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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. 

Adding UCSC CpG Annotations

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• 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.

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• 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.  The visualization can be supplemented with a special annotation file which can be built using a UCSC annotation file as the basis. Building and viewing the UCSC annotation file is available as an optional section of the tutorial, Optional: Adding UCSC CpG Island Annotations.