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Whole-genome annotations

CpG island annotations

The CgiMountatin track is a heatmap representation of CpG island strength. GC and CpG-rich CpG island cores are depicted in green, while regions with weaker CpG island characteristics, such as CpG island shores, fade towards blue. The annotation is based on 100 CpG island shadow annotations computed with CgiHunter. For each of these annotations the correlation with genomic DNA methylation was tested. Each annotation was ranked by this correlation. The tracks have been integrated in such a way that the highest ranking score for each region was retained.
The score of each region approximates the degree of hypomethylation of regions with a comparable CpG and GC density in human fibroblasts (100 - average methylation level in human fibroblasts).

SpeciesTypeView at UCSC
Human (Genome build hg18) CGI Mountatin track View
Human (Genome hg19) CGI Mountatin track View

Estimated germline methylation of ALU repeats

The Alu Judge Track applies the statistical model (Feuerbach et al., 2012) to predict which ALU repeat instance is methylated in the germline. The model uses for this prediction the 10-fold higher point mutaion rate of methylated CpGs compared to unmethylated CpGs. In consequence, ALU repeat copies, which become highly methylated in the germline after their transposition, carry a strong footprint of this epigenetic modification. Positive scores indicate that a repeat copy was only weakly methylated in the germline, while negative scores indicate strong DNA methylation. As described in the original publication the model is only applicable for repeats with a particular age and a certain number of CpGs in the ancestral sequence. Repeats that do not match these criteria are marked light grey.

SpeciesTypeMin. TransversionMax. TransversionMin. ancestral CpGsView at UCSC
Human Genome (hg18) AluJudge Track 1 % 4 % 10 View