DAVID Knowledgebase: a gene-centered database integrating heterogeneous gene annotation resources to facilitate high-throughput gene functional analysis
Top Cited Papers
Open Access
- 2 November 2007
- journal article
- database
- Published by Springer Nature in BMC Bioinformatics
- Vol. 8 (1) , 1-11
- https://doi.org/10.1186/1471-2105-8-426
Abstract
Background: Due to the complex and distributed nature of biological research, our current biological knowledge is spread over many redundant annotation databases maintained by many independent groups. Analysts usually need to visit many of these bioinformatics databases in order to integrate comprehensive annotation information for their genes, which becomes one of the bottlenecks, particularly for the analytic task associated with a large gene list. Thus, a highly centralized and ready-to-use gene-annotation knowledgebase is in demand for high throughput gene functional analysis. Description: The DAVID Knowledgebase is built around the DAVID Gene Concept, a single-linkage method to agglomerate tens of millions of gene/protein identifiers from a variety of public genomic resources into DAVID gene clusters. The grouping of such identifiers improves the cross-reference capability, particularly across NCBI and UniProt systems, enabling more than 40 publicly available functional annotation sources to be comprehensively integrated and centralized by the DAVID gene clusters. The simple, pair-wise, text format files which make up the DAVID Knowledgebase are freely downloadable for various data analysis uses. In addition, a well organized web interface allows users to query different types of heterogeneous annotations in a high-throughput manner. Conclusion: The DAVID Knowledgebase is designed to facilitate high throughput gene functional analysis. For a given gene list, it not only provides the quick accessibility to a wide range of heterogeneous annotation data in a centralized location, but also enriches the level of biological information for an individual gene. Moreover, the entire DAVID Knowledgebase is freely downloadable or searchable at http://david.abcc.ncifcrf.gov/knowledgebase/.Keywords
This publication has 21 references indexed in Scilit:
- IDconverter and IDClight: Conversion and annotation of gene and protein IDsBMC Bioinformatics, 2007
- ErmineJ: Tool for functional analysis of gene expression data setsBMC Bioinformatics, 2005
- Exploring relationships and mining data with the UCSC Gene Sorter: Figure 1.Genome Research, 2005
- Entrez Gene: gene-centered information at NCBINucleic Acids Research, 2004
- EnsMart: A Generic System for Fast and Flexible Access to Biological DataGenome Research, 2004
- UniProt: the Universal Protein knowledgebaseNucleic Acids Research, 2004
- GoMiner: a resource for biological interpretation of genomic and proteomic dataGenome Biology, 2003
- SOURCE: a unified genomic resource of functional annotations, ontologies, and gene expression dataNucleic Acids Research, 2003
- The Protein Information ResourceNucleic Acids Research, 2003
- RESOURCERER: a database for annotating and linking microarray resources within and across speciesGenome Biology, 2001