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. 2020 Feb 5;11:715. doi: 10.1038/s41467-020-14605-5

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© The Author(s) 2020

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. 3 — a Citrus plots showing the Spearman correlations between CNA-CESs in the reference dataset, depicted in bold, with CNA-CESs in the other three datasets. Blue lines indicate r > 0.5. Correlations are calculated based on the weights of genes in marked genomic regions of the CNA-CESs under investigation. Each scatterplot with marginal histograms shows the correlations versus their −log₁₀ transformed P values. The inset shows correlations > 0.5 having a P value < 0.05. b Example of a CNA-CESs in the GEO dataset that is highly correlated with a CNA-CES in the TCGA dataset with KRAS having a low degree of transcriptional adaptation to CNAs. Spearman correlation coefficient was derived using the genes mapping to the extreme-valued region from either of the CNA-CESs (n = 38). c Enrichment results using two-sided Welch’s t-test for the MSigDB Hallmark collection. A yellow bubble indicates enrichment for genes with a high degree of transcriptional adaptation to CNAs, and a blue bubble indicates a low degree. The size of the bubble corresponds to the significance level. Only CNA-CESs having at least 50 genes in their marked region were included. EMT: epithelial-mesenchymal transition; ROS: reactive oxygen species.