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. 2023 Feb 9;14:724. doi: 10.1038/s41467-023-36262-0

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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 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/.

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Fig. 6 — a Heatmap showing the Pearson correlation coefficients of global gene expression across the two APL patients and the induced/uninduced U937-PR9 cell line replicates. b Bar plot showing the number of regions overlapping with the 30,039 gained interactions identified in the U937-PR9 cell line model. The light blue bar illustrates the expected overlap of the gained regions as expected by chance, error bars indicate the range of 20,000 Monte Carlo Simulations. P indicates a significantly greater number of overlaps by chance, as determined by χ² test. The data used to subsample consisted of five independent interaction datasets—for each simulation a random set of interactions of the same size as the comparison set was taken. Mean error bars for each set of simulations are 2750, 2810, 3246, and 3980 for Patient #1, Patient #2, induced U937, and uninduced U937 datasets, respectively. c Venn diagram showing the overlap of interactions in the patient samples that correspond to gained interactions in the cell line model. The intersection contains 2956 fragments that interact with 1357 genes. d Scatter plot showing the mean expression correlation of the 1357 genes, comparing patients and induced U937-PR9 cells. Pearson correlation coefficient = 0.87. Positions of six genes relating to (e) are shown (blue dots). e–j Interaction landscape plots of six genes: AHR, VIM, TGFBR2, PTGER4, MYB, and CCNA1. The top panel in each plot shows the gained interactions after PML::RARA induction in the U937-PR9 cells, large blue dots indicate regions with a significant differential (gained) interaction, as determined by GOTHiC (ihw < = 0.01). The blue inverted peak tracks show the binding profiles of PML::RARA in U937-PR9 cells. Arc plots show the interactions for the induced U937-PR9 cells (blue), Patient #1 (light green), and Patient #2 (dark green). The colored arcs connect significant interactions to the gene promoter. Significant interactions are displayed as a red dot, and non-significant interactions as a blue dot. Each dot represents a unique HindIII fragment. Source data are provided as a Source data file.