Laboratory of Human Retrovirology and Immunoinformatics, Applied and Developmental Research Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA.
Clinical Services Program, Applied and Developmental Research Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD21702, USA.
Nucleic Acids Res. 2022 Jul 5;50(W1):W216-W221. doi: 10.1093/nar/gkac194.
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.
DAVID 是一个受欢迎的生物信息学资源系统，包括一个用于基因列表的功能注释和富集分析的网络服务器和网络服务。它由一个综合知识库和一组功能分析工具组成。在这里，我们报告了 2021 年的所有更新。DAVID Gene 系统进行了重建，以覆盖更多的生物体，将分类学覆盖率从 17399 增加到 55464。所有现有的注释类型都已根据新的 DAVID Gene 系统进行了更新（如果可用）。与上一个版本相比，更新后的知识库中大多数注释类型的基因-术语记录数量都显著增加。此外，我们还在知识库中纳入了新的注释，包括来自 PubChem 的小分子-基因相互作用、来自 DrugBank 的药物-基因相互作用、来自 Human Protein Atlas 的组织表达信息、来自 DisGeNET 的疾病信息以及来自 WikiPathways 和 PathBank 的途径。从 Uniprot Keyword 注释中拆分的十个亚组中的八个被分配到特定的类型。最后，我们添加了一个物种参数，用于上传基因符号列表，以最大限度地减少物种之间的歧义，这提高了列表上传的效率，并消除了用户的困惑。这些当前的更新显著扩展了知识库，并增强了 DAVID 的发现能力。
