DAVID: Database for Annotation, Visualization, and Integrated Discovery

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

8,806 citations recorded by the source corpus.

The distributed nature of biological knowledge poses a major challenge to the interpretation of genome-scale datasets, including those derived from microarray and proteomic studies. This report describes DAVID, a web-accessible program that integrates functional genomic annotations with intuitive graphical summaries. Lists of gene or protein identifiers are rapidly annotated and summarized according to shared categorical data for Gene Ontology, protein domain, and biochemical pathway membership. DAVID assists in the interpretation of genome-scale datasets by facilitating the transition from data collection to biological meaning.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/80e394ee3e1834091596e8b55c9ad9bf11456e09

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Citations in the corpus

Pscan: finding over-represented transcription factor binding site motifs in sequences from co-regulated or co-expressed genes (2009, methodology): “Other ID types (Aﬀy IDs, Entrez or ENSEMBL gene IDs and so on) can anyway be quickly converted in the format accepted by Pscan with tools like DAVID (15).”
seqMINER: an integrated ChIP-seq data interpretation platform (2010, methodology): “All visual features as well as the list of loci can be exported for further analysis with other methodologies [i.e. gene annotation (5), ontology (20)].”
FOXG1-dependent dysregulation of GABA/glutamate neuron differentiation in autism spectrum disorders (2015, neutral): “DAVID (Dennis et al., 2003) and MSigDB v4.”
Next-Generation Sequencing Technology: Current Trends and Advancements (2023, methodology): “Alignment of reads to reference Splice-aware aligner such as TopHat2 [123], HISAT2 [124], and STAR [125] Transcript quantiﬁcation featureCounts [126], HTSeq-count [127], Salmon [128], Kallisto [129] Differential gene expression analysis enrichment of gene categories DESeq2 [130], EdgeR [131], DAVID ”
The MicroRNA miR-124 promotes neuronal differentiation by triggering brain-specific alternative pre-mRNA splicing. (2007, methodology): “The likelihood of overrepresentation in the gene ontology (GO) biological process categories was generated using the Database for Annotation, Visualization, and Integrated Discovery (DAVID) 2.1 (Dennis et al., 2003; http://david.abcc.ncifcrf.gov/).”
The C. elegans TGF-β Dauer Pathway Regulates Longevity via Insulin Signaling (2007, positive): “To compare the biological roles that the genes regulated by each of these pathways might play, we submitted the lists of significantly up- and downregulated genes from both the adult TGF-b SAM analysis and from the TGF-b dauer arrays [5] to DAVID [10] for Gene Ontology (GO) analysis.”
DAVID Knowledgebase: a gene-centered database integrating heterogeneous gene annotation resources to facilitate high-throughput gene functional analysis (2007, methodology): “The work was originally conducted years ago to successfully serve as a comprehensive backend knowledgebase for various high throughput gene-annotation enrichment analytic tools in the DAVID and EASE packages [13,14].”
NOA: a novel Network Ontology Analysis method (2011, background): “Most tools such as FatiGO, DAVID, g:proﬁler and BiNGO are in this level.”
Autism and Increased Paternal Age Related Changes in Global Levels of Gene Expression Regulation (2011, methodology): “gov) Functional Annotation Bioinformatics Microarray Analysis[31,32] was used to assess gene lists for enriched biological themes.”
RECURRENT MUTATIONS IN THE U2AF1 SPLICING FACTOR IN MYELODYSPLASTIC SYNDROMES (2011, positive): “7b were performed as previously described 19,45,46 .”
Deconstructing the molecular portraits of breast cancer (2010, methodology): “Biologic analysis of microarray data was performed with DAVID annotation tool (http:// david.abcc.ncifcrf.gov/) (Dennis et al., 2003).”