Article

Dennis, G. et al. DAVID: Database for Annotation, Visualization, and Integrated Discovery. Genome Biol. 4, R60

Science Applications International Corporation-Frederick, Clinical Services Program, Laboratory of Immunopathogenesis and Bioinformatics, National Cancer Institute at Frederick, MD 21702, USA.
Genome biology (Impact Factor: 10.81). 02/2003; 4(5):P3. DOI: 10.1186/gb-2003-4-9-r60
Source: PubMed

ABSTRACT

Functional annotation of differentially expressed genes is a necessary and critical step in the analysis of microarray data. The distributed nature of biological knowledge frequently requires researchers to navigate through numerous web-accessible databases gathering information one gene at a time. A more judicious approach is to provide query-based access to an integrated database that disseminates biologically rich information across large datasets and displays graphic summaries of functional information.
Database for Annotation, Visualization, and Integrated Discovery (DAVID; http://www.david.niaid.nih.gov) addresses this need via four web-based analysis modules: 1) Annotation Tool - rapidly appends descriptive data from several public databases to lists of genes; 2) GoCharts - assigns genes to Gene Ontology functional categories based on user selected classifications and term specificity level; 3) KeggCharts - assigns genes to KEGG metabolic processes and enables users to view genes in the context of biochemical pathway maps; and 4) DomainCharts - groups genes according to PFAM conserved protein domains.
Analysis results and graphical displays remain dynamically linked to primary data and external data repositories, thereby furnishing in-depth as well as broad-based data coverage. The functionality provided by DAVID accelerates the analysis of genome-scale datasets by facilitating the transition from data collection to biological meaning.

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    • "al descriptions and Gene Ontology ( GO ) classifications . GO term enrichment and fold enrichment or depletion for gene lists of significantly up - and downregulated genes in kidney were determined . GO analysis for significant genes was performed using Kyoto Encyclopedia of Genes and Genomes ( KEGG ) and NIH DAVID Bioinformatics Resources 6 . 7 ( Dennis et al . , 2003 ) to identify regulated biological themes ."
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    • "The threshold for evaluating significance was obtained by applying a p-value of 0.05 FDR-Benjamini–Hochberg [9]. Integrated analysis of different functional databases was done using the functional annotation tool of the Database for Annotation, Visualization, and Integrated Discovery (DAVID) [10] using as background the set of genes that passed through the differential expression analysis filter. "

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    • "Ontologies enrichments related to BPA05 and BPA50 DEG were obtained by querying corresponding Entrez Gene IDs into the Database for Annotation, Visualization and Integrated Discovery (DAVID) (Dennis et al., 2003) and clustered for redundancy by the Functional Annotation Clustering of Gene Ontology (GO) terms so that each significant cluster included parent and children GO terms. Similarly, enrichments for KEGG pathways were obtained. "
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