DAVID (bioinformatics tool)

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DAVID (the Database for Annotation, Visualization and Integrated Discovery) is a free online bioinformatics resources developed by the Laboratory of Immunopathogenesis and Bioinformatics (LIB [1]). 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

Contents 1 Introduction to DAVID 2 Functionality Highlights 3 DAVID in Scientific Community 3.1 Citations 3.2 Recommendation 4 Publications

[edit] Introduction to DAVID

The newly updated 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. With DAVID (http://david.niaid.nih.gov), investigators gain more power to interpret the biological mechanisms associated with large gene lists.

[edit] Functionality Highlights

DAVID now 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:

    1. Identify enriched biological themes, particularly GO terms
    2. Discover enriched functional-related gene groups
    3. Cluster redundant annotation terms
    4. Visualize genes on BioCarta & KEGG pathway maps
    5. Display related many-genes-to-many-terms on 2-D view.
    6. Search for other functionally related genes not in the list 
    7. List interacting proteins
    8. Explore gene names in batch 
    9. Link gene-disease associations 
    10.Highlight protein functional domains and motifs 
    11.Redirect to related literatures 
    12.Convert gene identifers from one type to another.
    13.And more 

[edit] DAVID in Scientific Community

[edit] Citations

Hundreds of publications made use or referenced DAVID. Please see detail survey by Google Scholar

[edit] Recommendation

Many institutes and individual researchers recommend DAVID on their web page .

[edit] Publications

1. Sherman BT, Huang DW, Tan Q, Guo Y, Bour S, Liu D, Stephens R, Baseler MW, Lane HC, Lempicki RA. DAVID Knowledgebase: A Gene-centered Database Integrating Heterogeneous Gene Annotation Resources to Facilitate High-throughput Gene Functional Analysis. BMC Bioinformatics. 2007 Nov 2;8(1):426.

2. Huang DW, Sherman BT, Tan Q, Collins JR, Alvord WG, Roayaei J, Stephens R, Baseler MW, Lane HC, Lempicki RA. DAVID Gene Functional Classification Tool: A novel biological module-centric algorithm to functionally analyze large gene list. Genome Biol. 2007 Sep 4;8(9):R183.

3. Huang DW, Sherman BT, Tan Q, Kir J, Liu D, Bryant D, Guo Y, Stephens R, Baseler MW, Lane HC, Lempicki RA. DAVID Bioinformatics Resources: Expanded annotation database and novel algorithms to better extract biology from large gene lists. Nucleic Acids Res. 2007 Jul 1;35.

4. Hosack DA, Dennis G Jr, Sherman BT, Lane HC, Lempicki RA. Identifying biological themes within lists of genes with EASE. Genome Biol. 2003;4(10):R70.

5. Dennis G Jr, Sherman BT, Hosack DA, Yang J, Gao W, Lane HC, Lempicki RA. DAVID: Database for Annotation, Visualization, and Integrated Discovery. Genome Biol. 2003;4(5):P3.