Journal ArticleDOI
Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources.
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TLDR
By following this protocol, investigators are able to gain an in-depth understanding of the biological themes in lists of genes that are enriched in genome-scale studies.Abstract:
DAVID bioinformatics resources consists of an integrated biological knowledgebase and analytic tools aimed at systematically extracting biological meaning from large gene/protein lists. This protocol explains how to use DAVID, a high-throughput and integrated data-mining environment, to analyze gene lists derived from high-throughput genomic experiments. The procedure first requires uploading a gene list containing any number of common gene identifiers followed by analysis using one or more text and pathway-mining tools such as gene functional classification, functional annotation chart or clustering and functional annotation table. By following this protocol, investigators are able to gain an in-depth understanding of the biological themes in lists of genes that are enriched in genome-scale studies.read more
Citations
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Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists
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The Molecular Signatures Database Hallmark Gene Set Collection
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References
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Journal ArticleDOI
Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles
Aravind Subramanian,Pablo Tamayo,Vamsi K. Mootha,Sayan Mukherjee,Benjamin L. Ebert,Michael A. Gillette,Amanda G. Paulovich,Scott L. Pomeroy,Todd R. Golub,Eric S. Lander,Jill P. Mesirov +10 more
TL;DR: The Gene Set Enrichment Analysis (GSEA) method as discussed by the authors focuses on gene sets, that is, groups of genes that share common biological function, chromosomal location, or regulation.
Journal ArticleDOI
DAVID: Database for Annotation, Visualization, and Integrated Discovery
Glynn Dennis,Brad T. Sherman,Douglas A. Hosack,Jun Jun Yang,Wei Gao,H. Clifford Lane,Richard A. Lempicki +6 more
TL;DR: DAMID is a web-accessible program that integrates functional genomic annotations with intuitive graphical summaries that assists in the interpretation of genome-scale datasets by facilitating the transition from data collection to biological meaning.
Journal ArticleDOI
The DAVID Gene Functional Classification Tool: a novel biological module-centric algorithm to functionally analyze large gene lists
Da-Wei Huang,Brad T. Sherman,Qina Tan,Jack R. Collins,W. Gregory Alvord,Jean Roayaei,Robert S Stephens,Michael Baseler,H. Clifford Lane,Richard A. Lempicki +9 more
TL;DR: The DAVID Gene Functional Classification Tool 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, for efficient interpretation of gene lists in a network context.
Journal ArticleDOI
Identifying biological themes within lists of genes with EASE
TL;DR: EASE is a customizable software application for rapid biological interpretation of gene lists that result from the analysis of microarray, proteomics, SAGE and other high-throughput genomic data and is robust to varying methods of normalization, intensity calculation and statistical selection of genes.
Journal ArticleDOI
DAVID Bioinformatics Resources: expanded annotation database and novel algorithms to better extract biology from large gene lists
Da-Wei Huang,Brad T. Sherman,Qina Tan,Joseph Kir,David R. Liu,David Bryant,Yongjian Guo,Robert M. Stephens,Michael Baseler,H. Clifford Lane,Richard A. Lempicki +10 more
TL;DR: The expanded DAVID Knowledgebase now integrates almost all major and well-known public bioinformatics resources centralized by the DAVID Gene Concept, a single-linkage method to agglomerate tens of millions of diverse gene/protein identifiers and annotation terms from a variety of public bio informatics databases.
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