PGS Documentation

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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. 

 

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SubtitleTextAdding chromosome location to ANOVA results
AnchorNameAdding chromosome location to ANOVA results

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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)

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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

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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. 

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

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  • 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

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  • Select () from the quick action bar to save the filtered spreadsheet
  • Specify a name for the spreadsheet, we chose LCLs_vs_B_cells_CpG_Islands, using the Save File dialog
  • Select Save to save the spreadsheet

It is best practice to occasionally You may want to save the project you are working on. Let's take the opportunity to do this now. 

  • Select File from the main command toolbar
  • Select Save Project...
  • Specify a name for the project, we chose Methylation, using the Save File dialog
  • Select Save to save the project

Saving the project saves the identity and child-parent relationships of all spreadsheets displayed in the spreadsheet tree. This allows us to open all relevant spreadsheets for our analysis by selecting the project file. before proceeding to the next section of the tutorial.

 

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