DAVID Knowledgebase: a gene-centered database integrating heterogeneous gene annotation resources to facilitate high-throughput gene functional analysis

Table 2 An example of improved annotation coverage for an individual gene USP8 in the DAVID Knowledgebase.

Category (Resource)	Selected Annotation	Entrez Gene	UniProt	PIR iProClass	DAVID
Molecular Function (Gene Ontology)	GO:0004197:cysteine-type endopeptidase activity	√	√	√	√
	GO:0005515:protein binding	√	√	√	√
	GO:0004843:ubiquitin-specific protease activity	√	√	√	√
	GO:0008233: peptidase activity			√	√
	GO:0004221: ubiquitin thiolesterase activity			√	√
	GO:0016787: hydrolase activity			√	√
	GO:0008234: cysteine-type peptidase activity			√	√
Biological Process (Gene Ontology)	GO:0006512: ubiquitin cycle	√	√	√	√
	GO:0008283: cell proliferation	√	√	√	√
	GO:0006511: ubiquitin-dependent protein catabolic process	√	√	√	√
	GO:0007265: Ras protein signal transduction			√	√
Cellular Component (Gene Ontology)	GO:0005622: intracellular			√	√
Protein Domain (InterPro)	IPR001394:Peptidase_C19		√		√
	IPR001763:Rhodanese-like		√		√
Enzyme (EC)	EC 3.1.2.15: Ubiquitin thiolesterase		√		√
Protein 3-D Structure(PDB)	1WHB:Solution structure of the Rhodanese-like domain in human UBP8			√	√
	2A9U: Structure of the N-terminal domain of HumanUSP8			√	√
Disease Association (OMIM)	OMIM:603158: chronic myeloproliferative disorder	√	√		√

For the gene of USP8, the annotation coverage is partially overlapped among the independent resources of Entrez Gene, UniProt and PIR. After the integration around DAVID Gene Concept (Figure 1B), the DAVID Knowledgebase provides more comprehensive coverage of annotation in one centralized location for USP8 than that in each of the individual sources.

ISSN: 1471-2105