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. 2023 Oct 20;14:6669. doi: 10.1038/s41467-023-42371-7

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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. 4 — A Heatmap of gene expression using the 100 most differentially expressed genes between anatomical-molecular subgroups in a “one versus all others” manner. Top annotation indicates sample anatomical location. Genes of interest are listed at the left of the heatmap; expression levels are ranked from the lowest (gray, −2) to the highest (red). B, C Volcano plots showing differential gene expression analysis results of BG/IV SHH versus MYC (b) and BG/IV SHH versus CAL SHH (c). The x axis indicates the log2 transformed fold-change and the y axis indicates the reverse of the log10 transformed adjusted p-value. Horizontal red line corresponds to adjusted p-value equals to 0.05 and two vertical blue lines indicate log2(fold-change) respectively equal to = −1 (left) and 1 (right). Differentially expressed genes of interest are labeled. Negative binomial GLM and Wald test were applied for gene expression comparison and generated p-values were corrected using the Benjamini and Hochberg method. D, E Boxplots of ganglionic eminence gene expression in (A) human ATRT anatomical molecular subgroups (n = 39 total of independent samples: n_CNCS-MYC = 13, _nBG/IV-SHH = 8, n_CAL-SHH = 12, n_MCP/ICV-TYR = 6) and in (B) mouse RT subgroups (n = 16 total of independant samples: n_R26-SHH = 5, n_R26-MYC = 11). x axis indicates subgroups and y axis indicates the level of expression in log2(TPM + 1). The box part of the boxplots represents the interquartile range while the whisker bonds of the boxplots indicate the highest and smallest values within 1.5 times interquartile range above and below the 75th and 25th quantiles respectively. Source data are provided as a Source Data file.