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

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.

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.