Expression quantitative trait methylation across multiple cancer types with functional and therapeutic characterization using Onco-eQTM

Abstract

Abstract DNA methylation plays a crucial role in gene expression and tumorigenesis. Most pan-cancer resources primarily focus on genetic variants and their association with gene expression without clearly demonstrating how methylation itself regulates gene activity and clinical features. To address this gap, we developed Onco-eQTM, a web-based database that links DNA methylation at CpG sites to gene regulation and multiple functional and clinical layers across 27 cancer types. These layers include miRNA regulation and biological pathways, as well as immune cell infiltration and predicted drug response, enabling both functional and therapeutic interpretation. We analyzed 6880 TCGA samples and identified 5.25 million CpG–gene associations. Beyond gene expression, Onco-eQTM links CpG methylation to 4.52 million miRNA-related associations, 14.45 million drug-response associations, 13.6 million pathway activity associations from PARADIGM, and 3.55 million immune-infiltration associations covering 68 immune cell types. The database enables users to visualize how methylation impacts these biological and clinical factors. Onco-eQTM enables researchers to gain a deeper understanding of cancer-related methylation changes and identify potential therapeutic targets. The database is freely available at https://project.iith.ac.in/cgntlab/OncoeQTM/.