GeneMANIA has multiple methods to combine and weight networks to create the final composite network used to find similar genes. By default, GeneMANIA chooses the network weighting algorithm based on the length of the query list, using the precombined network for queries with less than five genes and the query-weighted method for five or more genes. However, through the advanced options panel, users can choose among seven specific options. These options include ones that depend on patterns of Gene Ontology co-annotation (called ‘Gene Ontology-based weighting’), those that depend only on the gene list (called ‘Assigned based on query genes’) or non-adaptive ones that assign equal weights to each selected network or selected data source. Table 1 shows the GeneMANIA weighting algorithms and the publications where they are described and validated.
