The old version of WebGestalt only included two types of functional categories (Table 1), whereas the new version covers six types (GO, Pathway, Network, Phenotype, Disease and Drug, and Chromosomal location) (Table 2). For the pathway collection, in addition to the KEGG database, WebGestalt has added data from Pathway Commons and WikiPathways. Because Pathway Commons collects and integrates nine centrally curated biological pathway databases and WikiPathways is a primary source for open community-based curation, adding these two resources has significantly increased the coverage of pathways in WebGestalt. Gene–phenotype association is one of the most important aspects biology. Therefore, we have added phenotype-associated gene sets defined by Mammalian Phenotype Ontology (15) and Human Phenotype Ontology (16) to WebGestalt. WebGestalt has also included gene sets defined by cytogenetic bands, which can help identify alterations related to chromosomal deletions or amplifications, dosage compensation and other regional effects. Table 2.Detailed information on the functional categories supported by WebGestaltTypeDatabaseMethodNo. of categoriesaNo. of organismsbData sourceGene OntologyBiological processCC24 2788Gene Ontology (http://www.geneontology.org/)Cellular componentCC30798Molecular functionCC95088PathwayKEGGCC3908R package KEGG.dbPathway CommonsCC16511http://www.pathwaycommons.org/pc/WikiPathwaysPC10188http://www.wikipathways.org/index.php/WikiPathwaysNetworkHierarchical protein interaction network moduleCA19932HPRD (http://www.hprd.org/)BioGrid (http://thebiogrid.org/)BOND (http://bond.unleashedinformatics.com/)DIP (http://dip.doe-mbi.ucla.edu/dip/)IntAct (http://www.ebi.ac.uk/intact/)MINT (http://mint.bio.uniroma2.it/mint/)Reactome (http://www.reactome.org/)MicroRNA
