Abstract 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.
Liu et al. (Tue,) studied this question.
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