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. 2020 Nov 17;12:175. doi: 10.1186/s13148-020-00965-8

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© The Author(s) 2020

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. 3 — 5hmC in HNSCC is highly correlated with gene expression. a Scatterplot showing the positive correlation between gene expression and hydroxymethylation in HPV(+) and HPV(−) samples (Pearson correlation coefficient = 0.62). The top half represents genes that are significantly up-regulated in HPV(+) tumors, and the right half represents genes that are significantly hyper-hydroxymethylated in HPV(+) tumors. b Scatterplot showing a strong correlation between log gene expression and log 5hmC of 5 kb intron region (chr9:21975000–21980000) of CDKN2A. HPV(+) samples were concentrated near the top right corner, indicating that both their gene expression and 5hmC coverage were higher compared with HPV(−) samples. c Spaghetti plot of log gene expression for top 20 genes with at least one DhMR in their promoter region for HPV(+) IMU, HPV(+) KRT and HPV(−) samples, respectively. d Heatmap showing the expression levels of sufficiently expressed genes with at least one HPV(+) DhMR in their promoter, which were mostly well clustered based on HPV status (marked with black and grey at the top). Most genes were significantly higher expressed in HPV(+) samples, such as CDKN2A. ↑ indicates genes that are also up-regulated in HPV(+) HNSCC, and ↓ indicates up-regulation in HPV(−) tumors. Keratin and EMT scores are measurements of keratinization level and EMT level, and T cell signature and B cell signature represent degree of immune response. Generally there was a higher level of keratinization and EMT in HPV(−) samples, while the immune response is more significant in HPV(+) samples. The detailed calculation can be found in Zhang et al. [9]. e Enrichment analysis results for gene expression vs hydroxymethylation by HPV status. Each dot represents one GO term, and the color denotes the significance (yellow: significant; blue: not significant). Signed p values are defined as > 0 to indicate up-regulation in HPV(+) samples or hyper-hydroxymethylation in HPV(+) samples, and < 0 to indicate upregulation in HPV(−) samples or hyper-hydroxymethylation in HPV(−) samples