Comprehensive Atlas of Cancer-Type-Specific Molecular Features from Comparative Analysis of TCGA Data

Cancer-type-specific molecular alterations often reflect the unique biological context of their tissue of origin and are more likely to represent relevant drivers rather than passenger events. We analyzed data from The Cancer Genome Atlas (TCGA) spanning 39 cancer types and 6 molecular platforms to create a comprehensive atlas of cancer-type-specific molecular features through unified comparative analyses. Simple nucleotide variation analysis characterized cancer-type-specific gene mutations and revealed heterogeneity among mutated genes within shared pathways. Copy number variation analysis characterized cancer-type-specific amplifications and deletions and demonstrated synergistic interactions between gene deletions and mutations. DNA methylation analysis identified candidate hypermethylated genes alongside well-established targets. Transcriptome profiling analysis revealed cancer-type-specific pathway enrichment reflecting tissue-of-origin functions or novel associations. Multiomics clustering analysis identified multi-cancer clusters and revealed consistent patterns across molecular platforms. These findings provide insights into cancer-type-specific molecular features and offer comprehensive visualizations as a reference resource for clinical application and hypothesis generation.