> For the complete documentation index, see [llms.txt](https://help.bioinsight.illumina.com/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://help.bioinsight.illumina.com/partek/partek-genomics-suite/tutorials/gene-expression-analysis-with-batch-effects/hierarchical-clustering-using-a-gene-list.md).

# Hierarchical clustering using a gene list

## Opening a gene list as a child spreadsheet

Gene lists can be visualized and their ability to distinguish samples evaluated using a hierarchical clustering heat map. Because of the batch effect in this data set, we will perform hierarchical clustering using batch-corrected intensity values. To do this, we need to open the *fourtreatments* list of differentially expressed genes as a child spreadsheet of the *batch-remove* spreadsheet

* Select **fourtreatments** from the spreadsheet tree
* Select (![](https://1384254481-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FJVEESmJAPppJ3ijFq5aR%2Fuploads%2Fgit-blob-2fbdd26c5f263e21cf832b591b2e715a6d93b541%2Fimage2017-8-29%2015_15_52.png?alt=media)) to close the spreadsheet
* Select **1-removeresult (batch-remove)** from the spreadsheet tree
* Select **File** from the main tool bar
* Select **Open as child...**
* Select **fourtreatments** using the file browser

The *fourtreatments* spreadsheet will open as a child spreadsheet of *batch-remove* (Figure 1).

![](https://1384254481-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FJVEESmJAPppJ3ijFq5aR%2Fuploads%2Fgit-blob-a5ff2d61a8392db74b420ca21477ef207c1a9154%2F2017-08-29%2015_20_09-Partek%20Genomics%20Suite%20-%201-removeresult_1%20\(fourtreatments\).png?alt=media)

Figure 1. The fourtreatments spreadsheet is open as a child spreadsheet of bath-remove. Visualizations performed using fourtreatments will pull intensity values from batch-remove.

Visualizations performed using the *fourtreatments* spreadsheet will now use intensity values from the *batch-remove* spreadsheet.

## Hierarchical clustering using a gene list

To invoke hierarchical clustering, follow the steps below.

* Select **Cluster Based on Significant Genes** from the *Visualization* section of the *Gene Expression* workflow
* Select **Hierarchical Clustering**
* Select **OK**
* Select **1-removeresult/1 (fourtreatments)** from the drop-down menu
* Select **Standardize** for *Expression normalization* (Figure 2)

![](https://1384254481-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FJVEESmJAPppJ3ijFq5aR%2Fuploads%2Fgit-blob-c1ecdca062269c65c06c912f3fba2d462a00b2cf%2F2017-08-29%2015_23_59-Cluster%20the%20significant%20genes.png?alt=media)

Figure 2. Configuring the Cluster the significant genes dialog

* Select **OK**

The hiearchical clustering heat map will open in a new tab (Figure 3).

![](https://1384254481-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FJVEESmJAPppJ3ijFq5aR%2Fuploads%2Fgit-blob-d7d925b3a721398d50da40f486502fad6bb9b6b8%2F2017-08-29%2015_26_47-Partek%20Genomics%20Suite%20-%201-removeresult%20\(batch-remove\).png?alt=media)

Figure 3. Hierarchical clustering of genes with significantly different expression across the treatment groups

Genes without changes in expression are given a value of zero and are colored black. Up-regulated genes have positive values and are displayed in red. Down-regulated genes have negative values and are displayed in green. Each sample is represented in a row while genes are represented as columns. Dendrograms illustrate clustering of samples and genes. To learn more about configuring the hierarchical clustering heat map, see the [Hierarchical Clustering Analysis](/partek/partek-genomics-suite/user-manual/hierarchical-clustering-analysis.md) user guide.

For detailed information about the methods used for clustering, refer to the Partek Manual **Chapter 8: Hierarchical & Partitioning Clustering**.

## Additional Assistance

If you need additional assistance, please visit [our support page](http://www.partek.com/support) to submit a help ticket or find phone numbers for regional support.


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