Fig. 6

Differentially expressed genes (DEGs) and hub genes in the ImmuneScoreH cluster (vs. the ImmuneScoreL cluster and healthy controls). FDR: false discovery rate, logFC: log(fold change). A Heatmaps of DEGs among healthy control samples and atheromatous plaques in the ImmuneScoreL and ImmuneScoreH clusters. B Bubble and circle plots showing the results from the KEGG pathway enrichment analysis of DEGs of atheromatous plaques in the ImmuneScoreH cluster (vs. ImmuneScoreL cluster and healthy controls). The top 10 KEGG pathways ranked by the FDR are shown. C Bubble and circle plots showing the results from the Gene Ontology (GO) enrichment analysis, including the biological process (BP), molecular function (MF), and cellular component (CC) categories, of DEGs of atheromatous plaque in the ImmuneScoreH cluster (vs. ImmuneScoreL cluster and healthy controls). The top 10 BP, MF and CC terms ranked by the FDR are shown. D PPI network of DEGs of plaques in the ImmuneScoreH cluster. E Nineteen hub genes of plaques in the ImmuneScoreH cluster. F UpSet plot demonstrating overlaps between the 698 DEGs (ImmuneScoreH cluster vs. other samples, Additional file 7: Supplementary Table 2), the 19 hub genes (E), 80 detected genes of interest (Fig. 5K) and 782 metagenes in ESTIMATE. G UpSet plot demonstrating overlaps between the 284 DEGs (ImmuneScoreH cluster vs. ImmuneScoreL cluster, Additional file 8: Supplementary Table 3), 19 hub genes (E), 80 detected genes of interest (Fig. 5K) and 782 metagenes in ESTIMATE. HLA: human leukocyte antigen, PTPN6: protein tyrosine phosphatase non-receptor type 6, VAMP8: vesicle-associated membrane protein 8, ITGB2: integrin subunit beta 2, ITGAM: integrin subunit alpha M, CXCL1: C-X-C motif chemokine ligand 1, CYBA: cytochrome B-245 alpha chain, CYBB: cytochrome B-245 beta chain (also known as NADPH oxidase 2), FCER1G: Fc receptor gamma chain, LCK: lymphocyte cell-specific protein-tyrosine kinase, PTPRJ: protein tyrosine phosphatase receptor type J (also known as SCC1 or DEP1)