Enrichment analysis of differentially methylated CpGs.

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Enrichment analysis of differentially methylated CpGs. Enrichment analysis of differentially methylated CpGs. (A) Enrichment analysis of significant differentially methylated CpGs upon KD of transcripts 1+3 (25 hyper- and 327 hypomethylated CpGs) and of transcript 2 (8,536 hyper- and 369 hypomethylated CpGs) as compared with all CpGs on the microarray in relation to CGIs (left panels) and gene regions (right panels). Two kb upstream or downstream of CGIs were termed as shore region (“north” [N] and “south” [S], respectively); 2 kb flanking regions next to the shores were defined as shelf regions; and all other CpG sites were referred to as “open sea”; TSS1500 and TSS200 = 1,500 and 200 bp upstream of transcription start site, respectively. Significance was calculated by hypergeometric distribution; *P < 0.05, **P < 0.01, ***P < 0.001. (B, C) Motive enrichment analysis of DMRs (flanking 50 bp of significant CpGs) for KD of transcripts 1+3 (B) and transcript 2 (C). (D) GO classification of genes with significant DNAm changes upon KD of transcripts 1+3 and transcript 2. Tanja Božić et al. LSA 2018;1:e201800153 © 2018 Božić et al.