Extended Data Fig. 4. Integrative cross-correlation analysis of RNA-seq and aggregated mass cytometry data corroborated the atherosclerotic plasma-driven inflammatory signature and intracellular signaling.

A. Heatmap of a sub-network of cytokine DEGs in response to atherosclerotic plasma (atherosclerosis, n = 20 biologically independent samples, males=10) vs. pooled healthy plasma (healthy, n = 12 biologically independent samples), showing z-score of transcripts with absolute log₂ fold change >1.2 and normalized sequence counts >4 associated with cytokine activity (GO:0005125). B. Co-expression Pearson correlation analysis of DEGs in response to atherosclerotic plasma (atherosclerosis, n = 20 biologically independent samples, males=10) vs. pooled healthy plasma (healthy, n = 12 biologically independent samples), filtered for cytokine activity (GO:0005125). C. Enriched GO terms from gene expression data in response to atherosclerotic plasma (n = 20 biologically independent samples; males=10) vs. pooled healthy plasma (n = 12 biologically independent samples). D. Hierarchically ordered heatmap of Pearson’s correlations between gene expression and phosphoprotein-cell type pairs in response to atherosclerotic plasma (n = 20 biologically independent samples, males=10) vs. pooled healthy plasma (healthy, n = 12 biologically independent samples). Only DEGs in healthy PBMCs, in response to atherosclerotic plasma, belonging to the enriched GO terms are included. E. Pairs of phosphoprotein and cell-type with the highest median cross-correlation with RNA-seq data. Box plots showing the median and range (min to max). F. Enriched TFs obtained by analyzing upregulated DEGs in healthy PBMCs, in response to atherosclerotic plasma, against ChIP-seq libraries and position weight matrix (PWM) predictions. G. Enriched TFs obtained by analyzing downregulated DEGs in healthy PBMCs, in response to atherosclerotic plasma, against ChIP-seq libraries and position weight matrix (PWM) predictions.