Cited by 9,327Bioinformatics and Genomic NetworksGenomics and Phylogenetic StudiesBiomedical Text Mining and Ontologies

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DAVID: Database for Annotation, Visualization, and Integrated Discovery

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Dennis, Glynn, Sherman, Brad T, Hosack, Douglas A, Yang, Jun, Gao, Wei, Lane, H Clifford, Lempicki, Richard A·2003·Genome Biology

DOI 10.1186/gb-2003-4-5-p3PMC PMC193660

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Abstract

BACKGROUND: 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. RESULTS: 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. CONCLUSIONS: 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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Gene Ontology: tool for the unification of biology
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KEGG: Kyoto Encyclopedia of Genes and Genomes
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Database resources of the National Center for Biotechnology Information: update
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“16,17 The raw data file for the RNAseq has been deposited in Gene Expression Omnibus with the accession code GSE273139.”

Authors: Dennis, G., Sherman, B. T., Hosack, D. A., Yang, J., Gao, W., Lane, H. C., & Lempicki, R. A.
Affiliations: National Cancer Institute (US)
National Institutes of Health (US)
Corresponding author: Dennis, Glynn
ORCID: Sherman, Brad T
Gao, Wei
Lane, H Clifford
Lempicki, Richard A
Venue: Genome Biology
Publisher: Springer Science and Business Media LLC
Published: 2003-04-03
Volume: 4
Issue: 5
Pages: P3-P3
ISSN: 1465-6906 (ISSN-L)
1474-760X
DOI: 10.1186/gb-2003-4-5-p3
PMC: PMC193660
OpenAlex: W2122683221
Cited by: 9,327
References: 16
Citations by year: 2026: 164 · 2025: 352 · 2024: 394 · 2023: 412 · 2022: 486 · 2021: 528 · 2020: 459 · 2019: 429 · 2018: 392 · 2017: 413 · 2016: 377 · 2015: 456 · 2014: 437 · 2013: 484 · 2012: 527
FWCI: 38.46
Type: journal article
Language: en
Open access: gold
doi.org
Licence: www.springer.com/tdm (tdm)
Locations: Genome biology (publishedVersion)
Europe PMC (PubMed Central) (publishedVersion, other-oa)
PubMed Central (publishedVersion, other-oa)
PubMed (publishedVersion)
Funders: U.S. Public Health Service (N01-C056000)
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
Health Sciences › Medicine › Health Informatics › Biomedical Text Mining and Ontologies
Keywords: David, functional annotation, differentially expressed genes, microarray data analysis, Gene Ontology, KEGG pathways, online databases, gene function classification
MeSH terms: Humans, Leukocytes, Mononuclear, Macrophages, HIV-1, Computational Biology, Internet, Oligonucleotide Array Sequence Analysis, Gene Expression Profiling, Databases, Nucleic Acid

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