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Gene Set Enrichment and Pathway Analysis


GeneMANIA is an online platform for discovery of enrichment of interactions from a user-provided gene list; and also has a downloadable plug-in for use with Cytoscape.

While it does not allow for upload of experimental values, its network interaction functionality resembles that of licensed pathway and network analysis products.

GeneMANIA draws networks of interactions for a list of user-supplied objects from data available from 9 species. It uses data from GO annotations, NCI-Nature's Pathway Commons database, NCBI, Ensembl, EMBL-EBI, other databases, and published literature to inform network interactions. The program draws dynamic, object-weighted networks based on pathways, physical or genetic interactions, co-localization, co-expression, or predicted interactions from published literature. Users can omit or include specific interaction types when submitting object lists, or when viewing results.