# Performing biological interpretation

* [Enrichment analysis](#enrichment-analysis)
* [KEGG enrichment analysis](#kegg-enrichment-analysis)

To learn more about the biology underlying gene expression changes, we can use gene ontology (GO) or pathway enrichment analysis. Enrichment analysis identifies over-represented GO terms or pathways in a filtered list of genes.

## Enrichment analysis

* Click the **Filtered feature list** data node
* Click **Biological interpretation** in the task menu
* Click **Gene set enrichment** then select **Gene set database** to perform GO enrichment analysis (Figure 1)

![Figure 1. Invoking enrichment analysis](https://1384254481-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FJVEESmJAPppJ3ijFq5aR%2Fuploads%2Fgit-blob-169ebf3a947edb98e0fa5786e977ad6819463915%2Fbulk%20seq%20tut%20perform%20gene%20set%20enrichment%20from%20task%20menu.png?alt=media)

* Select the latest gene set from geneontology.org from the *Gene set database* drop-down menu
* Click **Finish**

A gene set enrichment task node and data node will be added to the pipeline (Figure 2).

![Figure 2. Gene set enrichment task node and data node](https://1384254481-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FJVEESmJAPppJ3ijFq5aR%2Fuploads%2Fgit-blob-c8f490bb9307f7a204797362a1e79151ca38ef1a%2Fbulk%20seq%20tut%20task%20graph%20after%20gene%20set%20enrichment.png?alt=media)

* Double-click the **Gene set enrichment** task node to open the task report (Figure 3)

![Figure 3. Viewing the GO enrichment task report](https://1384254481-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FJVEESmJAPppJ3ijFq5aR%2Fuploads%2Fgit-blob-589de259e7ace11c485e75f09547f66873f031ec%2Fbulk%20seq%20tut%20gene%20set%20enrichment%20report.png?alt=media)

The *gene set enrichment* task report lists GO terms by ascending p-value with the most significant GO term at the top of the list. Also included are the enrichment score, the number of genes from that GO term in the list, and the number of genes from that GO term that are not in the list.

To view the genes associated with each GO term, select ![](https://1384254481-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FJVEESmJAPppJ3ijFq5aR%2Fuploads%2Fgit-blob-6f33880235899116af19939988b2b3aa2f5f4f55%2Fnotebook-icon.png?alt=media) to open the extra details page. To view additional information about a GO term, click the blue gene set ID in the first column to open the linked geneontology.org entry in a new browser tab.

For more information about GO enrichment analysis, please see the [Gene Set Enrichment](https://help.connected.illumina.com/partek/partek-flow/user-manual/task-menu/biological-interpretation/gene-set-enrichment) user guide.

## KEGG enrichment analysis

KEGG enrichment analysis identifies pathways that are over-represented in a gene list data node.

* Click the **Filtered feature list** data node
* Click **Biological interpretation** in the task menu
* Click **Gene set enrichment** then select **KEGG database**
* Click **Finish** in the configuration dialog to run KEGG analysis with the *Homo sapiens* KEGG database

A *Pathway* enrichment task node and data node will be added to the pipeline (Figure 4).

![Figure 4. Pathway enrichment task node and data node](https://1384254481-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FJVEESmJAPppJ3ijFq5aR%2Fuploads%2Fgit-blob-b35665629ee7848833aa3415ff463d171a8b43af%2Fbulk%20seq%20tut%20task%20graph%20with%20gene%20set%20enrichment.png?alt=media)

* Double-click the **Pathway enrichment** task node to open the task report

The *Pathway enrichment* task report is similar to the *gene set* e*nrichment analysis* task report (Figure 5).

![Figure 5. Pathway enrichment task report](https://1384254481-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FJVEESmJAPppJ3ijFq5aR%2Fuploads%2Fgit-blob-591a9fd6c8d66cd11fb7324141ae918d3fb0d970%2Fbulk%20seq%20tut%20pathway%20enrichment%20report.png?alt=media)

To view an interactive KEGG pathway map, click the pathway ID (*Gene set* column).

## 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.