Bladder Cancer Cohort Analysis

The RNA-seq data and clinical annotation were collected from the bladder cancer patient cohort (139). Patients were clustered using cytokine expressions (genes in KEGG_CYTOKINE_CYTOKINE_INTERACTIONS pathway) by uniform manifold approximation and projection (UMAP) dimension reduction using “uwot” with parameters n_neighbors = 40; learning_rate = 0.1; min_dist = 0.001; number of PC = 10. The clustering resulted in two clusters. DEGs between two clusters were identified by the R package “Seurat.” Finally, ESRRA activities were compared among UMAP clusters, immune phenotypes, and Lund2 classification of bladder cancer (140). The significance of comparisons was determined using the Wilcoxon test for pairwise comparison and the Kruskal–Wallis test for group-wise comparison.