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

Area of Science:

• Bioinformatics
• Computational Biology
• Genomics

Background:

• Gene Ontology (GO) enrichment analysis is crucial for interpreting complex biological data.
• Identifying significantly overrepresented GO terms reveals shared biological functions within gene sets.
• Effective visualization of enrichment results is essential for biological interpretation.

Purpose of the Study:

• To introduce FunSet, a novel web server for performing and visualizing GO enrichment analysis.
• To provide a tool that enhances the biological interpretation of enrichment results through advanced visualization.

Main Methods:

• FunSet identifies statistically overrepresented GO terms by comparing a target gene set against a background set.
• Enriched terms are visualized in a 2D plot reflecting semantic similarity.
• Includes options for spectral clustering to group terms and identify representative terms for each cluster.

Main Results:

• FunSet offers interactive and programmatic access to enrichment analysis.
• Results can be downloaded in tabular, graphical (SVG), or data (JSON, CSV) formats.
• Provides access to historical ontology and annotation data for enhanced reproducibility.

Conclusions:

• FunSet facilitates the comprehensive analysis and interpretation of Gene Ontology enrichment.
• The tool supports data download and ensures reproducibility through access to historical data.
• Open-source availability of FunSet promotes wider adoption and contribution in bioinformatics research.