FatiGOplus

FatiGOplus performs functional profiling of genome-scale experiments to interpret microarray and other high-throughput data by annotating gene sets with Gene Ontology (GO), KEGG pathways, Interpro motifs, Swissprot keywords, text-mined bioentities, regulatory motifs and interactome structural features.

Key Features:

• Functional annotations: Provides annotations including Gene Ontology (GO) terms, KEGG pathways, Interpro motifs, Swissprot keywords and text-mined bioentities related to diseases and chemical compounds.
• Microarray focus: Targets interpretation of microarray data within genome-scale experiments.
• Regulatory information: Incorporates predicted regulatory targets from Transfac and CisRed.
• miRNA motif predictions: Includes miRNA target motif predictions to infer potential activation or deactivation in gene samples.
• Interactome structural data: Integrates structural information on gene product location and connectivity within the interactome.
• Enrichment analysis on coordinates: Performs enrichment analysis of functional terms using chromosomal coordinates.
• Integration with Babelomics and FatiScan: Operates within the Babelomics suite with indexing and computational efficiency and includes FatiScan to identify groups of functionally related genes with coordinated behavior while addressing multiple-testing challenges.

Scientific Applications:

• Microarray experiments: Interprets differential expression patterns by linking genes to GO terms, pathways, motifs and regulatory signals.
• Proteomics and genome-scale studies: Supports functional profiling in proteomics and other high-throughput genomic experiments.
• Regulatory network analysis: Aids inference of regulatory activation or deactivation through Transfac, CisRed and miRNA motif predictions.
• Systems biology hypothesis testing: Facilitates testing of systems biology hypotheses by identifying coordinated functional gene groups and assessing enrichment across genomic coordinates.

Methodology:

Uses functional annotation aggregation (GO, KEGG, Interpro, Swissprot), text-mining for bioentities, predicted regulatory targets from Transfac and CisRed, miRNA target motif predictions, enrichment analysis on chromosomal coordinates, integration of interactome structural data, and the FatiScan method that identifies coordinated gene groups while accounting for multiple-testing; implemented with indexing and computational efficiency within the Babelomics suite.