The list, LCLs vs B cells, includes differentially methylated loci for locations across the genome; however, in many cases we may want to focus on loci located in particular regions of the genome. To filter our list to include only regions of interest, we can use the annotations provided by Illumina and the interactive filter in Partek Genomics Suite. 

CpG islands are regions of the genome with an atypically high frequency of CpG sites. CpG islands and their surrounding regions (termed shelf and shore) include many gene promoters and altered methylation in these regions can have a disproportionate effect on gene expression. For example, hyper-methylation of promoter CpG islands is a common mechanism for down-regulating gene expression in cancer. 


Now, we can filter probes by their relation to CpG islands.

For categorical columns, the interactive filter displays each category of the selected column as a colored bar. For 4. Relation_to_UCSC_CpG_Island, each bar represents one of the categories of the UCSC annotation . To filter out a category, left-click on its bar. Right clicking on a bar will include only the selected category. A pop up balloon will show the category label as you mouse over each bar. 

The yellow and black bar on the right-hand side of the spreadsheet panel shows the fraction of excluded cells in black and included cells in yellow. Right-clicking this bar brings up an option to clear the filter. 

Now that we have filtered out probes that are not in CpG islands, we will create a spreadsheet containing only these probes. 

You may want to save the project before proceeding to the next section of the tutorial.