Fig. 2: DNA methylation in HLA-I genes in prostate cancer.
From: Reversible epigenetic alterations regulate class I HLA loss in prostate cancer
a Approximate locations of probes within the HLA-I CpG islands. b Methylation levels in the promoter or intragenic regions of the HLA-I CpG islands in normal (blue circle; n = 49) and primary tumor (red circle; n = 332 for HLA-B, n = 333 for HLA-A and HLA-C) samples represented by mean beta value determined by microarray analysis. c Methylation levels in the promoter or intragenic regions of the HLA-I CpG islands in primary tumor samples stratified by gene expression level. Low expression: z-score < −1.96, med expression 1.96 < z-score > −1.96, high expression: z-score >1.96. See figure for n number for each condition. d Detection of HLA-A methylation in primary, adjacent benign, and metastatic lesions by COMPARE-MS. Location of amplicon is indicated. e ATAC-seq from PRAD data set at two promoter regions in each HLA-I gene (n = 26). Samples are ordered on RNA-seq signal from PRAD data set (top row on each heat map). f Correlation of ATAC-seq signal to gene expression in each HLA-I gene (n = 26). Distal promoter (black circle) proximal promoter (gray circle).
