Here, we describe a unique, one-stop online assembly of computational software tools (summarized in Table 1 and Figure 1) that enables biomedical researchers to (i) perform gene list enrichment analysis (ToppFun), (ii) perform candidate gene prioritization based on functional annotations (ToppGene), (iii) perform candidate gene prioritization based on protein interactions network analysis (ToppNet) and (iv) identify and rank candidate genes in the interactome based on both functional annotations and PPIN analysis (ToppGeNet). Instructions and ‘help’ for each of these modules can be accessed from the homepage. The database is updated periodically, and the current status of the data (versions and coverage) can also be accessed from the homepage (‘Database details’). Additionally, several examples with stepwise instructions are provided to demonstrate the utility of these applications (see ‘Supplementary’ section from ToppGene homepage). Table 1.Summary of ToppGene suite applicationsApplicationDescriptionInputOutputToppFunDetects functional enrichment of input gene list based on Transcriptome (gene expression), Proteome (protein domains and interactions), Regulome (TFBS and miRNA), Ontologies (GO, Pathway), Phenotype (human disease and mouse phenotype), Pharmacome (Drug–Gene associations) and Bibliome (literature co-citation).Supported identifiers include NCBI Entrez gene IDs, approved
