query genes. For example, if the query genes are part of a protein complex, GeneMANIA will predict additional members of that complex using primarily physical interactions (which highly connect the query genes); or if the query genes are protein kinases, GeneMANIA will suggest other protein kinases by using the protein domain similarity network. Networks are assigned weights based on how relevant they are to the query genes, and non-relevant networks will receive zero weights and not be shown in the results. Finally, GeneMANIA is a general purpose network search engine that supports selecting networks to search out of hundreds of options to identify a set of connections among query genes (the network weighting method should be set to ‘equal by network’ in this case). This is particularly useful when used in the Cytoscape app to find a network of interactions to process further using Cytoscape’s analysis features.
