DAVID: Database for Annotation, Visualization, and Integrated Discovery

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: 10.47). 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; 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.

Download full-text


Available from: Richard A Lempicki, Jul 28, 2015
    • "Functional enrichment analysis. DAVID (Dennis et al., 2003) and MSigDB v4.0 (Subramanian et al., 2005) were used to test differentially expressed genes and WGCNA modules for overrepresentation in Gene Ontologies and Canonical Pathways. "
    [Show abstract] [Hide abstract]
    ABSTRACT: Autism spectrum disorder (ASD) is a disorder of brain development. Most cases lack a clear etiology or genetic basis, and the difficulty of re-enacting human brain development has precluded understanding of ASD pathophysiology. Here we use three-dimensional neural cultures (organoids) derived from induced pluripotent stem cells (iPSCs) to investigate neurodevelopmental alterations in individuals with severe idiopathic ASD. While no known underlying genomic mutation could be identified, transcriptome and gene network analyses revealed upregulation of genes involved in cell proliferation, neuronal differentiation, and synaptic assembly. ASD-derived organoids exhibit an accelerated cell cycle and overproduction of GABAergic inhibitory neurons. Using RNA interference, we show that overexpression of the transcription factor FOXG1 is responsible for the overproduction of GABAergic neurons. Altered expression of gene network modules and FOXG1 are positively correlated with symptom severity. Our data suggest that a shift toward GABAergic neuron fate caused by FOXG1 is a developmental precursor of ASD. Copyright © 2015 Elsevier Inc. All rights reserved.
    Cell 07/2015; 162(2):375-390. DOI:10.1016/j.cell.2015.06.034 · 33.12 Impact Factor
  • Source
    • "The DEGs were subjected to gene ontology (GO) and pathway analysis using the Database for Annotation, Visualization, and Integrated Discovery (DAVID) (Dennis et al., 2003; Huang et al., 2009) to find overrepresentations of GO terms in the biological process (BP) category at level 5 (GOTERM_BP_5) and KEGG pathways. As background, the Homo sapiens (human) whole genome was used. "
    [Show abstract] [Hide abstract]
    ABSTRACT: The increased use of silver nanoparticles (AgNPs) in foods and cosmetics has raised public safety concerns. However, only limited knowledge exists on the effect of AgNPs on the cellular transcriptome. This study evaluated global gene expression profiles of human liver HepG2 cells exposed to 20 and 50 nm AgNPs for 4 and 24 h at 2.5 µg ml(-1) . Exposure to 20 nm AgNPs resulted in 811 altered genes after 4 h, but much less after 24 h. Exposure to 50 nm AgNPs showed minimal altered genes at both exposure times. The HepG2 cells responded to the toxic insult of AgNPs by transiently upregulating stress response genes such as metallothioneins and heat shock proteins. Functional analysis of the altered genes showed more than 20 major biological processes were affected, of which metabolism, development, cell differentiation and cell death were the most dominant categories. Several cellular pathways were also impacted by AgNP exposure, including the p53 signaling pathway and the NRF2-mediated oxidative stress response pathway, which may lead to increased oxidative stress and DNA damage in the cell and potentially result in genotoxicity and carcinogenicity. Together, these results indicate that HepG2 cells underwent a multitude of cellular processes in response to the toxic insult of AgNP exposure, and suggest that toxicogenomic characterization of human HepG2 cells could serve as an alternative model for assessing toxicities of NPs. Published 2015. This article is a U.S. Government work and is in the public domain in the USA. Published 2015. This article is a U.S. Government work and is in the public domain in the USA.
    Journal of Applied Toxicology 05/2015; DOI:10.1002/jat.3170 · 3.17 Impact Factor
  • Source
    • "The gene ontology analysis (Pavlidis et al., 2004) which aids in the identification of molecular function, biological process and cellular locations of large-scale transcriptome data was monitored for all the initially filtered genes using DAVID web server (Dennis et al., 2003). The hypergeometric distribution count N2 and FDR b0.05 were set as threshold criteria to identify the functional gene ontology of the mined gene set. "
    [Show abstract] [Hide abstract]
    ABSTRACT: Psoriasis is a chronic disease of the skin characterized by hyper proliferation and inflammation of the epidermis and dermal components of the skin. T-cell-dependent inflammatory process in skin governs the pathogenesis of psoriasis. An insilico search strategy was utilized to identify psoriatic therapeutic drug targets. The gene expression profiling of psoriatic skin identified a total of 427 differentially expressed genes (DEGs). Gene ontology investigation of DEGs identified genes involved in calcium binding, apoptosis, keratinisation, lipid transportation and homeostasis apart from immune mediated processes. The protein interaction networks identified proteins involved in various signaling mechanisms with high degree of interconnections. The gene modules derived from the main network were enriched with rich kinome. These sub-networks were dominated by the presence of non-receptor kinase family members which are major signal transmitters in immune response. The computational approach has aided in the identification of non-receptor kinases as potential targets for psoriasis drug development. Copyright © 2015. Published by Elsevier B.V.
    Gene 04/2015; 566(2). DOI:10.1016/j.gene.2015.04.030 · 2.08 Impact Factor
Show more