VIRGO

VIRGO predicts gene functions by constructing Functional Linkage Networks from gene expression and molecular interaction data and propagating Gene Ontology annotations to prioritize and assign confidence estimates to unannotated and lineage-specific genes.

Key Features:

• Functional Linkage Network (FLN) Construction: Constructs a Functional Linkage Network (FLN) from gene expression data and molecular interaction information.
• Gene Annotation Propagation: Labels genes with Gene Ontology annotations and propagates those annotations across the FLN to predict functions for genes lacking sequence or structural homology.
• Confidence Estimates and Prioritization: Assigns confidence estimates to predicted functions and prioritizes predictions for experimental validation.
• Propagation Diagrams for Visualization: Generates propagation diagrams that trace the flow of evidence within the FLN supporting each functional prediction.

Scientific Applications:

• Systems biology and functional genomics: Annotates genes of unknown function in systems biology and functional genomics by integrating diverse biological evidence.
• Target identification for medical, diagnostic, and pharmacogenomic studies: Prioritizes candidate genes for medical, diagnostic, or pharmacogenomic follow-up using network-derived functional predictions and confidence estimates.
• Lineage-specific and orphan gene analysis: Predicts functions for lineage-specific or organism-specific genes that lack sequence or structural homology to known genes.
• Integration with high-throughput experimental screens: Incorporates data from DNA chips and protein-protein interaction screens to inform and strengthen functional predictions.

Methodology:

Constructs an FLN from gene expression and molecular interaction data, labels genes with Gene Ontology annotations and propagates those annotations across the network, assigns confidence estimates to predictions, and produces propagation diagrams tracing evidence flow.