title: DAVID Bioinformatics Resources: expanded annotation database and novel algorithms to better extract biology from large gene lists.
abstract: All tools in the DAVID Bioinformatics Resources aim to provide functional interpretation of large lists of genes derived from genomic studies. The newly updated DAVID Bioinformatics Resources consists of the DAVID Knowledgebase and five integrated, web-based functional annotation tool suites: the DAVID Gene Functional Classification Tool, the DAVID Functional Annotation Tool, the DAVID Gene ID Conversion Tool, the DAVID Gene Name Viewer and the DAVID NIAID Pathogen Genome Browser. 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 bioinformatics databases. For any uploaded gene list, the DAVID Resources now provides not only the typical gene-term enrichment analysis, but also new tools and functions that allow users to condense large gene lists into gene functional groups, convert between gene/protein identifiers, visualize many-genes-to-many-terms relationships, cluster redundant and heterogeneous terms into groups, search for interesting and related genes or terms, dynamically view genes from their lists on bio-pathways and more. With DAVID (http://david.niaid.nih.gov), investigators gain more power to interpret the biological mechanisms associated with large gene lists.
authors.affiliation: Laboratory of Immunopathogenesis and Bioinformatics, SAIC-Frederick, Inc., National Cancer Institute at Frederick, MD 21702, USA.
authors.forename: Da Wei
authors.initials: DW
authors.lastname: Huang
authors.forename: Brad T
authors.initials: BT
authors.lastname: Sherman
authors.forename: Qina
authors.initials: Q
authors.lastname: Tan
authors.forename: Joseph
authors.initials: J
authors.lastname: Kir
authors.forename: David
authors.initials: D
authors.lastname: Liu
authors.forename: David
authors.initials: D
authors.lastname: Bryant
authors.forename: Yongjian
authors.initials: Y
authors.lastname: Guo
authors.forename: Robert
authors.initials: R
authors.lastname: Stephens
authors.forename: Michael W
authors.initials: MW
authors.lastname: Baseler
authors.forename: H Clifford
authors.initials: HC
authors.lastname: Lane
authors.forename: Richard A
authors.initials: RA
authors.lastname: Lempicki
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D003627:Data Interpretation, Statistical; D030541:Databases, Genetic; D030561:Databases, Nucleic Acid; D020869:Gene Expression Profiling / Q000706:statistics & numerical data*; D023281:Genomics; D006801:Humans; D016247:Information Storage and Retrieval / Q000379:methods*; D020407:Internet; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods; D010363:Pattern Recognition, Automated; D012984:Software