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

. 2023 Jul 14;14:4214. doi: 10.1038/s41467-023-39919-y

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

© 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 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. 3 — a iGraph layout of the A compartment clusters after UMAP dimensionality reduction and Louvain clustering. Each circle represents an A compartment. Colors represent the ten clusters that were identified. The size of the circles is proportional to the level of co-accessibility of that A compartment, showing that clusters 1, 2, 3, and 5 have the highest levels of co-accessibility. The A compartment cluster coverage of enhancer (b), promoter (c), and quiescent (d) ChromHMM chromatin states are indicated with boxplots. Overall p values (top) correspond to the two-sided Kruskal–Wallis test comparing the coverage across the A compartment clusters. The p value map below the plot denotes which pairwise differences are significant (p < 0.05) in the post hoc Dunn test, after correcting for multiple testing using the Holm procedure. The number of compartments in each cluster is listed in Supplementary Table 4. e Violin plots with inlaid boxplots show the number of pCHi-C interactions per promoter in the four A compartment clusters. The overall p value corresponds to the two-sided Kruskal–Wallis test and the pairwise comparisons denote the p values from the post hoc Dunn test, after correcting for multiple testing using the Holm procedure. The violin plot shows the kernel probability density of the data. f Boxplots show the proportion of ATAC peaks in the cluster A compartments that are upregulated (higher accessibility in D1 relative to PAd) or downregulated (lower accessibility in D1 relative to PAd) after 24 h of PAd differentiation into adipocytes. The p values correspond to the two-sided paired Wilcoxon rank-sum test for differences between the proportion of up- or down-regulated peaks in each of the compartment clusters separately. See also Supplementary Figs. 7, 8, Supplementary Data 5, 6, and Supplementary Table 4. For all boxplots, the center represents the median gene density of the compartment type, the upper and lower bounds of the box represent the 75th and 25th percentile, respectively, and the upper and lower whiskers represent the highest (non-outlier) and lowest (non-outlier) values, respectively. Source data are provided as a Source Data file.