Figure 1
From: Cellular dissection of psoriasis for transcriptome analyses and the post-GWAS era
Gene set enrichment analysis: Psoriasis DEGs overlap significantly with genes altered in other skin diseases and in cytokine-treated KCs. We identified 1019 PP-increased DEGs and 885 PP-decreased DEGs (n = 216 patients) and evaluated how these genes were altered in other skin diseases or experiments with cytokine-treated KCs. (A) Comparison with skin diseases. Psoriasis DEGs were compared to ranked gene lists generated from microarray studies comparing diseased skin samples with normal or uninvolved skin. Barplots show GSEA area statistics calculated for each comparison (i.e., area between foreground and background detection rate curves; see parts C and D). Positive area statistics indicate that psoriasis DEGs are disproportionately elevated in a given skin disease, while negative statistics indicate that psoriasis DEGs are disproportionately repressed. The analysis was performed with respect to PP-increased DEGs and PP-decreased DEGs, and comparisons are ranked according to the maximum p-value from the two analyses (Wilcoxon rank sum test). The top-ranked 10 comparisons are shown (of 51 included in our screen). (B) Comparison with cytokine-treated KCs. The analysis was repeated with respect to ranked gene lists generated from microarray experiments in which cultured KCs were treated with cytokines. Left margin labels list the concentration of cytokine (per mL) and the duration of treatment. The top-ranked 10 comparisons are shown (of 46 included in our screen). Most experiments were performed with primary NHEKs (** denotes experiments performed using reconstituted epidermis). (C) GSEA analysis of psoriasis-increased DEGs and squamous cell carcinoma (SCC). Genes were ranked according to how strongly they were increased in SCC as compared to normal skin (GEO series GSE7553). The figure shows the cumulative overlap between psoriasis-increased DEGs and this ranked gene list. Significance of this overlap is proportional to the area between this curve and the diagonal (i.e., grey region). Yellow hashmarks (top) denote the 100 DEGs most strongly elevated in psoriasis lesions (i.e., highest PP/PN fold-change). (D) GSEA analysis of psoriasis-decreased DEGs and SCC. Yellow hashmarks (top) denote the 100 DEGs most strongly repressed in psoriasis lesions (i.e., lowest PP/PN fold-change).