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To quantify the amount of variation in DNA methylation explained by genomic context, we considered the correlation between genomic context and principal components (PCs) of methylation levels across all 100 samples (Figure 4). We found that many of the features derived from a CpG site’s genomic context appear to be correlated with the first principal component (PC1). The methylation status of upstream and downstream neighboring CpG sites and a co-localized DNAse I hypersensitive (DHS) site are the most highly correlated features, with Pearson’s correlation r=[0.58,0.59] (P0.5 (P<2.2?10 ?16 ) with PC1, including co-localized active TFBSs ELF1 (ETS-related transcription factor 1), MAZ (Myc-associated zinc finger protein), MXI1 (MAX-interacting protein 1) and RUNX3 (Runt-related transcription factor 3), and co-localized histone modification trimethylation of histone H3 at lysine 4 (H3K4me3), suggesting that they may be useful in predicting DNA methylation status (Additional file 1: Figure S3). 67,P<2.2?10 ?16 ) [53,54].

Correlation matrix regarding anticipate possess with first 10 Pcs out-of methylation levels. The newest x-axis represents among the 122 keeps; the fresh y-axis is short for Personal computers step 1 as a consequence of ten. Tone match Pearson’s relationship, just like the shown from the legend. Desktop computer, dominant part.

Binary methylation reputation prediction

These observations about patterns of DNA methylation suggest that correlation in DNA methylation is local and dependent on genomic context. More >

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