Integration of Genome-Wide DNA Methylation and Transcription Uncovered Aberrant Methylation-Regulated Genes and Pathways in the Peripheral Blood Mononuclear Cells of Systemic Sclerosis
Identification of differentially expressed genes between systemic sclerosis and normal. (a) Volcano plot of the differential gene expression analysis. X-axis: fold change difference (log 2 scale); y-axis: BH-adjusted p values for each probe (- log10 scale). The vertical dotted lines represent absolute cutoff value of 1.5-fold change. The horizontal dotted line represents the significant cutoff of p < 0.05 (see Supplementary Table 2). (b) Two-dimensional hierarchical clustering of differential gene expression probes. Probes are shown in rows; samples are shown in columns. (c) Canonical pathway analysis of the differentially expressed genes in PBMC from SSc patients as compared with normal controls. Statistically significant pathways were shown. The y-axis indicates percentage of differential expression genes involved in the pathway. The y-axis shows BH-adjusted p-value of enrichment analysis.