gCocoa

gCocoa performs functional enrichment and annotation of gene lists to identify statistically significant Gene Ontology (GO) terms, pathways, and other functional datasets for comparative analysis across multiple gene sets and species.

Key Features:

• Functional annotation and enrichment analysis: Interprets flat and ranked gene lists to identify statistically significant Gene Ontology (GO) terms, pathways, and related gene function annotations.
• Gene identifier translation: Translates hundreds of gene identifiers across multiple species to enable integration and comparison of datasets.
• Comparative analysis of multiple gene sets: Performs comparative analyses across multiple gene sets simultaneously to support cross-set interpretation.
• Comprehensive species support: Supports an extensive range of 213 species, including mammals, other vertebrates, plants, insects, and fungi.
• Timely data updates: Synchronizes genome and pathway information with the Ensembl database through quarterly updates.
• Expanded functional datasets (2016 update): Includes transcription factor binding site predictions, Mendelian disease annotations, protein expression and complexes, and gene mappings of human genetic polymorphisms.

Scientific Applications:

• High-throughput data interpretation: Interprets gene lists from RNA sequencing and ChIP-seq experiments to derive functional insights.
• Biological process and disease mechanism discovery: Identifies enriched biological processes and potential disease mechanisms from experimental gene lists.
• Cross-species gene function analysis: Facilitates exploration of gene function and annotations across multiple species via identifier translation and broad species coverage.

Methodology:

Performs statistical enrichment to identify significant GO terms and pathways from flat and ranked gene lists, translates gene identifiers across species, conducts comparative analyses of multiple gene sets, synchronizes genome and pathway data with Ensembl on a quarterly basis, and incorporates transcription factor binding site predictions, Mendelian disease annotations, protein expression and complexes, and gene mappings of human genetic polymorphisms.