Tissue Memory Score captures proximal tubular identity loss and independently stratifies survival in clear cell renal cell carcinoma

This deposit contains the locked computational artefacts, analytical scripts, processed analytic sets, and numerical outputs supporting the construction and clinical evaluation of the Tissue Memory Score (TMS) in clear cell renal cell carcinoma (ccRCC). TMS is an atlas-referenced continuous RNA-seq metric defined as the negative Euclidean distance from a tumour projection in a locked GTEx V8 healthy-tissue principal-component space to the matched healthy-tissue centroid. The prespecified primary analysis uses TCGA-KIRC primary tumours (n = 540). The deposit covers the platform-robust (rank-based) TMS formulation, the censored CPTAC-3 ccRCC overall-survival replication, the E-MTAB-1980 microarray external replication, the disease-specific survival analysis, the bootstrap-median Shapley variance decomposition, the reclassification and decision-curve clinical-utility analyses, and the ISUP grade and driver-mutation mechanism analyses. CPTAC-3 projection transferability, TCGA-LIHC exploratory analyses, GSE76427 platform-incompatibility diagnostics, and seven non-KIRC TCGA cohorts (boundary conditions) are also included. The deposited materials support computational reproducibility of the manuscript analyses. This repository is not a clinical-use software package and does not provide a validated diagnostic, prognostic, or treatment-selection assay.