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. 2024 Jun 13;25:156. doi: 10.1186/s13059-024-03300-z

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© 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/. 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. 5 — Species-specific oCGIs in species-specific peaks are associated with gene expression changes. A Schematic illustrating our method for assigning oCGIs and peaks to genes as described in the text and Additional file 1: Figure S42, using a pairwise comparison of rat and pig as an example. Left: A gene associated with a rat-only oCGI in a rat-only H3K27ac peak, which means the gene is assigned to the “rat-only set” (A-only set) of genes. Right: A gene associated with a pig-only oCGI in a pig-only H3K27ac peak, which means the gene is assigned to the “pig-only set” (B-only set) of genes. B The log₂-transformed TPM ratio for genes in the A-only set and the B-only set for each indicated species pair and histone modification using data from adult brain. Points indicate median values for the A-only set (dark blue) and the B-only set (light blue) and lines indicate the interquartile range. All values in the A-only set and B-only set were normalized to the median TPM ratio across resampling rounds from the background set. Stars indicate a significant difference between the observed median and the expected median (q < 0.05, resampling test to compare to the background set, BH-corrected; see Additional file 1: Fig. S42 and “Methods”)