Figures_Rheumatology_RHE-20-0645.R1
Figure 1. Whole gene expression profiling and functional enrichment analysis.
A) Hierarchical clustering analysis. B, C and D) The top 20 enriched terms using genes in cluster 1 (B), 2 (C) and 3 (D) identified in the hierarchical clustering analysis. Count (%) is the percentage of all of the provided genes that are found in the given ontology term. Log10(P) is the p-value in log base 10. ACA, anti-centromere antibody; ATA, anti-topoisomerase antibody; dcSSc, diffuse cutaneous systemic sclerosis; GO, gene ontology; lcSSc, limited cutaneous systemic sclerosis; None, seronegative patients; RNAP, anti-RNA polymerase III antibody; RNP, anti-U1 RNP antibody.
Figure 2. Differentially expressed genes (DEGs) in systemic sclerosis (SSc) patient skin lesions compared to healthy controls (HCs).
A, B, C, D and E) Volcano plot of None (A), ACA (B), RNP (C), RNAP (D) and ATA (E) autoantibodies. The red and blue points indicate the upregulated and downregulated transcripts compared to the controls, respectively. The top 10 significantly upregulated and downregulated transcripts are annotated by the gene name. The p-value was adjusted with the Benjamini-Hochberg procedure and is shown as the false discovery rate (FDR). F and G) Venn diagram of upregulated DEGs (F) and downregulated DEGs (G). ACA, anti-centromere antibody; ATA, anti-topoisomerase antibody; None, seronegative patients; RNAP, anti-RNA polymerase III antibody; RNP, anti-U1 RNP antibody.
Figure 3. Functional enrichment analysis using differentially expressed genes (DEGs).
A, B, C, D, E and F) The top 20 enriched terms using the DEGs from ACA (A), RNP (B), RNAP (C and E) and ATA (D and F) autoantibodies. Count (%) is the percentage of all of the provided genes that are found in the given ontology term. Log10(P) is the p-value in log base 10. ACA, anti-centromere antibody; ATA, anti-topoisomerase antibody; GO, gene ontology; None, seronegative patients; RNAP, anti-RNA polymerase III antibody; RNP, anti-U1 RNP antibody.
Figure 4. Functional enrichment analysis using non-overlapping differentially expressed genes (DEGs).
A, B, C, D and E) The top 20 enriched terms using non-overlapping DEGs from ACA (A), RNP (B), RNAP (C and D) and ATA (E) autoantibodies. Count (%) is the percentage of all of the provided genes that are found in the given ontology term. Log10(P) is the p-value in log base 10. ACA, anti-centromere antibody; ATA, anti-topoisomerase antibody; GO, gene ontology; None, seronegative patients; RNAP, anti-RNA polymerase III antibody; RNP, anti-U1 RNP antibody.
Figure 5. Analysis of cell type-specific expression in skin specimens according to the type of autoantibody.
A) Hierarchical clustering analysis. (B) Correlation between cell signature score and mRSS. ****, p<0.0001; ***, p<0.001; **, p<0.01; *, p<0.05; using Spearman’s rank correlation test. (C) Cell signature score boxplot according to the autoantibody. ****, p<0.0001; ***, p<0.001; **, p<0.01; *, p<0.05; ns, not significant; using the Kruskal-Wallis (global p-value) and Wilcoxon rank sum tests (p-value between groups). ACA, anti-centromere antibody; ATA, anti-topoisomerase antibody; Dif, diffuse cutaneous systemic sclerosis; EC, endothelial cells; Mφ/Mono, macrophages/monocytes; Lim, limited cutaneous systemic sclerosis; MDC, myeloid dendric cells; mRSS, modified Rodnan skin thickness score; NK, natural killer; None, seronegative patients; RNAP, anti-RNA polymerase III antibody; RNP, anti-U1 RNP antibody.
