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. 2023 May 15;14:2514. doi: 10.1038/s41467-023-38093-5

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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. 5 — A WGCNA of human macrophages cultured on HD and LD decellularized tissue showing clusters of co-expressed genes as dendrogram. Numbers indicate different modules (gene programs). N = 16 HD MAM samples, N = 15 LD MAM samples. B Cluster dendrogram of module eigenvalues (MEs) showing associated gene programs from WGCNA of human macrophages cultured on high and low disease decellularized tissue. N = 16 HD MAM samples, N = 15 LD MAM samples. C Heatmap of association of ME with gsva scores of the HD vs. LD, up and down. Pearson’s r-values with two-sided alternative hypothesis testing are noted for the significant correlations p < 0.05. N = 16 HD MAM samples, N = 15 LD MAM samples. D Bar plots for significantly enriched gene ontology biological processes in clusters 8, 9, 10, and 1, 2, 12 gene programs. Broken line denotes adjusted p = 0.05. Hypergeometric test with multiple comparisons correction using the Bonferroni method. N = 16 HD MAM samples, N = 15 LD MAM samples. E Boxplot of selected DE HD MAM genes termed HD MAM signature. Boxplots illustrate median (center of the box) with the upper (Q3: 75th percentile) and lower (Q1: 25th percentile) quartiles (ends of the box); The whiskers correspond to Q3 + 1.5 x Interquartile Range (IQR) to Q1 − 1.5 x IQR; Dots beyond the whiskers show potential outliers. Two-way ANOVA, p = 4.272e−12. N = 16 HD MAM samples, N = 15 LD MAM samples. F Correlation scatter plots of gsva scores from gene lists. GSVA scores were calculated from the MAM RNAseq dataset using the gene lists indicated next to the scatterplots and R package gsva. Correlation coefficient corresponds to Pearson’s correlation. Line was fitted with linear model (lm) with 95% confidence interval displayed. p values and correlation coefficients correspond to Pearson’s method, with two-sided alternative hypothesis testing. N = 16 HD MAM samples, N = 15 LD MAM samples.