Fig. 6: IPF fibroblast-derived matrix has a distinct matrisome.

a Schematic of experimental design for MS-proteomics of CDMs from control (n = 3 in duplicate) and IPF (n = 3 in duplicate) HLFs. Created with BioRender.com. b GO Biological Pathways using DAVID v6.8 functional annotation tool for 154 matrisome proteins identified in CDMs (one-sided Fisher’s exact test, Benjamini–Hochberg adjusted P value). c Radar plot of protein abundance according to matrisome categories identified in control (black) and IPF (red) CDMs. d PCA of 154 matrisome proteins identified in control and IPF CDMs. Unit variance scaling is applied to rows; SVD with imputation is used to calculate principal components. Prediction ellipses are such that with probability 0.95, a new observation from the same group will fall inside the ellipse. e Heatmap with hierarchical clustering of normalised abundance of each protein identified. Rows and columns using correlation distance and average linkage. Rows are centred and unit variance scaling is applied. f Volcano plot showing significant differentially expressed proteins between IPF CDMs and control CDMs, upregulated proteins (red), downregulated proteins (blue). One-way ANOVA, Benjamini–Hochberg adjusted P value, significance defined as a fold change >2 or <2, P < 0.05. g Venn diagram showing shared GO biological processes for significantly differentially expressed proteins. h Protein-protein interaction network using STRING⁴¹ v11 using matrisome proteins with an abundance ratio >2 or <2, P < 0.05. Source data are provided as a Source Data file.