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

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.

1700029I15Rik orchestrates the biosynthesis of acrosomal membrane proteins required for sperm–egg fusion

“…b , GO and KEGG analyses of the highly associated interacting proteins. Functional annotations of interactome were conducted using the DAVID knowledgebase 31 . Only the 31 proteins concurrently detected in at least two replicates of the co-IP/MS experiments were analysed.…”

3’UTR-directed, kinase proximal mRNA decay inhibits C/EBPβ phosphorylation/activation to suppress senescence in tumor cells

“…1C). The GRE-bound protein list was analyzed by gene ontology (DAVID, GOTERM_BP) (Sherman et al, 2022) to identify enriched biological processes (Fig. 1D).…”

“…(D) Gene ontology analysis of proteins preferentially binding to the GRE. GRE-enriched proteins were analyzed for associations with pathways/biological processes using DAVID (Sherman et al, 2022). GO terms for the 20 highest ranking biological processes are shown, ranked by p-value.…”

“…Using a threshold FDR of 0.1, all proteins whose ratio of GRE-bound PSMs to GFP-bound PSMs was at least 2.0 were selected. The 324 proteins that show a significant preference for binding to GRE were submitted to DAVID (2021 Release) (Sherman et al, 2022) for functional analyses.…”

CK2 signaling from TOLLIP-dependent perinuclear endosomes is an essential feature ofKRASandNRASmutant cancers

“…The amino acid sequence around the phosphorylation site of phospho-peptides was examined to determine if it represented a CK2 phosphorylation motif, [S|T]xx[D|E] 43 . DAVID analysis 68 was performed to determine functional annotation of the potential CK2 phospho-peptides. Functional classifications based on Molecular Function (GOTERM_MF_DIRECT) and Biological Processes (GOTERM_BP_DIRECT) were obtained and plotted.…”