FunSet: An open-source software and web server for performing and displaying Gene Ontology enrichment analysis

Research output: Contribution to journalArticle

1 Citation (Scopus)

Abstract

Background: Gene Ontology enrichment analysis provides an effective way to extract meaningful information from complex biological datasets. By identifying terms that are significantly overrepresented in a gene set, researchers can uncover biological features shared by genes. In addition to extracting enriched terms, it is also important to visualize the results in a way that is conducive to biological interpretation. Results: Here we present FunSet, a new web server to perform and visualize enrichment analysis. The web server identifies Gene Ontology terms that are statistically overrepresented in a target set with respect to a background set. The enriched terms are displayed in a 2D plot that captures the semantic similarity between terms, with the option to cluster terms via spectral clustering and identify a representative term for each cluster. FunSet can be used interactively or programmatically, and allows users to download the enrichment results both in tabular form and in graphical form as SVG files or in data format as JSON or csv. To enhance reproducibility of the analyses, users have access to historical data for the ontology and the annotations. The source code for the standalone program and the web server are made available with an open-source license.

Original languageEnglish (US)
Article number359
JournalBMC bioinformatics
Volume20
Issue number1
DOIs
StatePublished - Jun 27 2019

Fingerprint

Gene Ontology
Open Source Software
Web Server
Ontology
Servers
Software
Genes
Licensure
Term
Semantics
Cluster Analysis
Research Personnel
Gene
Spectral Clustering
Semantic Similarity
Historical Data
Reproducibility
Open source software
Open Source
Annotation

Keywords

  • Functional Enrichment
  • Gene Ontology
  • Web Tools

ASJC Scopus subject areas

  • Structural Biology
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Applied Mathematics

Cite this

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abstract = "Background: Gene Ontology enrichment analysis provides an effective way to extract meaningful information from complex biological datasets. By identifying terms that are significantly overrepresented in a gene set, researchers can uncover biological features shared by genes. In addition to extracting enriched terms, it is also important to visualize the results in a way that is conducive to biological interpretation. Results: Here we present FunSet, a new web server to perform and visualize enrichment analysis. The web server identifies Gene Ontology terms that are statistically overrepresented in a target set with respect to a background set. The enriched terms are displayed in a 2D plot that captures the semantic similarity between terms, with the option to cluster terms via spectral clustering and identify a representative term for each cluster. FunSet can be used interactively or programmatically, and allows users to download the enrichment results both in tabular form and in graphical form as SVG files or in data format as JSON or csv. To enhance reproducibility of the analyses, users have access to historical data for the ontology and the annotations. The source code for the standalone program and the web server are made available with an open-source license.",
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