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. 2021 Jan 4;22:7. doi: 10.1186/s13059-020-02230-w

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© The Author(s) 2021

Open AccessThis 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 licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence 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 licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.

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Fig. 5 — Analysis of upper tract urothelial carcinomas (UTUC) DNA methylation. a Unsupervised clustering of most variable DNA methylation probes in UTUC showing two epi-clusters: EpiC-C1(high) and EpiC-C2(low). b Percentage and distribution of differentially DNA methylation probes (blue) between EpiC-high and EpiC-low subgroups across different genomic regions annotated by EPIC arrays (red). Note that there is no enrichment identified in specific genomic regions. c Single-sample Gene Set Enrichment Analysis (ssGSEA) showing pathways enriched in EpiC-high relative to EpiC-low cluster. d Boxplot showing significantly higher MeTIL score in EpiC-high subgroup than that in EpiC-low subgroup (P = 0.003). e Count of mutations in SWI/SNF family genes in EpiC-high and EpiC-low clusters. f Frequency of mutations affecting SWI/SNF family genes in EpiC-high versus EpiC-low UTUC subgroups. Note that 9 out of 18 (50%) UTUC samples in the EpiC-high subgroup harbored mutations as compared to none in the EpiC-low subgroup. g Forest plot showing that the DMBcluster of EpiC-high and EpiC-low is a significant prognostic factor as compared to other major clinicopathological features for either overall survival or progression-free survival