Fig. 1: The m6A landscape of localized prostate cancer.
From: The landscape of N6-methyladenosine in localized primary prostate cancer
a, Top to bottom, bar plots. The number of MeTPeak peaks across samples ordered from greatest to smallest. The number of genomic rearrangements (GRs) identified in each sample. The number of single-nucleotide variants (SNVs) identified in each sample. The PGA40 as a proxy of the total CNAs for each sample. The Conti PRS50 calculated for each sample. Top heatmap shows the associated clinical covariates including ISUP Grade Group, anatomical T category, PSA, age, IDC/CA, biochemical relapse (BCR) and metastasis. Bottom heatmap, complementary molecular profiling data collected for each sample including germline polymorphisms in samples of European ancestry18, somatic CNAs and simple somatic mutations17, DNA methylome18, H3K27ac20, ultra-deep RNA-seq19 and proteomics2. SSM, simple somatic mutation; N/A, not available. b–e, Exemplar plots for AR (the inset magnifies the region highlighted in yellow; b), MYC (c), TP53 (d) and PTEN (e). In the top polygon plots, the median IP (green) and input (purple) coverage (reads per kilobase per million mapped reads-normalized bigWig files) is represented using lines, while background colors represent the range of IP and input coverage across samples. Exons identified in GENCODE version 34 are annotated below in dark blue. Bottom heatmaps represent the distribution of IP and input coverage (log1p transformed) across samples (y axis), and darker colors correspond to greater read coverage. Samples are clustered using Euclidean distance and Ward’s minimum variance method with squared distances. chr, chromosome. f, Top bar plot, the number of peaks uniquely found in a given number of samples. Bottom scatterplot, the median adjusted m6A abundance of a joint peak (y axis) versus the number of samples in which the peak is identified (x axis). Colors indicate the deciles of the adjusted m6A abundance. Multiple joint peaks can be identified in a single gene, but the most prevalent and abundant peaks for a given gene are labeled where applicable. g, Distribution of the normalized mutual information (MI) for each data type pair. For visualization, values < 10−4 are shown as 10−4. Top heatmap indicates data type pair. Subsequent heatmaps show the number of genes with data available for each data type pair, numbers of genes for which mutual information is significant (Q < 0.1) and percentage of significant genes.
