Laboratory of Human Retrovirology and Immunoinformatics, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, United States.
Bioinformatics. 2024 Oct 1;40(10). doi: 10.1093/bioinformatics/btae615.
The Database for Annotation, Visualization, and Integrated Discovery (DAVID) is a web-based bioinformatics system for the functional interpretation of large lists of genes/proteins generated from high-throughput assays. It has been cited in 72 287 papers since its debut in 2003 as of 23 July 2024. The analysis is usually limited to the species of study. However, the knowledge of genes may be incomplete or unavailable for some species. Model organisms have been studied more extensively and analyzing gene lists in the context of these species can offer valuable insights, helping users better understand the genes and biological themes in their species of interest.
We developed DAVID Ortholog for the conversion of gene lists between species. We utilized the ortholog data downloaded from Orthologous MAtrix (OMA) and Ensembl Compara as the base for the conversion. The OMA ortholog IDs and Ensembl gene IDs were converted to DAVID gene IDs and the pairing information of these IDs from these two sources was integrated into the DAVID Knowledgebase. DAVID Ortholog can convert the user's source gene list to an ortholog list of a desired species and the downstream DAVID analysis, in the context of that species, can be continued seamlessly, allowing users to further understand the biological meaning of their gene list based on the functional annotation found for the orthologs.
数据库注释、可视化和综合发现（DAVID）是一个基于网络的生物信息学系统，用于对高通量测定产生的大量基因/蛋白质列表进行功能解释。截至 2024 年 7 月 23 日，自 2003 年首次亮相以来，它已在 72287 篇论文中被引用。分析通常仅限于研究的物种。然而，对于某些物种，基因的知识可能不完整或不可用。模式生物已被更广泛地研究，在这些物种的背景下分析基因列表可以提供有价值的见解，帮助用户更好地理解其感兴趣物种中的基因和生物学主题。
我们开发了 DAVID Ortholog，用于在物种之间转换基因列表。我们利用从 Orthologous MAtrix (OMA) 和 Ensembl Compara 下载的同源数据作为转换的基础。OMA 同源 ID 和 Ensembl 基因 ID 被转换为 DAVID 基因 ID，这两个来源的这些 ID 的配对信息被整合到 DAVID 知识库中。DAVID Ortholog 可以将用户的源基因列表转换为所需物种的同源列表，并且可以在该物种的背景下继续进行下游 DAVID 分析，从而允许用户根据为同源物找到的功能注释进一步理解其基因列表的生物学意义。
