Optional: Add UCSC CpG island annotations

Partek Genomics Suite software can view annotation .BED files as tracks in the Genome Viewer. We can add a CpG islands track to the Genome Viewer using the UCSC Genome Browser CpG islands annotation.

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

Figure 1. Navigating to the Table Browser at the UCSC Genome Browser website

Configure the Table Browser page as shown (Figure 2)

Figure 2. Configuring the Table Browser to output CpG Islands BED file

Set assembly to Feb. 2009 (GRCh37/hg19)
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)

Figure 3. Importing the CpG Islands map BED file

Select the file cpg.bed

The BED file will open as a new spreadsheet.

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 in the Determining the average values for a region list section of Starting with a list of genomic regions.

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