Fig. 4: Pathway analyses of DNA methylation genes in RB.
From: Characterizing DNA methylation signatures of retinoblastoma using aqueous humor liquid biopsy
A Significantly differential DNA methylation in RB versus retina. Each dot represents one probe. −log10(p value) for each probe were plotted on the y-axis while the β value difference between RB tumors and normal retina were plotted on the x-axis. The P value was calculated using two-sided Welch’s t-tests. The β value change cutoffs of +/−0.3 were shown. Probe locations were shown in red for promoter, blue for gene body and gray for other location. B Genes regulated by DNA methylation in RB versus normal retina. DNA methylation changes were plotted on the x-axis (Δβ > 0.3 or <−0.3). Gene expression changes were plotted on the y-axis (Log2FC > 1 or <−1). Only the probes located in promoter (red) and gene body (blue) were plotted. C Graphical summary of the IPA pathway analysis of the genes identified in B shows enrichment of several tumor-associated pathways. Source data are provided as a Source Data file. D The estrogen-mediated S-phase Entry pathway is activated by the upregulation of many pathway components (shown in red) identified in B. E Promoter DNA hypomethylation of the genes highlighted in D.
