Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA.
Hum Mutat. 2010 Mar;31(3):219-28. doi: 10.1002/humu.21176.
Identification and annotation of mutated genes or proteins involved in oncogenesis and tumor progression are crucial for both cancer biology and clinical applications. We have developed a human Cancer Proteome Variation Database (CanProVar) by integrating information on protein sequence variations from various public resources, with a focus on cancer-related variations (crVAR). We have also built a user-friendly interface for querying the database. The current version of CanProVar comprises 8,570 crVARs in 2,921 proteins derived from existing genome variation databases and recently published large-scale cancer genome resequencing studies. It also includes 41,541 non-cancer specific variations (ncsVARs) in 30,322 proteins derived from the dbSNP database. CanProVar provides quick access to known crVARs in protein sequences along with related cancer samples, relevant publications, data sources, and functional information such as Gene Ontology (GO) annotations for the proteins, protein domains in which the variation occurs, and protein interaction partners with crVARs. CanProVar also helps reveal functional characteristics of crVARs and proteins bearing these variations. Our analysis showed that crVARs were enriched in certain protein domains. We also showed that proteins bearing crVARs were more likely to interact with each other in the protein interaction network. CanProVar can be accessed from http://bioinfo.vanderbilt.edu/canprovar.
鉴定和注释参与肿瘤发生和肿瘤进展的突变基因或蛋白质对于癌症生物学和临床应用都至关重要。我们通过整合来自各种公共资源的蛋白质序列变异信息，开发了一个人类癌症蛋白质组变异数据库（CanProVar），重点关注与癌症相关的变异（crVAR）。我们还为查询数据库构建了一个用户友好的界面。当前版本的 CanProVar 包含来自现有基因组变异数据库和最近发表的大规模癌症基因组重测序研究的 2921 种蛋白质中的 8570 种 crVAR 和 30322 种蛋白质中的 41541 种非癌症特异性变异（ncsVAR）。CanProVar 提供了对蛋白质序列中已知 crVAR 以及相关癌症样本、相关出版物、数据源以及蛋白质功能信息（如基因本体论（GO）注释）的快速访问，其中包括发生变异的蛋白质结构域以及与 crVAR 相互作用的蛋白质。CanProVar 还可以帮助揭示 crVAR 和携带这些变异的蛋白质的功能特征。我们的分析表明，crVAR 富集在某些蛋白质结构域中。我们还表明，携带 crVAR 的蛋白质在蛋白质相互作用网络中更有可能相互作用。CanProVar 可通过以下网址访问：http://bioinfo.vanderbilt.edu/canprovar。
