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Fig. 3 | Genome Biology

Fig. 3

From: Comprehensive analyses of partially methylated domains and differentially methylated regions in esophageal cancer reveal both cell-type- and cancer-specific epigenetic regulation

Fig. 3

Subtype-specific PMDs control cell-type-specific functions. A, B In both EAC (A) and ESCC (B), genes covered by PMDs are expressed at lower levels than those in non-PMDs in a cancer-specific manner. C, D Cistrome-GO enrichment analyses using either EAC-specific (C) or ESCC-specific (D) PMDs and the downregulated genes within them. The top 15 most significant pathways are shown, and the number of genes enriched in each pathway is shown on the right. E Two representative genome windows showing the methylation profiles of EAC-specific (left panel) and ESCC-specific PMDs (right panel). CGI regions were masked using the annotation from Irizarry et al. [39]. F Volcano plots showing that genes residing within genome domains in E are downregulated in corresponding cancer subtypes. The differentially expressed genes were identified with the average expression level (FPKM) ≥ 0.1, adjusted p-value < 0.05 and absolute fold-change > 2. Expression RNA-seq in C, D, F are from the TCGA ESCA project, including 76 ESCC and 78 EAC samples

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Genome Biology

ISSN: 1474-760X

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