Multi-Omic Pan-Cancer data from TCGA.

Data consist of three omic blocks from The Cancer Genome Atlas (TCGA), containing whole-genome profiles of -Gene expression (file GE.RData), -DNA methylation (file METH.RData), and -Copy number variants (file CNV.RData). Omic profiles consist of information from 5,408 tumor samples across 33 cancer types (as matrix rows), and 60,112 features (expression of 20,319 genes, methylation of 28,241 CpG islands, and copy number variant intensity for 11,552 genes). GE profiles by sample corresponded with the logarithm of RNA-Seq counts by gene (Illumina HiSeq RNA V2 platform). METH profiles corresponded with CpG sites B-values from the Illumina HM450 platform, summarized at the CpG island level, using the maximum connectivity approach from the WGCNA R package (Langfelder and Horvath 2008) , and further transformed into M-values (M=beta/(1-beta); Du et al. 2010). Omic blocks were adjusted for batch and tissue specific effects (see Gonzalez-Reymundez and Vazquez (2020) and references therein for further details on quality controls and data edition).本数据集包含来自癌症基因组图谱（The Cancer Genome Atlas, TCGA）的三组组学区块，涵盖全基因组层面的三类组学图谱：基因表达（文件GE.RData）、DNA甲基化（文件METH.RData）以及拷贝数变异（文件CNV.RData）。该组学图谱包含覆盖33种癌症类型的5408个肿瘤样本（以矩阵行作为样本维度），总计60112个特征，具体包括20319个基因的表达量、28241个CpG岛（CpG island）的甲基化水平，以及11552个基因的拷贝数变异强度。样本对应的基因表达图谱为基于Illumina HiSeq RNA V2测序平台得到的基因RNA测序（RNA-Seq）计数的对数值。DNA甲基化图谱对应Illumina HM450平台获取的CpG位点B值，采用WGCNA R软件包（WGCNA R package）的最大连通性方法（Langfelder与Horvath, 2008）在CpG岛层面进行汇总，并进一步转换为M值（计算公式为M=β/(1-β)；Du等, 2010）。所有组学区块均已针对批次效应与组织特异性效应完成校正，有关质量控制与数据整理的详细信息，请参阅Gonzalez-Reymundez与Vazquez (2020)及其中引用的相关文献。