DOMINO

DOMINO identifies active modules in gene networks by integrating gene activity profiles to detect subnetworks with significant accumulated activity and reveal condition-specific molecular processes in omics studies.

Key Features:

• DOMINO algorithm: A novel active module identification (AMI) algorithm reported to detect active modules with improved empirical validation rates compared to existing methods.
• Gene network and gene activity profile input: Accepts a gene network together with a gene activity profile to identify subnetworks enriched for accumulated activity signals.
• Gene Ontology (GO) enrichment analysis: Performs GO enrichment analysis to characterize the biological functions of identified modules.
• Module visualization: Generates visual representations of identified active modules.
• Customizable output formats: Exports results in formats intended for downstream customized analyses.
• Multi-organism compatibility: Supports various gene identifiers across different organisms.

Scientific Applications:

• Active module identification in omics studies: Detects subnetworks that capture coordinated activity signals in omics datasets to highlight biologically relevant modules.
• Detection of condition-specific molecular processes: Identifies molecular processes that are over-represented under specific biological conditions.
• Network-based systems biology analyses: Enables network-centric interpretation of gene activity profiles in bioinformatics and systems biology studies.
• Multi-organism and comparative analyses: Facilitates analyses across different organisms through support for multiple gene identifier types.

Methodology:

Executes the DOMINO AMI algorithm on an input gene network and gene activity profile, performs Gene Ontology (GO) enrichment analysis of identified modules, and produces module visualizations and exportable result files.