The Cancer Genome Atlas (TCGA)

We recently reported the immune classification of TCGA MIBC tumours[15]. The publicly available global transcriptomic sequencing (RNA-Seq) data from 412 MIBC cases, with the corresponding clinical information was downloaded from TCGA data portal (https://gdc-portal.nci.nih.gov/), now part of the National Cancer Institute’s Genetic Data Commons. From a cohort of 344 previously untreated MIBC cases we further selected those cases that specifically belonged to the luminal (n = 121) and basal (n = 68) subtypes. From the MSig database a list of 113 T cell cytotoxicity associated genes were selected and their expression levels evaluated between the luminal and basal subtypes.