TP53-based tripartite classification reveals three distinct mutation patterns across pan-cancer

We conducted a comprehensive pan-cancer analysis of gene mutation frequencies across 45,259 samples from 41,988 patients, which were classified into three categories: TP53_top, TP53_plus, and Non_TP53. Intersection analysis of mutated genes revealed heterogeneous overlaps among 61 cancers. Based on sample quantity, mutation frequency, and distribution patterns, 95 significantly mutated genes with 80,524 unique mutations were identified and categorized into three groups: SinglePoint-SingleCan, SinglePoint-MultiCan, and MultiPoints-MultiCan. These findings delineate two strategies for precision medicine development: SinglePoint specificity and MultiPoints compatibility. Furthermore, we identified 26 mutated transcription factors (TFs) and 476 downstream targets across 19 regulatory networks, which were categorized into three groups: TP53-Solo, TP53-Multi, and Non_TP53. Additionally, we mapped 47 mutated signaling pathway networks across 52 cancers, highlighting diverse dysregulated phenotypes and potential therapeutic targets downstream or upstream of these mutated genes. The integration of pan-cancer genotypes and phenotypes provides a blueprint for developing precision therapies tailored to mutation-specific, multi-variant, and context-dependent targeting.