The DAVID Gene Functional Classification Tool: a novel biological module-centric algorithm to functionally analyze large gene lists
By Danzhi Huang, Brad T. Sherman, Qina Tan, J. Collins, Gregory Alvord, Jean A. Roayaei, Robert M. Stephens, M. Baseler, C. Lane, Richard A. Lempicki. Genome Biology, 2007
2,300 citations recorded by the source corpus.
The DAVID Gene Functional Classification Tool http://david.abcc.ncifcrf.gov uses a novel agglomeration algorithm to condense a list of genes or associated biological terms into organized classes of related genes or biology, called biological modules. This organization is accomplished by mining the complex biological co-occurrences found in multiple sources of functional annotation. It is a powerful method to group functionally related genes and terms into a manageable number of biological modules for efficient interpretation of gene lists in a network context.
Subfields: Molecular Biology
View Paper: https://www.semanticscholar.org/paper/70e0e13f11abb01c4a71a1b95cb2f473eb04e7e5
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In Molecular Biology
- Danzhi Huang
- Richard A. Lempicki
- Brad T. Sherman
- Gary D. Bader
- Daniele Merico
- Ruth Isserlin
- Robert M. Stephens
- Andrew Emili
Citations in the corpus
- pathfindR: An R Package for Comprehensive Identification of Enriched Pathways in Omics Data Through Active Subnetworks (2019, methodology): “In order to establish representative pathways among similar groups of pathways, we propose that clustering can be performed either via hierarchical clustering (default) or via a fuzzy clustering method as described by Huang et al. (2007).”
- Enrichment Map: A Network-Based Method for Gene-Set Enrichment Visualization and Interpretation (2010, methodology): “DAVID [12,29,30] utilizes fuzzy gene clusters, pre-computed on the basis of annotation similarity among all genes, to sort enriched gene-sets into different yet partially overlapping groups; results are then displayed in a tabular format.”
- Extracting Biological Meaning from Large Gene Lists with DAVID (2009, methodology): “This protocol describes several DAVID tools, all of which aim at extracting biological meaning from large gene lists (Huang et al., 2007a,b).”
- GLK Transcription Factors Coordinate Expression of the Photosynthetic Apparatus in Arabidopsis[W][OA] (2009, methodology): “To assess the degree to which these classifications are overrepresentative of Arabidopsis proteins as a whole, the GLK1upregulated genes were submitted to enrichment analysis using the DAVID Functional Annotation tool (Huang et al., 2007).”