# Make comparisons using Compute biomarkers and Biological interpretation

* [Compute biomarkers](#compute-biomarkers)
* [Create a list](#create-a-list)
* [Biological Interpretation](#biological-interpretation)

We will compare the classification (FASN expression) we previously made based on expression levels of the FASN gene. Here, we will compare FASN high and FASN low cells to identify genes and pathways.

## Compute biomarkers

* Select the Normalized counts node and choose **Compute biomarkers** from the *Statistics* drop-down

![](https://1384254481-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FJVEESmJAPppJ3ijFq5aR%2Fuploads%2Fgit-blob-bf7603f4413031f28e4610d4cd21029625464279%2Fimage2023-7-26_9-47-57.png?alt=media)

* Choose the "FASN expression" attribute
* Do not select **Split by sample**
* Click Finish

![](https://1384254481-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FJVEESmJAPppJ3ijFq5aR%2Fuploads%2Fgit-blob-960184df565fbc6106157a2fc17928feede95c61%2Fimage2023-7-26_9-30-9.png?alt=media)

This results in a Biomarkers report.

* Double-click the **Biomarkers** results node to open the report

![](https://1384254481-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FJVEESmJAPppJ3ijFq5aR%2Fuploads%2Fgit-blob-f0d6c49fa6dd5fc1151470eea1172987e4303df2%2Fimage2023-7-26_9-34-11.png?alt=media)

The top features are reported for the comparison.

* **Download** this table with more than 10 features using the Download option ![image2023-7-26\_9-38-10](https://1384254481-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FJVEESmJAPppJ3ijFq5aR%2Fuploads%2Fgit-blob-f67090262d7098cbe979ce4bafcc731dae7404e0%2Fblue-download-button.png?alt=media)

![](https://1384254481-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FJVEESmJAPppJ3ijFq5aR%2Fuploads%2Fgit-blob-7ff5c39c2bc80a06f96f57ad215ab4c63d8b4c6d%2Fimage2023-7-28_12-39-43.png?alt=media)

[Please click here for more information on differential analysis methods.](https://help.connected.illumina.com/partek/partek-flow/user-manual/task-menu/differential-analysis)

## Create a list

We will create a list using [List management](https://help.connected.illumina.com/partek/partek-flow/user-manual/settings/components/lists) with these 10 genes, so that we can use this list in the Gene set enrichment task.

* Click your **username** in the top right corner
* Select **Settings** from the drop-down
* Choose **Lists** from the **Components** drop-down in the menu on the left

![](https://1384254481-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FJVEESmJAPppJ3ijFq5aR%2Fuploads%2Fgit-blob-31acfda85608eeea9e5911d2e5e35b1a653ccb8a%2Fimage2023-7-26_10-3-11.png?alt=media)

* Use the **+ New list** button to add these 10 genes

![](https://1384254481-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FJVEESmJAPppJ3ijFq5aR%2Fuploads%2Fgit-blob-f016101904a6f0f2bd1055f0d152897710532bec%2Fimage2023-7-26_10-5-1.png?alt=media)

* Choose **Text** as the list option
* Give the list a **Name** and **Description**
* Enter the 10 genes in column format as shown below
* Click **Add list**

![](https://1384254481-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FJVEESmJAPppJ3ijFq5aR%2Fuploads%2Fgit-blob-cf974c239479d1da21a7a822d88ca69a2ad20545%2Fimage2023-7-26_10-10-53.png?alt=media)

The list has been added and can now be used for further analysis. The **Actions** button can be used to modify this list if necessary, as shown below.

![](https://1384254481-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FJVEESmJAPppJ3ijFq5aR%2Fuploads%2Fgit-blob-b7c0e6b29cfb1290f72939ef1b5605265ac7eeb7%2Fimage2023-7-26_10-13-19.png?alt=media)

## Biological Interpretation

Here we are going to perform [Gene Set Enrichment](https://help.connected.illumina.com/partek/partek-flow/user-manual/task-menu/biological-interpretation/gene-set-enrichment) on our top 10 features for the FASN high group that we have added as a list called "Top 10 FASN high Features".

* Go to the **Analyses tab**
* Select the Normalized counts node
* Choose **Gene set enrichment** from the *Biological interpretation* drop-down in the task menu

![](https://1384254481-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FJVEESmJAPppJ3ijFq5aR%2Fuploads%2Fgit-blob-d64c8321163336a1256e0a09967d6459b71ec9de%2Fimage2023-7-26_10-34-58.png?alt=media)

* Use the KEGG database for pathway enrichment
* Check **Specify background gene list**
* Select "Top 10 FASN high Features" as the **Background gene list**
* Click **Finish**

![](https://1384254481-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FJVEESmJAPppJ3ijFq5aR%2Fuploads%2Fgit-blob-6df670c9b7b87d3141ca97c722b56d56d53db452%2Fimage2023-7-26_10-38-53.png?alt=media)

This results in a Pathway enrichment report, as shown below.

* Double-click the report to view the pathways involved in this list of genes

![](https://1384254481-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FJVEESmJAPppJ3ijFq5aR%2Fuploads%2Fgit-blob-f36dafd74747254767d81d68b01e2597d5798543%2Fimage2023-7-26_10-50-1.png?alt=media)

Please click [here](https://help.connected.illumina.com/partek/partek-flow/user-manual/task-menu/biological-interpretation) for more information on Biological interpretation.

## 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.