Multi-gradient Permutation Survival Analysis Identifies Mitosis and Immune Signatures Steadily Associated with Cancer Patient Prognosis

The inconsistency of the association between genes and cancer prognosis is often attributed to many variables that contribute to patient survival. Whether there exist the Genes Steadily Associated with Prognosis (GEARs) and what their functions are remain largely elusive. We have developed a novel method called “Multi-gradient Permutation Survival Analysis” (MEMORY) to screen the GEARs using RNA-seq data from the TCGA database. Then we employed a network construction approach to identify hub genes from GEARs, and utilized them for cancer classification. In the case of LUAD, the GEARs were found to be related to mitosis. Our analysis suggested that LUAD cell lines carryingPIK3CAmutations exhibit increased drug resistance. For BRCA, the GEARs were related to immunity. The analysis revealed thatCDH1mutation might influence immune infiltration through the EMT process in BRCA. We further explored the prognostic relevance of mitosis and immunity through their respective scores. This study offers significant biological insights into GEARs and highlights their potential as robust prognostic indicators across diverse cancer types.