g:Profiler-interoperable web service for functional enrichment analysis and gene identifier mapping (2023 update)

Area of Science:

• Bioinformatics
• Computational Biology
• Genomics

Background:

• Functional enrichment analysis is crucial for interpreting large gene lists in biological research.
• Existing tools require comprehensive databases and user-friendly interfaces for efficient analysis.
• g:Profiler has been a long-standing resource for gene list analysis since 2007.

Purpose of the Study:

• To introduce updates to the g:Profiler tool, enhancing its functional enrichment analysis capabilities.
• To present a novel filtering method for highlighting Gene Ontology (GO) driver terms.
• To improve the visualization of GO term significance and context.

Main Methods:

• Integration of multiple biological databases (Gene Ontology, KEGG, TRANSFAC).
• Development of interactive user interfaces and programmatic access.
• Implementation of a new filtering algorithm for GO driver terms.
• Introduction of new graph visualizations for GO term analysis.

Main Results:

• g:Profiler supports 849 species and custom annotations for any organism.
• Maintains historical database versions since 2015 to ensure research reproducibility.
• The new filtering method effectively highlights key GO driver terms.
• Enhanced visualizations provide broader context for significant GO terms.

Conclusions:

• g:Profiler remains a leading, reliable, and up-to-date tool for functional enrichment analysis.
• The recent updates improve the analysis and interpretation of gene lists, particularly for GO terms.
• The tool's accessibility and comprehensive features make it invaluable for genetics, biology, and medical researchers.