如何看懂从TCGA下载的甲基化数据

如何看懂从TCGA下载的甲基化数据

从TCGA下载的甲基化数据是包含了样品中不同甲基化位点的甲基化程度β值和位点的注释信息。该数据的表头解释如下:

Composite ElementA unique ID for the array probe associated with a CpG site
Beta ValueRepresents the ratio between the methylated array intensity and total array intensity, falls between 0 (lower levels of methylation) and 1 (higher levels of methylation)
ChromosomeThe chromosome in which the probe binding site is located
StartThe start of the CpG site on the chromosome
EndThe end of the CpG site on the chromosome
Gene SymbolThe symbol for genes associated with the CpG site. Genes that fall within 1,500 bp upstream of the transcription start site (TSS) to the end of the gene body are used.
Gene TypeA general classification for each gene (e.g. protein coding, miRNA, pseudogene)
Transcript IDEnsembl transcript IDs for each transcript associated with the genes detailed above
Position to TSSDistance in base pairs from the CpG site to each associated transcript's start site
CGI CoordinateThe start and end coordinates of the CpG island associated with the CpG site
Feature Type

The position of the CpG site in reference to the island: Island, N_Shore or S_Shore (0-2 kb upstream or downstream from CGI), or N_Shelf or S_Shelf (2-4 kbp upstream or downstream from CGI)


如果您想学习TCGA数据挖掘,请学习的我TCGA系列课程:

TCGA-甲基化生存分析

TCGA-生存分析

TCGA-基因差异表达分析

TCGA-ceRNA调控网络分析

TCGA-转录因子调控

  • 发表于 2019-02-18 17:23
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  • 分类:TCGA

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