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

. 2024 Apr 15;21(6):974–982. doi: 10.1038/s41592-024-02239-0

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

© The Author(s) 2024

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/.

PMC Copyright notice

Extended Data Fig. 3 — a, Comparison of pairwise 3D distance matrix measured, ensemble LiMCA and bulk Hi-C contact map. b, Histogram of expression level distribution for NFKB1 (left), IKZF2 (middle) and MYC (right). c, Histogram showing the distribution of detected gene numbers (left), RNA counts (middle) and contact numbers between NFKB-high and NFKB1-low group. n.s., no significance, two-sided Mann-Whitney U rank test. d, Differential contact matrix around NFKB1 (chr4: 102.3–102.8 Mb) between NFKB1-high and low groups. e, Downsample analysis for NFKB1 gene. Left: contact matrices around NFKB1 (chr4: 102.3–102.8 Mb), representing ensemble Hi-C data from NFKB-high (top left) and NFKB1-low (bottom right). Middle: Differential matrix between NFKB-high and NFKB1-low group. Right: Normalized contact frequency plot, centered at NFKB1 upstream enhancer. f, The same as e, but cells are randomly grouped. g-h, The same as c, showing downsampled groups (g) and randomly assigned groups (h). n.s., no significance, two-sided Mann-Whitney U rank test. i, Left: Ensemble contact maps comparing IKZF2-high and (bottom left) and IKZF2-low (top right). Right: 4 C visualization of interactions between enhancer and the expressed gene, viewpoint centered at downstream enhancer. The green dot/line shows the position of candidate enhancer and the yellow dots/lines represent the position of TSS and TTS. j, The same as i but for MYC. k, Expressed genes spatial distribution of a representative GM12878 cell, genes are colored by gene number within 300 nm. l, Dotplot showing the median gene cluster size within 300 nm for expressed genes and randomly selected genes, the same cell was connected with line (n = 68). Two-sided Wilcoxon signed-rank test for paired data. m, Scatter-plot of expression level versus the normalized radial position at 20 kb resolution of a representative GM12878 cells. n, Correlation distribution of normalized radial position versus expression level among single cells. o, The same as i, but for mean expression level versus median radial position across cell population at 1 Mb resolution.