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. 2022 Apr 25;3(4):505–517. doi: 10.1038/s43018-022-00356-3

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© The Author(s), under exclusive licence to Springer Nature America, Inc. 2022

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. 3 — a, Rank-ordered plot showing Spearman rank correlation between gene expression in malignant cells inferred by BayesPrism and macrophage fraction in the TCGA-GBM dataset. The top ten positive and negative outlier genes are marked in red; purple circles highlight experimentally validated regulators of macrophage infiltration in GBM, or genes whose expression correlates with macrophage infiltration in IVY GAP. b,c, Boxplots showing BayesPrism-inferred percentage of macrophage infiltration for regions with low (ISH control) or high (ISH high) expression of two target genes, PI3 (b) and POSTN (c). Colors indicate anatomic structures associated with ISH experiments. Boxes mark the 25th percentile (bottom), median (central bar) and 75th percentile (top); whiskers represent extreme values within 1.5-fold of interquartile range. Statistical significance was determined by two-sided t-test. Sample size of PI3 was n = 3 for ISH control and n = 12 for ISH high; sample size of POSTN was n = 3 for ISH control and n = 10 for ISH high, with n representing the number of independent patients. Uncorrected P values are reported. d, Barplot showing normalized gene set enrichment score of genes ranked by correlation with macrophage cell fraction in GBM, as computed in a. Only the top 20 semantically nonredundant most enriched biological processes were selected for visualization. Padj, multiple testing-corrected P values were determined using the Benjamini–Hochberg method. e–g, Cartoons summarizing three patterns of relationship between biological processes and infiltration of nonmalignant cell types: IFN-α/γ (e), mesenchymal activation/EMT (f) and keratinization (g). Red arrows and blue flat-headed arrows denote positive and negative correlations, respectively. Shapes represent the tumor types of nonmalignant cells. Macro., macrophage; endo., endothelial cell; peri., pericyte.

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