Figure - PMC

Skip to main content

An official website of the United States government

Here's how you know

Here's how you know

Official websites use .gov
A .gov website belongs to an official government organization in the United States.

Secure .gov websites use HTTPS
A lock ( ) or https:// means you've safely connected to the .gov website. Share sensitive information only on official, secure websites.

View full-text article in PMC

. 2020 Oct 27;11:5414. doi: 10.1038/s41467-020-18955-y

Search in PMC
Search in PubMed
View in NLM Catalog
Add to search

© 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/.

PMC Copyright notice

Fig. 2 — a HumanMethylation450 profiles of GCTB tumor tissue samples (green), GCTB stromal cells (GCTB-SC in pink, wt in blue, mut in red) and healthy nontumoral stromal cells (nt-SC, violet). Heatmap displays 10,000 CpG sites with highest variance across all samples. Agglomerative, hierarchical clustering of rows (CpGs) and columns (samples) was performed with average-linkage based on Euclidean distance metric. b Principal component analysis of HumanMethylation450 array-based DNA methylation profiles of GCTB tumor tissue (triangles), GCTB stromal cells (GCTB-SC, circles) and nontumoral stromal cells (nt-SC, rectangles). Samples with wildtype (wt) and mutant (mut) H3F3A status are shown in blue and red, respectively. Each data point represents one patient. c–e Hierarchical clustering with correlation distance of DNA methylation (c), chromatin accessibility (d) and H3K27me3 (e) profiles in nt-SC (violet) and stromal cells (pink). H3.3 mutational groups in blue (H3.3 WT) and red (H3.3 MUT). Heatmaps represent pairwise Pearson correlation coefficients (r) between respective modification profiles of two cell lines. Dendrograms were obtained with agglomerative hierarchical clustering with 1-r distance and average linkage. Heatmap color codes represent the H3.3 mutational status (inner), and the cell type (outer). UPI, Unified patient identifier. f Stratification of epigenetic differences using MSC-specific chromatin states as defined by ChromHMM. For DNA methylation difference between average methylation levels of all CpGs falling into corresponding states in H3.3 WT and H3.3 MUT cells is presented. For chromatin accessibility and histone post-translational modifications (PTMs), the standardized difference (delta over root-mean-square of deltas in each row) between average normalized read counts over all regions of a state is shown (values are only row-wise comparable). Mnemonics for the ChromHMM states are defined by the Roadmap project (TssA, active TSS; TssFlnk, active TSS flanking regions; Tx, transcribed regions; TxFlnk, transcription franking regions; TxWk, weakly transcribed regions; Enh, enhancers; EnhG, genic enhancers, ZNF/Rpts; zinc finger genes and repeats; TssBiv, bivalent TSS; BivFlnk, flanking bivalent regions; EnhBiv, bivalent enhancer; ReprPC, Polycomb repressed; ReprPCWk, weak Polycomb repressed; Quies, quiescent). All analyzed stromal cell lines with their UPIs are listed in Supplementary Data 1.