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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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