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To illustrate the capabilities and customization options of hierarchical clustering in Partek Genomics Suite, we will explore an example of hierarchical clustering drawn from the tutorial Gene Expression Analysis. The data set in this tutorial includes gene expression data from patients with or without Down syndrome. Using this data set, 23 highly differentially expressed genes between Down syndrome and normal patient tissues were identified. These 23 differentially regulated genes were then used to perform hierarchical clustering of the samples. Follow the steps outlined in Hierarchical Clustering and Adding Information to Gene Lists to perform hierarchical clustering and launch the Hierarchical Clustering tab (Figure 1).

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The sample attributes are now labeled with group titles (Figure 2).

Adding a Sample Attribute to the Heat Map

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Color blocks indicating the tissue of each sample have been added to the row labels and sample legend (Figure 3).

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The bottom row has moved to the top of the heat map (Figure 5). 

Changing Heat Map Colors

The minimum, maximum, and midpoint colors of the heart map intensity plot can be customized. 

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The selected dendogram column will be in bold and the selected rows will be highlighted. 

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The same steps can be used to zoom into columns or rows. Here, we have zoomed in on the rows, but not columns to show the expression levels of the selected genes for all samples (Figure 8). 

To reset zoom select () on the x-axis to show all columns and the y-axis to show all rows

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