The new version of WebGestalt has significantly increased the coverage of organisms, gene identifiers and functional categories, has enabled enrichment analysis against some unique data sources including the publicly curated WikiPathways database, hierarchical network modules, phenotype ontology, and disease and drug-associated gene sets, and has implemented new visualization features for presenting pathway, phenotype and network enrichment analysis results. As shown in Table 3, many unique features allow WebGestalt to maintain strong competitiveness among a large number of software applications related to functional enrichment analysis (26). However, WebGesalt is still far from perfect. For example, DAVID contains information about protein domains, Swiss-Prot keywords and Panther pathways, which is not included in WebGestalt. Thus, in the future, we will continuously update WebGestalt to support more gene identifiers and curated functional categories, develop and adopt novel computational methods to define new functional categories, and improve the intuitiveness and friendliness of the user interface. Table 3.Features unique to WebGestalt or shared with other toolsaMultiple-organism support✓✓✓✓ Gene identifier Public database✓✓✓✓ Affymetrix✓✓✓✓ Agilent✓✓✓✓ Codelink✓✓✓ SNP✓✓✓ Functional category GO✓✓✓✓ KEGG✓✓✓✓ Pathway Commons✓LbLL WikiPathways✓ Hierarchical protein interaction network
