ArticleNucleic acids research2010
FunSimMat update: new features for exploring functional similarity.
Article in Nucleic acids research, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers, 1 of them a synthesis that pooled it.
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16 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Dense genotyping of immune-related disease regions identifies nine new risk loci for primary sclerosing cholangitis.Nature genetics · 2013Pooled it
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- Semantic similarity and machine learning with ontologies.Briefings in bioinformatics · 2021Review
- Predicting candidate genes from phenotypes, functions and anatomical site of expression.Bioinformatics (Oxford, England) · 2021Article
- Inferring ontology graph structures using OWL reasoning.BMC bioinformatics · 2018Article
- InteGO2: a web tool for measuring and visualizing gene semantic similarities using Gene Ontology.BMC genomics · 2016Article
- The role of ontologies in biological and biomedical research: a functional perspective.Briefings in bioinformatics · 2015Article
- Abundant genetic overlap between blood lipids and immune-mediated diseases indicates shared molecular genetic mechanisms.PloS one · 2015Article
- FSim: a novel functional similarity search algorithm and tool for discovering functionally related gene products.BioMed research international · 2014Article
- Drug-target interaction prediction by integrating chemical, genomic, functional and pharmacological data.Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing · 2014Article
- Chapter 15: disease gene prioritization.PLoS computational biology · 2013Article
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- Specificity of linear motifs that bind to a common mitogen-activated protein kinase docking groove.Science signaling · 2012Article
- Mining GO annotations for improving annotation consistency.PloS one · 2012Article
- Improving disease gene prioritization using the semantic similarity of Gene Ontology terms.Bioinformatics (Oxford, England) · 2010Article
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2 authors.
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Abstract
Quantifying the functional similarity of genes and their products based on Gene Ontology annotation is an important tool for diverse applications like the analysis of gene expression data, the prediction and validation of protein functions and interactions, and the prioritization of disease genes. The Functional Similarity Matrix (FunSimMat, http://www.funsimmat.de) is a comprehensive database providing various precomputed functional similarity values for proteins in UniProtKB and for protein families in Pfam and SMART. With this update, we significantly increase the coverage of FunSimMat by adding data from the Gene Ontology Annotation project as well as new functional similarity measures. The applicability of the database is greatly extended by the implementation of a new Gene Ontology-based method for disease gene prioritization. Two new visualization tools allow an interactive analysis of the functional relationships between proteins or protein families. This is enhanced further by the introduction of an automatically derived hierarchy of annotation classes. Additional changes include a revised user front-end and a new RESTlike interface for improving the user-friendliness and online accessibility of FunSimMat.
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