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Fig. 2 | Clinical Epigenetics

Fig. 2

From: Association of expression of epigenetic molecular factors with DNA methylation and sensitivity to chemotherapeutic agents in cancer cell lines

Fig. 2

Overall design of the study. a Analysis of direct associations between GMD expression and drug response. b A two-step approach to identify possible indirect GMD effects on drug response. Epigenetic targets significantly associated with GMD expression were identified first, and then, the correlation of methylation of these significant targets with drug response was analyzed. c. Analysis of average DNA methylation values. In each analysis, we examined associations in all cancer categories combined (pancancer analysis) and in individual cancer types with ≥ 10 cell lines. GMD expression data included RNA-seq RPKM values for 72 GMDs. Epigenome-wide DNA methylation data included beta-values for 424,840 individual probes and gene region-averaged values for 93,591gene regions from 20,643 genes and noncoding RNA. Average epigenome-wide methylation values were computed as a mean of beta-values for 424,840 probes which passed the QC and filtering. Drug response measures consisted of 275 log(IC50) values for 255 anticancer agents obtained from CCLE and GDSC datasets. The criteria for identifying significant strong associations are provided below each diagram. pFDR, p-value adjusted for false discovery rate according to Benjamini–Hochberg procedure

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