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Partek Genomics Suite enables you to visualize each probe and compare the methylation between the groups at a single CpG site level. The visualization can be supplemented with a special annotation file which can be built using a UCSC annotation file as the basis.

Genomics Suite Documentation > Visualize methylation at each locus > figure32.png

Genomics Suite Documentation > Visualize methylation at each locus > figure33.png

Adding UCSC CpG Annotations

Go to UCSC Genome Browser
Select Table Browser under Tools in the main command bar of the webpage (Figure 1)

Genomics Suite Documentation > Visualize methylation at each locus > 2017-06-30 14_59_17-UCSC Genome Browser Home.png

Configure the Table Browser page as shown (Figure 2)

Genomics Suite Documentation > Visualize methylation at each locus > 2017-06-30 15_01_28-Table Browser.png

Set group to Regulation
Set track to CpG Islands
Set table to cpgIslandExt
Set output format to BED
Set output file to cpg.bed
Select get output

The Output cpgIslandExt as BED page will open.

Select get BED to download a compressed folder containing the BED file
Unzip the file using 7-Zip, WinRAR, or a similar program of your choice to a location you will be able to find

Next, we can import the BED file into Partek Genomics Suite.

Select Genomic Database... under Import under File in the main toolbar in Partek Genomics Suite (Figure 3)

Genomics Suite Documentation > Visualize methylation at each locus > appendix1.png

Select the file cpg.bed

The BED file will open as a new spreadsheet (Figure 5).

Change the spreadsheet name to UCSC CpG Island Annotation and save it

For this region list, you can also calculate the average beta values for the probes in each island per sample and detect differential methylated CpG islands regions. Detailed information on how to get average beta value for each CpG can be found from the Determining the average values for a region list section of Help>On-line Tutorials>User Guides> List.