Obtain Methylation Signatures

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) 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)

Figure 1. Selecting Heirarchical Clustering for clustering method

Select OK
Verify that (CpG of interest) is selected in the drop-down menu
Select Standardize for Expression normalization (Figure 2)

Figure 2. Selecting spreadsheet and normalization method for clustering

Select OK

The heat map will be displayed on the Hierarchical Clustering tab (Figure 3).

Figure 3. Hierarchical clustering with heat map invoked on a list of significant CpG loci

The experimental groups are rows, while the CpG loci from the (LCLs vs. B 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 samples are colored red and LCLs samples are colored orange in the dendrogram on the the left-hand side of the heat map.

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