GeneMANIA

GeneMANIA predicts gene function and gene–gene associations by extending query gene lists using integrated genomics and proteomics networks to identify functionally similar genes.

Key Features:

• Gene function hypothesis generation: Extends a list of query genes by identifying functionally similar genes using integrated genomic and proteomic datasets.
• Data integration: Integrates datasets from GEO, BioGRID, Pathway Commons, IRefIndex, I2D and organism-specific functional genomics datasets.
• Predictive value weighting: Computes weights that indicate the predictive value of each dataset for a given query.
• Cytoscape plugin and network support: Provides a Cytoscape plugin implementing a guilt-by-association approach and supporting over 800 networks with the ability to add interaction networks and expression profile data.
• Organism support: Supports Arabidopsis thaliana, Caenorhabditis elegans, Drosophila melanogaster, Mus musculus, Homo sapiens, Rattus norvegicus and Saccharomyces cerevisiae.
• User-defined datasets: Allows uploading and analysis of user-provided interaction networks and expression profile datasets.

Scientific Applications:

• Gene function prediction: Predicts functions of unknown genes by associating them with functionally similar genes in integrated networks.
• Candidate gene prioritization: Prioritizes genes for experimental validation and functional assays based on network-based similarity and dataset weights.
• Gene Ontology enrichment exploration: Identifies enriched Gene Ontology categories among genes associated with a query set.
• Benchmarking and evaluation: Enables performance assessment as demonstrated by benchmarks on yeast and mouse datasets.

Methodology:

Extends query gene lists by integrating genomic, proteomic and expression-profile networks, applies a guilt-by-association algorithm, and computes dataset-specific weights indicating predictive value while supporting addition of user networks and expression data.