OncoDB 2.0: a comprehensive platform for integrated pan-cancer omics analysis

OncoDB was initially developed to advance cancer research by integrating RNA expression profiles, DNA methylation patterns, clinical annotations, and oncoviral signatures derived from the Cancer Genome Atlas (TCGA) and Genotype-Tissue Expression datasets. We now present OncoDB 2.0, an extensively expanded platform that offers a more comprehensive and integrated view of cancer omics. The updated version includes an atlas of somatic mutations discovered from combined DNA and RNA sequencing, enabling in-depth investigation of mutation patterns across tumor types and their association with clinical features. Furthermore, we have integrated proteomic data from the Clinical Proteomic Tumor Analysis Consortium (CPTAC) and chromatin accessibility data from TCGA, offering new dimensions for oncogene regulation studies. OncoDB 2.0 also introduces advanced multi-omics analysis modules that facilitate the combined exploration of RNA expression, DNA methylation, and somatic mutations, allowing researchers to examine complex cross-omic relationships with greater depth and flexibility. Together, these enhancements make OncoDB 2.0 a robust and invaluable tool for the cancer research community. OncoDB 2.0 is freely available at https://oncodb.org.