PGS Documentation

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The significant CpG loci detected in the previous step actually form a methylation signature that differentiates , which we shall now visualise by a heat map.

  • Select the (LCLs vs. B cells) cells spreadsheet in the spreadsheet pane on the left
  • Select Cluster Based on Significant Genes from the Visualization panel of the Illumina BeadArray Methylation workflow
  • Select Hierarchical Clustering for Specify Method (Figure 1)

Numbered figure captions
SubtitleTextSelecting Heirarchical Clustering for clustering method
AnchorNameSelecting clustering method

  • Select OK
  • Verify that (CpG of interest) that LCLs vs. B cells is selected in the drop-down menu
  • Select Standardize for Expression normalization (Figure 2)

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Numbered figure captions
SubtitleTextHierarchical clustering with heat map invoked on a list of significant CpG loci
AnchorNameheat map

The experimental groups are rows, while the CpG loci from the (LCLs vs. B cells) cells spreadsheet are columns. Methylation levels are compared between the LCLs and B cells groups. CpG loci with higher methylation are colored red, CpG loci with lower methylation are colored green. B cells LCLs samples are colored red and LCLs orange and B cells samples are colored orange in red in the dendrogram on the the left-hand side of the heat map. 

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