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. 2021 Apr 16;12:2301. doi: 10.1038/s41467-021-22465-w

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© The Author(s) 2021

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 6 — a Summary of classification results and stage distribution for all tumors, tumors with microarray data and tumors with RNA-Seq data (1228 tumors were classified in total and 1225 of these were assigned to a class). b Association of tumor stage, tumor grade and FGFR3 and TP53 mutation status with transcriptomic classes. P-values were calculated using two-sided Fisher’s exact test. c Kaplan–Meier plot of progression-free survival (PFS) for 511 patients stratified by transcriptomic class. The p-value was calculated using two-sided log-rank test. d Association of regulon activities (active vs. repressed status) with transcriptomic classes in the UROMOL cohort (including samples with positive silhouette scores, n = 505) and transcriptomic classes in the independent cohorts (pooled). The heatmap illustrates BH-adjusted p-values from two-sided Fisher’s exact tests. e Pathway enrichment scores within transcriptomic classes in the UROMOL cohort (including samples with positive silhouette scores, n = 505) and transcriptomic classes in the independent cohorts (pooled). Asterisks indicate significant association between pathway and class (one class vs. all other classes, two-sided Wilcoxon rank-sum test, BH-adjusted p-value below 0.05). Triangles indicate direction swaps of pathway enrichment in the independent cohorts compared to the UROMOL cohort. GSVA gene set variation analysis. Source data are provided as a Source data file.