ccmGDB: a database for cancer cell metabolism genes.
ccmGDB: a database for cancer cell metabolism genes.
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DOI：
10.1093/nar/gkv1128
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发表时间：
2016-01-04
影响因子：
14.9
通讯作者：
Zhao Z
中科院分区：
文献类型：
--
作者：
Kim P;Cheng F;Zhao J;Zhao Z
越来越多的证据表明，细胞中代谢的重新布线是癌症的一个重要标志。据估计，死于代谢紊乱的患者占晚期癌症患者的30%。因此，对癌细胞代谢基因进行系统的注释势在必行。在这里，我们提出了ccmGDB（癌症细胞代谢基因数据库），一个全面的注释数据库，在癌症细胞代谢基因，可在http://bioinfo.mc.vanderbilt.edu/ccmGDB。我们为30多种癌症类型中的2000多个细胞代谢基因组装，策划和整合遗传，基因组，转录组，蛋白质组学，生物网络和功能信息。总共，我们整合了超过260 000个体细胞改变，包括非同义突变，拷贝数变异和结构变异。我们还整合了各种原发性肿瘤的RNA-Seq数据，1000多个癌细胞系的基因表达微阵列数据和蛋白质表达数据。此外，我们构建了癌症或组织类型特异性的，基于基因共表达的蛋白质相互作用网络和药物-靶标相互作用网络。使用这些系统注释，ccmGDB门户网站提供6个类别：基因摘要，表型信息，体细胞突变，基因和蛋白质表达，基因共表达网络和药物药理学信息，并提供用户友好的界面供浏览和搜索。ccmGDB被开发和维护为癌症研究社区的有用资源。
Accumulating evidence has demonstrated that rewiring of metabolism in cells is an important hallmark of cancer. The percentage of patients killed by metabolic disorder has been estimated to be 30% of the advanced-stage cancer patients. Thus, a systematic annotation of cancer cell metabolism genes is imperative. Here, we present ccmGDB (Cancer Cell Metabolism Gene DataBase), a comprehensive annotation database for cell metabolism genes in cancer, available at http://bioinfo.mc.vanderbilt.edu/ccmGDB. We assembled, curated, and integrated genetic, genomic, transcriptomic, proteomic, biological network and functional information for over 2000 cell metabolism genes in more than 30 cancer types. In total, we integrated over 260 000 somatic alterations including non-synonymous mutations, copy number variants and structural variants. We also integrated RNA-Seq data in various primary tumors, gene expression microarray data in over 1000 cancer cell lines and protein expression data. Furthermore, we constructed cancer or tissue type-specific, gene co-expression based protein interaction networks and drug-target interaction networks. Using these systematic annotations, the ccmGDB portal site provides 6 categories: gene summary, phenotypic information, somatic mutations, gene and protein expression, gene co-expression network and drug pharmacological information with a user-friendly interface for browsing and searching. ccmGDB is developed and maintained as a useful resource for the cancer research community.