DAVID (bioinformatics tool)

From Wikipedia, the free encyclopedia
Jump to: navigation, search
DAVID Bioinformatics Resources
Original author(s) Da-Wei Huang, Brad Sherman, Richard A. Lempicki,
Developer(s) Laboratory of Immunopathogenesis and Bioinformatics
Stable release 6.7 / 27 January 2010; 4 years ago (2010-01-27)
Type Bioinformatics
License proprietary
Website http://david.abcc.ncifcrf.gov/home.jsp

DAVID (the Database for Annotation, Visualization and Integrated Discovery) is a free online bioinformatics resource developed by the Laboratory of Immunopathogenesis and Bioinformatics (LIB).[1][2][3][4][5][6] All tools in the DAVID Bioinformatics Resources aim to provide functional interpretation of large lists of genes derived from genomic studies, e.g. microarray and proteomics studies. DAVID can be found at http://david.niaid.nih.gov or http://david.abcc.ncifcrf.gov

The DAVID Bioinformatics Resources consists of the DAVID Knowledgebase and five integrated, web-based functional annotation tool suites: the DAVID Gene Functional Classification Tool, the DAVID Functional Annotation Tool, the DAVID Gene ID Conversion Tool, the DAVID Gene Name Viewer and the DAVID NIAID Pathogen Genome Browser. The expanded DAVID Knowledgebase now integrates almost all major and well-known public bioinformatics resources centralized by the DAVID Gene Concept, a single-linkage method to agglomerate tens of millions of diverse gene/protein identifiers and annotation terms from a variety of public bioinformatics databases. For any uploaded gene list, the DAVID Resources now provides not only the typical gene-term enrichment analysis, but also new tools and functions that allow users to condense large gene lists into gene functional groups, convert between gene/protein identifiers, visualize many-genes-to-many-terms relationships, cluster redundant and heterogeneous terms into groups, search for interesting and related genes or terms, dynamically view genes from their lists on bio-pathways and more.

Functionality[edit]

DAVID provides a comprehensive set of functional annotation tools for investigators to understand biological meaning behind large list of genes. For any given gene list, DAVID tools are able to:

  • Identify enriched biological themes, particularly GO terms
  • Discover enriched functional-related gene groups
  • Cluster redundant annotation terms
  • Visualize genes on BioCarta & KEGG pathway maps
  • Display related many-genes-to-many-terms on 2-D view.
  • Search for other functionally related genes not in the list
  • List interacting proteins
  • Explore gene names in batch
  • Link gene-disease associations
  • Highlight protein functional domains and motifs
  • Redirect to related literatures
  • Convert gene identifiers from one type to another.

External links[edit]

References[edit]

  1. ^ Huang DW, Lempicki RA (2009). "Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources.". Nature Protocols 4 (1): 44–57. doi:10.1038/nprot.2008.211. PMID 19131956. 
  2. ^ Sherman BT, Huang DW, Tan Q, Guo Y, Bour S, Liu D, Stephens R, Baseler MW, Lane HC, Lempicki RA (2007). "DAVID Knowledgebase: a gene-centered database integrating heterogeneous gene annotation resources to facilitate high-throughput gene functional analysis". BMC Bioinformatics 8: 426. doi:10.1186/1471-2105-8-426. PMC 2186358. PMID 17980028. 
  3. ^ Huang DW, Sherman BT, Tan Q, Collins JR, Alvord WG, Roayaei J, Stephens R, Baseler MW, Lane HC, Lempicki RA (2007). "The DAVID Gene Functional Classification Tool: a novel biological module-centric algorithm to functionally analyze large gene lists". Genome Biol 8 (9): R183. doi:10.1186/gb-2007-8-9-r183. PMC 2375021. PMID 17784955. 
  4. ^ Huang Da, HC; Sherman, BT; Tan, Q; Kir, J; Liu, D; Bryant, D; Guo, Y; Stephens, R et al. (2007). "DAVID Bioinformatics Resources: expanded annotation database and novel algorithms to better extract biology from large gene lists". Nucleic Acids Research 35 (Web Server issue): W169–75. doi:10.1093/nar/gkm415. PMC 1933169. PMID 17576678. 
  5. ^ Hosack; Dennis Jr, G; Sherman, BT; Lane, HC; Lempicki, RA (2003). "Identifying biological themes within lists of genes with EASE.". Genome Biology 4 (10): R70. doi:10.1186/gb-2003-4-10-r70. PMC 328459. PMID 14519205. 
  6. ^ Dennis Jr; Sherman, BT; Hosack, DA; Yang, J; Gao, W; Lane, HC; Lempicki, RA (2003). "DAVID: Database for Annotation, Visualization, and Integrated Discovery.". Genome Biology 4 (5): P3. doi:10.1186/gb-2003-4-5-p3. PMID 12734009.