Another important consideration for enrichment analysis tools is to update and expand the collection of functional categories. Most of these tools integrate multiple centrally curated functional databases, such as Gene Ontology (GO) (5), KEGG (6), Pathway Commons (7) and MSigDB (8). In contrast to centrally curated databases, open, collaborative platforms that allow for broader participation by the entire biology community, such as WikiPathways (9), have become a new model for community-based curation of biological data. This new model enhances and complements ongoing effort of centrally curated databases and holds great potential to significantly enhance our knowledge on functional categories. In addition to manual curation, computational analysis represents an alternative approach for building functional categories. For example, motif gene sets derived from comparative genomic analysis of conserved cis-regulatory motifs have been included in MSigDB. Recently, it has been shown that large gene and protein interaction networks can be used to infer ontologies whose coverage and power are comparable to those manually curated by the GO consortium (10). We have also built GLAD4U (11), a tool that derives and prioritizes gene lists
