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. 2022 Jul 5;50(W1):W216-W221.
doi: 10.1093/nar/gkac194.

DAVID: a web server for functional enrichment analysis and functional annotation of gene lists (2021 update)

Brad T Sherman  1 , Ming Hao  1 , Ju Qiu  1 , Xiaoli Jiao  1 , Michael W Baseler  2 , H Clifford Lane  3 , Tomozumi Imamichi  1 , Weizhong Chang  1
Affiliations

DAVID: a web server for functional enrichment analysis and functional annotation of gene lists (2021 update)

Brad T Sherman et al. Nucleic Acids Res. .

Abstract

DAVID is a popular bioinformatics resource system including a web server and web service for functional annotation and enrichment analyses of gene lists. It consists of a comprehensive knowledgebase and a set of functional analysis tools. Here, we report all updates made in 2021. The DAVID Gene system was rebuilt to gain coverage of more organisms, which increased the taxonomy coverage from 17 399 to 55 464. All existing annotation types have been updated, if available, based on the new DAVID Gene system. Compared with the last version, the number of gene-term records for most annotation types within the updated Knowledgebase have significantly increased. Moreover, we have incorporated new annotations in the Knowledgebase including small molecule-gene interactions from PubChem, drug-gene interactions from DrugBank, tissue expression information from the Human Protein Atlas, disease information from DisGeNET, and pathways from WikiPathways and PathBank. Eight of ten subgroups split from Uniprot Keyword annotation were assigned to specific types. Finally, we added a species parameter for uploading a list of gene symbols to minimize the ambiguity between species, which increases the efficiency of the list upload and eliminates confusion for users. These current updates have significantly expanded the Knowledgebase and enhanced the discovery power of DAVID.

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Figures

Graphical Abstract
Graphical Abstract
DAVID: a web server for functional enrichment analysis and functional annotation of gene lists (2021 update).
Figure 1.
Figure 1.
Updated DAVID Gene System. (A) Integrated Knowledgebase. The DAVID Gene system was rebuilt based on the NCBI Entrez Gene system and Uniprot Knowledgebase. The categories with new annotation types are coloured green. (B) Analytical Tools. The six DAVID analytical tools were connected to the updated Knowledgebase for comprehensive functional annotation and enrichment analysis of gene/protein lists.
Figure 2.
Figure 2.
Significant Expansion of the DAVID Knowledgebase. (A) DAVID Taxonomy Coverage. The number of taxonomies in DAVID has increased significantly for all kingdoms due to the increased coverage resulting from the new DAVID Gene system. (B) Major Gene Identifier Type Counts and (C) Significant Increase in Gene-Term Records for Default DAVID Annotation Types. Significant increases in gene-term records are due to both increased annotation from the source databases as well as the increased coverage of the new DAVID Gene System.
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