Methylation chart

Anonymous 11 years ago • updated by 11 years ago • 3

Dear colleagues,

I am comparing a bed of exons against the corresponding full-genes bed file. By looking at "DNA methylation (ENCODE)" I can see higher bars for full-genes (e.g. 75% unmethylated for genes compared to 5% unmethylated for exons).

Below, it can be read:

Chart description: The bar chart visualizes the percentage of regions in the selected region set that overlap with any of the listed genomic and epigenomic features on the x-axis.

And this is what I do not understand. The plot suggests more methylation on exons, but the chart description refers to percentages of regions that overlap with a given epigenomic feature. Then, if an exon intersects with a methylated region, then the corresponding gene should intersect too. What am I missing here?

Many thanks for EpiExplorer, it is really helpful,

Best,

Federico

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11 years ago

Dear Federico,

The methylation chart reports what percent of the regions in your datasets that can be considered methylated or unmethylated based on their methylation ratio for a specific tissue. The methylation ratio of each region (e.g. exon, gene, promoter, CpG island) is computed by averaging the methylation for every CpG for which there is methylation data available for the tissue. If the ratio is below 0.33 the region is considered unmethylated and if it is above 0.66 it is considered methylated.

Hope this helps,

best,

konstantin

11 years ago

Many thanks, Konstantin, thats exactly what I wanted to know.

Federico

11 years ago

Dear Konstantin, I have a related question. I have been exporing the original methylation files and was wondering which thresholds does EpiExplorer use for read coverage and percentage of reads with methylation. In UCSC they recommend requiring at least 10 reads and they assign colors depending on what fraction of the reads is found to be methylated.

Thanks again,

Federico

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