Integration of Genome-Wide DNA Methylation and Transcription Uncovered Aberrant Methylation-Regulated Genes and Pathways in the Peripheral Blood Mononuclear Cells of Systemic Sclerosis

Figure 1

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.

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