PGS Documentation

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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. 

Figure 1. Browsing to location from spreadsheet with differentially expressed genes
Figure 2. Viewing location in Genome Viewer
 

Adding UCSC CpG Annotations

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

Figure 3. Navigating to the Table Browser at the UCSC Genome Browser website

  • Configure the Table Browser page as shown (Figure 2) 

Figure 4. Configuring the Table Browser to output CpG Islands BED file
  • 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 5. Importing the CpG Islands map BED file
  • 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.  

 

Additional Assistance

If you need additional assistance, please visit our support page to submit a help ticket or find phone numbers for regional support.

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