OncoDB: an interactive online database for analysis of gene expression and viral infection in cancer.
OncoDB: an interactive online database for analysis of gene expression and viral infection in cancer.
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OncoDB：用于分析癌症中基因表达和病毒感染的交互式在线数据库。
DOI：
10.1093/nar/gkab970
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发表时间：
2022-01-07
影响因子：
14.9
通讯作者：
Wang X
中科院分区：
文献类型：
--
作者：
Tang G;Cho M;Wang X
大规模的多组学数据集，最突出的是来自TCGA联盟，已向公众提供人类癌症的系统表征。然而，到目前为止，缺乏相应的在线资源来利用这些有价值的数据来研究基因表达失调和病毒感染，这是癌症发展和进展的两个主要原因。为了解决这些未满足的需求，我们建立了OncoDB，这是一个在线数据库资源，用于探索与癌症临床特征相关的基因表达异常模式以及病毒感染。具体来说，OncoDB整合了TCGA研究中超过10000名癌症患者以及GTEx研究中正常组织的RNA-seq、DNA甲基化和相关临床数据。OncoDB的另一个独特之处在于它专注于肿瘤病毒。通过挖掘TCGA RNA-seq数据，我们已经确定了六种主要的肿瘤病毒，并进一步将病毒感染与宿主基因表达和临床结果的变化相关联。所有分析结果都集成在OncoDB中，并具有灵活的Web界面，可搜索与癌症患者的RNA表达，DNA甲基化，病毒感染和临床特征相关的数据。OncoDB可以在http://oncodb.org上免费访问。
Large-scale multi-omics datasets, most prominently from the TCGA consortium, have been made available to the public for systematic characterization of human cancers. However, to date, there is a lack of corresponding online resources to utilize these valuable data to study gene expression dysregulation and viral infection, two major causes for cancer development and progression. To address these unmet needs, we established OncoDB, an online database resource to explore abnormal patterns in gene expression as well as viral infection that are correlated to clinical features in cancer. Specifically, OncoDB integrated RNA-seq, DNA methylation, and related clinical data from over 10 000 cancer patients in the TCGA study as well as from normal tissues in the GTEx study. Another unique aspect of OncoDB is its focus on oncoviruses. By mining TCGA RNA-seq data, we have identified six major oncoviruses across cancer types and further correlated viral infection to changes in host gene expression and clinical outcomes. All the analysis results are integratively presented in OncoDB with a flexible web interface to search for data related to RNA expression, DNA methylation, viral infection, and clinical features of the cancer patients. OncoDB is freely accessible at http://oncodb.org.
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影响因子：
7.3
作者：
Gao J;Aksoy BA;Dogrusoz U;Dresdner G;Gross B;Sumer SO;Sun Y;Jacobsen A;Sinha R;Larsson E;Cerami E;Sander C;Schultz N
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Schultz N
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影响因子：
14.9
作者：
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影响因子：
30.8
作者：
Weinstein, John N.;Collisson, Eric A.;Mills, Gordon B.;Shaw, Kenna R. Mills;Ozenberger, Brad A.;Ellrott, Kyle;Shmulevich, Ilya;Sander, Chris;Stuart, Joshua M.
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Stuart, Joshua M.
影响因子：
6
作者：
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影响因子：
64.5
作者：
Liu J;Lichtenberg T;Hoadley KA;Poisson LM;Lazar AJ;Cherniack AD;Kovatich AJ;Benz CC;Levine DA;Lee AV;Omberg L;Wolf DM;Shriver CD;Thorsson V;Cancer Genome Atlas Research Network;Hu H
通讯作者：
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