Obtain methylation signatures
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Partek
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The significant CpG loci detected in the previous step actually form a methylation signature that differentiates between LCLs and B cells. We can build and visualize this methylation signature using clustering and a heat map.
Select the LCLs_vs_Bcells_CpG_Islands 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 LCLs_vs_Bcells_CpG_Islands is selected in the drop-down menu
Verify that Standardize is selected 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. LCLs samples are colored orange and B cells samples are colored red in the dendrogram on the the left-hand side of the heat map.
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