CMAtlas: a comprehensive DNA methylation atlas for exploring epigenetic alterations in 34 human cancer types

Motivation Aberrant DNA methylation is a fundamental epigenetic hallmark of cancer. However, existing resources often lack technological diversity and comprehensive cancer coverage. Furthermore, most platforms fail to achieve deep multi-omics integration and tend to ignore cancer-type-specific methylation features, limiting their utility in precision oncology and drug discovery. Results We developed CMAtlas (Cancer Methylation Atlas), a comprehensive platform integrating 13,753 samples across 34 cancer types. By applying technology-tailored pipelines to data from various profiling technologies, we identified 830,725 tumor-specific differentially methylated elements (DMEs) and 1,480,098 differentially methylated regions (DMRs), alongside 1,154,256 cancer-type-specific DMEs and 329,154 DMRs. The platform demonstrates high cross-platform consistency and strong concordance between tumor tissues and cell lines, ensuring the robustness of our findings. All DMEs and DMRs are annotated with multi-omics data (RNA expression, somatic mutations, and chromatin accessibility) and clinical relevance (survival associations and cell-free DNA profiling). We further demonstrate the utility of CMAtlas by identifying prognostic aberrant methylation in colorectal cancer driver genes. Availability CMAtlas is freely accessible at {{https://cmatlas.renlab.cn/}}. The platform offers an intuitive web interface supporting gene-centric and cancer-centric queries, alongside customizable analysis modules designed to facilitate user-specific research needs. Supplementary information Supplementary data are available at Bioinformatics online.