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. 2019 Jun 5;27(3):147–167. doi: 10.1038/s41417-019-0109-7

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© The Author(s) 2019

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 — PROM1 and PROM2 gene signatures are predominantly amplified and significantly co-expressed in neuroendocrine prostate cancer (NEPC) and bladder cancer. a We used the Oncoprint feature of cBioPortal to determine the copy number alteration frequency of each individual gene of the PROM1 (a) cluster (PROM1, PROM2, GRP, ZNF157, FRZB, CLDN10, PIP5K1B, CDHR1, CX3CL1, and PDZD2) and the PROM2 (b) cluster (PROM2, PROM1, EHF, FAM110C, SGPP2, ADGRG1, CWH43, PRRG2, TSPAN1, and ELF3) within selected cancer subtypes. The alterations included missense mutations (green), amplifications (red), deep deletions (blue), or no alterations (grey). c and d Mutual exclusivity panel analysis revealed the co-occurrence of alterations of PROM1 gene signatures and correlations between PROM1 gene copy number and mRNA expression. The correlation between PROM1 CNAs and mRNA levels was investigated using the cBioPortal for Cancer Genomics. Data are shown for the 107 NEPC samples in which CNAs were available. The search criteria were: “neuroendocrine prostate cancer (NEPC), mutation, and putative copy-number alterations adjusted by ploidy and purity with CLONET.” The x-axis is divided according to the copy number status of the tumor and the Y-axis represents PROM1 mRNA levels. e and f Mutual exclusivity panel analysis revealed the co-occurrence of alterations of PROM2 gene signatures and correlation between PROM2 gene copy number and mRNA expression. The correlation between PROM2 CNAs and mRNA levels was investigated using cBioPortal for Cancer Genomics. Data are shown from the 402 bladder cancer (TCGA PanCan Atlas) samples in which CNAs were available. The search criteria were “Bladder cancer (TCGA PanCan Atlus), mutation, putative copy-number alterations from GISTIC, and mRNA expression z-Scores (U133 microarray only).” The x-axis is divided according to the copy number status of the tumor and the Y-axis represents PROM2 mRNA level