PGS Documentation

Page tree

Versions Compared


  • This line was added.
  • This line was removed.
  • Formatting was changed.


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, altered hyper-methylation of promoter CpG islands is a common mechanism for down-regulating gene expression changes in cancer. 


Numbered figure captions
SubtitleTextAdding chromosome location to ANOVA results
AnchorNameAdding chromosome location to ANOVA results


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. 

  • LeftRight-click the unlabeled column Island column to filter it out other columns (Figure 3)

Numbered figure captions
SubtitleTextUsing Interactive Filter tool to filter out probes by annotation. When pointed to a categorical column, the Interactive Filter tool summarises the content of the column by a column chart. Left-click to exclude a category (two columns were excluded, so they are grayed out), right-click to include only
AnchorNameUsing the Interactive Filter

Image RemovedImage Added

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 or near CpG islands, we will create a spreadsheet containing only these probes. 


Numbered figure captions
SubtitleTextCloning a filtered spreadsheet creates a new spreadsheet with only the included cells
AnchorNameCloning a filtered spreadsheet

Image RemovedImage Added

  • Select Clone
  • Rename the new spreadsheet LCLs_vs_B_cells_CpG_Islands using the Clone Spreadsheet dialog
  • Select mvalues from the Create new spreadsheet as a child spreadsheet: drop-down menu (Figure 5)
  • Select OK