MethCNA: a database for integrating genomic and epigenomic data in human cancer
MethCNA: a database for integrating genomic and epigenomic data in human cancer
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MethCNA：整合人类癌症基因组和表观基因组数据的数据库
DOI：
10.1186/s12864-018-4525-0
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发表时间：
2018-02-13
期刊：
影响因子：
4.4
通讯作者：
Cai, Haoyang
中科院分区：
文献类型：
--
作者：
Deng, Gaofeng;Yang, Jian;Cai, Haoyang
DNA甲基化和拷贝数改变数据的整合有望为癌症发生和发展的潜在分子机制提供有价值的见解。然而，如果单独进行，这些数据集的生成和处理是昂贵和耗时的。Illumina Infinium HumanMethylation450 BeadChip最初设计用于评估DNA甲基化水平，允许使用生物信息学工具调用拷贝数变体。结果近年来积累了大量不同癌症类型的Infinium HumanMethylation450数据，为大规模数据分析提供了宝贵的资源。在这里，我们提出了methna，一个综合数据库的基因组和表观基因组数据整合在人类癌症。在当前的版本中，MethCNA包含了大约10000个肿瘤样本，代表了37种癌症类型。所有原始阵列数据均来自The Cancer Genome Atlas和NCBI Gene Expression Omnibus数据库，并使用整合多种计算资源和工具的流水线进行分析。获得归一化拷贝数畸变数据和DNA甲基化改变。我们为数据挖掘和可视化提供了一个用户友好的web界面。结论：Illumina Infinium HumanMethylation450芯片能够对来自同一DNA样本的基因组和表观基因组数据进行查询和整合，从而有助于区分癌症中的驱动突变和乘客突变。我们期望MethCNA将使研究人员能够探索DNA甲基化和拷贝数改变模式，识别癌症的关键致癌驱动因素，并协助开发靶向治疗。methna可在http://cgma.scu.edu.cn/MethCNA上公开获取。
BackgroundThe integration of DNA methylation and copy number alteration data promises to provide valuable insight into the underlying molecular mechanisms responsible for cancer initiation and progression. However, the generation and processing of these datasets are costly and time-consuming if carried out separately. The Illumina Infinium HumanMethylation450 BeadChip, initially designed for the evaluation of DNA methylation levels, allows copy number variant calling using bioinformatics tools.ResultsA substantial amount of Infinium HumanMethylation450 data across various cancer types has been accumulated in recent years and is a valuable resource for large-scale data analysis. Here we present MethCNA, a comprehensive database for genomic and epigenomic data integration in human cancer. In the current release, MethCNA contains about 10,000 tumor samples representing 37 cancer types. All raw array data were collected from The Cancer Genome Atlas and NCBI Gene Expression Omnibus database and analyzed using a pipeline that integrated multiple computational resources and tools. The normalized copy number aberration data and DNA methylation alterations were obtained. We provide a user-friendly web-interface for data mining and visualization.ConclusionsThe Illumina Infinium HumanMethylation450 BeadChip enables the interrogation and integration of both genomic and epigenomic data from exactly the same DNA specimen, and thus can aid in distinguishing driver from passenger mutations in cancer. We expect MethCNA will enable researchers to explore DNA methylation and copy number alteration patterns, identify key oncogenic drivers in cancer, and assist in the development of targeted therapies. MethCNA is publicly available online at http://cgma.scu.edu.cn/MethCNA .