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. 2023 Jul 11;11:113. doi: 10.1186/s40478-023-01610-0

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© The Author(s) 2023

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 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. 2 — Analysis of genes expression and its relation to the DNA methylation profile. (a) Heatmap of 4275 top most variably expressed genes and their clustering showing lack of clear overlap between methylation and expression-based chordoma clusters (b) Fraction of genes differentially expressed between chordoma subtypes as well as chordomas and nucleus pulposus that are under DNA methylation control (as defined by significant correlation of mean promoter methylation with gene expression), the blue dot-and-dash line indicates the level of methylation control of the genome in general (c) Volcano plot of differentially expressed genes identified in chordoma—nucleus pulposus comparison (d) Volcano plot of differentially expressed genes found in chordoma I—chordoma C comparison (e) DMR relation to DEGs in chordoma I—chordoma C comparison, height of the bars represents number of genes/DMRs (f) Role of DNA methylation in TBXT (brachyury) gene. Difference in the methylation levels of CpGs at TBXT locus with DMPs labeled with *(for adj.p < 0.05), **(for adj.p < 0.001) or ***(for p-value <9*10⁻⁸) (left panel), difference in TBXT expression of (middle panel) and correlation between TBXT promoter methylation and expression levels (right panel); p-values are shown for chordoma-nucleus pulposus comparison (g) Difference in the methylation levels of CpGs at PTPRCAP locus with DMPs labeled with *(for adj.p < 0.05), **(for adj.p < 0.001) or ***(for p-value < 9*10⁻⁸) (left panel), difference in PTPRCAP expression of (middle panel) and correlation between PTPRCAP promoter methylation and expression levels (right panel) (h) Position of TBXT (brachyury) and PTPRCAP genes on their chromosomes, along with EPIC methylation probes position and DMR