Table 1.

Summary of ToppGene suite applications

Application	Description	Input	Output
ToppFun	Detects 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 human gene symbols, NCBI Reference Sequence accession numbers; single gene list.	HTML output; Tab-delimited downloadable text file; graphical charts
ToppGene	Prioritize or rank candidate genes based on functional similarity to training gene list.	Same as above but with two gene lists (training and test)	HTML output
ToppNet	Prioritize or rank candidate genes based on topological features in protein–protein interaction network.	Same as above	HTML output; Cytoscape-compatible input file; graphical networks
ToppGeNet	Identify and prioritize the neighboring genes of the ‘seeds’ in protein–protein interaction network based on functional similarity to the ‘seed’ list (ToppGene) or topological features in protein–protein interaction network (ToppNet).	Single gene list	Same as above