantic Similarity and Particularity: Application to the Comparison of Gene Sets and Metabolic Pathways Using GO and ChEBI.

scientific article published on 31 July 2015

Optimal Threshold Determination for Interpreting Semantic Similarity and Particularity: Application to the Comparison of Gene Sets and Metabolic Pathways Using GO and ChEBI. is …
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scholarly articleQ13442814

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P819ADS bibcode2015PLoSO..1033579B
P356DOI10.1371/JOURNAL.PONE.0133579
P932PMC publication ID4521860
P698PubMed publication ID26230274
P5875ResearchGate publication ID281240911

P50authorCharles BettembourgQ85606313
P2093author name stringOlivier Dameron
Christian Diot
P2860cites workA Mathematical Theory of CommunicationQ724029
A Topology-Based Metric for Measuring Term Similarity in the Gene OntologyQ35990752
GOSemSim: an R package for measuring semantic similarity among GO terms and gene productsQ38375582
A new method to measure the semantic similarity of GO termsQ38398724
Correlation between gene expression and GO semantic similarityQ38403038
Semantic particularity measure for functional characterization of gene sets using gene ontology.Q38437022
Evaluation of gene ontology semantic similarities on protein interaction datasetsQ38455092
Assessing identity, redundancy and confounds in Gene Ontology annotations over timeQ38458235
A graph-based semantic similarity measure for the gene ontologyQ38481218
Improved detection of overrepresentation of Gene-Ontology annotations with parent child analysisQ38515564
Database resources of the National Center for Biotechnology InformationQ56337611
Semantic similarity in biomedical ontologiesQ21145359
Semantic Similarity for Automatic Classification of Chemical CompoundsQ21563489
Gene ontology: tool for the unification of biologyQ23781406
ChEBI: a database and ontology for chemical entities of biological interestQ24650818
The PANTHER database of protein families, subfamilies, functions and pathwaysQ24795605
Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene listsQ28131785
Semantic similarity measures as tools for exploring the gene ontologyQ28211764
Reactome: a database of reactions, pathways and biological processesQ28298042
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The Gene Ontology Annotation (GOA) Database: sharing knowledge in Uniprot with Gene OntologyQ29616014
Coexpression analysis of human genes across many microarray data setsQ30936126
How to decide which are the most pertinent overly-represented features during gene set enrichment analysisQ33298548
Gene Ontology term overlap as a measure of gene functional similarityQ33357701
A relation based measure of semantic similarity for Gene Ontology annotationsQ33382540
GO-based functional dissimilarity of gene setsQ34008003
Identifying informative subsets of the Gene Ontology with information bottleneck methodsQ34149135
On the Use of Gene Ontology Annotations to Assess Functional Similarity among Orthologs and Paralogs: A Short ReportQ34167857
A knowledge-based clustering algorithm driven by Gene OntologyQ34356455
Transcriptional regulation of metabolismQ34511703
PPAR expression and function during vertebrate developmentQ34570161
Improving the measurement of semantic similarity between gene ontology terms and gene products: insights from an edge- and IC-based hybrid methodQ34761563
Use and misuse of the gene ontology annotationsQ34778304
Measuring the evolution of ontology complexity: the gene ontology case study.Q35022572
Predictive Integration of Gene Ontology-Driven Similarity and Functional InteractionsQ35090749
P275copyright licenseCreative Commons Attribution 4.0 InternationalQ20007257
P6216copyright statuscopyrightedQ50423863
P433issue7
P407language of work or nameEnglishQ1860
P921main subjectmetabolic pathwayQ68685
semantic similarityQ2268914
P304page(s)e0133579
P577publication date2015-07-31
P1433published inPLOS OneQ564954
P1476titleOptimal Threshold Determination for Interpreting Semantic Similarity and Particularity: Application to the Comparison of Gene Sets and Metabolic Pathways Using GO and ChEBI
P478volume10

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cites work (P2860)
Q38389436Gene Ontology semantic similarity tools: survey on features and challenges for biological knowledge discovery
Q92035472SMAC, a computational system to link literature, biomedical and expression data

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