# Analyzing pathway enrichment in Partek Pathway

Partek Pathway is a separate program from Partek Genomics Suite with a distinct user interface (Figure 1).

![](https://1384254481-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FJVEESmJAPppJ3ijFq5aR%2Fuploads%2Fgit-blob-081cc5020c6c33d6c317a30be7c3998f3ea4a5d5%2F2017-08-21%2014_46_20-Partek%20Pathway%20-%20GABAergic%20synapse.png?alt=media)

Figure 1. Partek Pathway

The *Project Elements* panel (Figure 2) displays the selected pathway, the original gene list, the Pathway Enrichment spreadsheet, and the library references that were used for the pathway analysis. The *Project Elements* panel is used to navigate between open pathway diagrams and spreadsheets.

![](https://1384254481-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FJVEESmJAPppJ3ijFq5aR%2Fuploads%2Fgit-blob-c7f14e622ab2b102c868406de657ec96404a2c74%2F2017-08-21%2015_22_54-Partek%20Pathway%20-%20GABAergic%20synapse.png?alt=media)

Figure 2. Project Elements panel

* Select the **Brain vs. Heart** spreadsheet under *Gene Lists*

The *Brain vs. Heart* gene list we created earlier will open (Figure 3). The spreadsheet can be sorted by any column by left-clicking a column header; the first click will sort by ascending values, the second click will switch to descending values.

![](https://1384254481-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FJVEESmJAPppJ3ijFq5aR%2Fuploads%2Fgit-blob-e71c03919e82891d796783a00dfe4efbba64dc41%2F2017-08-21%2015_42_18-Partek%20Pathway%20-%20Marker%20List.png?alt=media)

Figure 3. Viewing a gene list in Partek Pathway

* Select the **Pathway-Enrichment** spreadsheet under *Pathway Lists*

The *Pathway-Enrichment.txt* spreadsheet will open (Figure 4). This spreadsheet has the same contents as the *Pathway-Enrichment.txt* spreadsheet in Partek Genomics Suite. Selecting any of the pathway names will open its pathway diagram. The spreadsheet can be sorted by any column.

![](https://1384254481-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FJVEESmJAPppJ3ijFq5aR%2Fuploads%2Fgit-blob-3eee1300c1d01a9153d28bb9c56edae4131a59f8%2F2017-08-21%2015_46_40-Partek%20Pathway%20-%20Pathway%20List.png?alt=media)

Figure 4. Viewing the Pathway Enrichment spreadsheet in Partek Pathway

* Select the **GABAergic synapse** pathway on the *Pathway-Enrichment* spreadsheet or the Project Elements panel

The *GABAergic synapse* pathway diagram will open. Genes in the pathway are shown as boxes. The color of the boxes is set by the *Configuration* panel (Figure 5).

![](https://1384254481-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FJVEESmJAPppJ3ijFq5aR%2Fuploads%2Fgit-blob-6e8c284b33048f4260392ee84e787fb8a70b6392%2F2017-08-21%2015_58_11-.png?alt=media)

Figure 5. The Configuration panel

Any numerical column from the source gene list can be used to color the gene boxes. While significant p-values indicate a difference between the categories, they give no information about upregulation or downregulation of the pathway. We can overlay fold-change information on the pathway diagram.

* Select **Brain vs. Heart: Fold-Change(Brain vs. Heart)** from the drop-down menu

The pathway diagram now shows fold change for each gene in the pathway included in the gene list (Figure 6). Genes not in the gene list remain black.

![](https://1384254481-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FJVEESmJAPppJ3ijFq5aR%2Fuploads%2Fgit-blob-fa5236aca17091274f28dff239977cdf90d938e2%2F2017-08-21%2016_20_12-Partek%20Pathway%20-%20GABAergic%20synapse.png?alt=media)

Figure 6. GABAergic synapse pathway diagram showing fold-changes for genes in the gene list

The colors and range of can be changed using the *Color By* panel.

* Select the red color square next to *Max*
* Select yellow from the color picker interface
* Select **OK**
* Select the green color square next to *Min*
* Select pale blue from the color picker interface
* Select **OK**

We can see that all the colored genes in the *GABAergic synapse* pathway are yellow (Figure 7), indicating that they are up-regulated.

![](https://1384254481-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FJVEESmJAPppJ3ijFq5aR%2Fuploads%2Fgit-blob-8de247be8ed6efd67c94e8f9293b4bd64d57d8c2%2F2017-08-21%2016_30_55-Partek%20Pathway%20-%20GABAergic%20synapse.png?alt=media)

Figure 7. Changing colors in the Pathway Diagram; up-regulated genes are yellow and down-regulated genes are teal

We can select a gene to learn more about it.

* Select (![alt text](https://1384254481-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FJVEESmJAPppJ3ijFq5aR%2Fuploads%2Fgit-blob-45d3ffdf94292c9996fa53ce35f55f9cdb2cbfb7%2Fimage2017-8-21%2016_36_35.png?alt=media)) to activate Selection Mode
* Right-click *GABAB* (Figure 8)

![](https://1384254481-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FJVEESmJAPppJ3ijFq5aR%2Fuploads%2Fgit-blob-d01d0eeca5ab2b29b6d1e61da05065e39b44e2c1%2F2017-08-22%2011_31_29-.png?alt=media)

Figure 8. Learn more about any gene on a pathway diagram by right-clicking

Options available include:

*Look up on KEGG -* opens the KEGG page for the pathway on GenomeNet (genome.jp) in your web browser

*Ensembl* - under *External Links*, opens the page for the selected Ensembl ID on ensemble.org

*UniProt* - under *External Links,* opens the page for the selected UniProt ID on uniprot.org

*Jump to \_\_\_ on "\_\_\_"* - opens the source gene list in Partek Pathway to the row of the selected gene

Selecting (![](https://1384254481-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FJVEESmJAPppJ3ijFq5aR%2Fuploads%2Fgit-blob-a4fc24be459019581becce71c6ee21950d83b237%2Fimage2017-8-22%2010_31_25.png?alt=media)) activates Navigation Mode. This enables navigation on large pathway diagrams by left-clicking and dragging to move the view.

The pathway database can be searched for genes of interest using the *Search* panel.

* Select (![](https://1384254481-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FJVEESmJAPppJ3ijFq5aR%2Fuploads%2Fgit-blob-72ce13114844ffe72d9637960d25c097dfdd1cd6%2Fimage2017-8-22%2010_40_24.png?alt=media)) to open the search panel
* Type **NSF** in the search box
* Select (![](https://1384254481-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FJVEESmJAPppJ3ijFq5aR%2Fuploads%2Fgit-blob-9cb655dbd2ff12cdc99d32db9d3a4ff8c814732c%2Fimage2017-8-22%2010_42_57.png?alt=media)) to search

Pathways containing NSF appear on the right-hand side in the Search Results section in alphabetical order (Figure 9).

![](https://1384254481-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FJVEESmJAPppJ3ijFq5aR%2Fuploads%2Fgit-blob-207260a05aaf79b6192c9523e8d42325608d4344%2F2017-08-22%2010_52_54-Partek%20Pathway%20-%20GABAergic%20synapse.png?alt=media)

Figure 9. Using the search panel to find pathways containing a gene of interest

If multiple species or libraries have been loaded, the Filter Options section on the left-hand side can be used to choose which species and libraries to search.

* Double click on **Synaptic vesicle cycle** in the Search Results section

The selected pathway, Synaptic vesicle cycle, will open in the *Pathway Diagram* panel (Figure 10).

* Select (![](https://1384254481-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FJVEESmJAPppJ3ijFq5aR%2Fuploads%2Fgit-blob-03ac890b2ec650028fc46457502c4368021f61ae%2Fimage2017-8-22%2011_3_50.png?alt=media)) to minimize the *Search* panel

![](https://1384254481-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FJVEESmJAPppJ3ijFq5aR%2Fuploads%2Fgit-blob-b50bf3744553b5cf275296880190c0aad29b7d18%2F2017-08-22%2010_56_07-Partek%20Pathway%20-%20Synaptic%20vesicle%20cycle.png?alt=media)

Figure 10. Opening a pathway diagram from search results

On the right-hand side of the Partek Pathway window, we see the *Pathway Detail* panel (Figure 11).

![](https://1384254481-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FJVEESmJAPppJ3ijFq5aR%2Fuploads%2Fgit-blob-aa2f4178dd2c5e9f2d9bc0270fb583ffc1319c56%2F2017-08-22%2011_34_03-.png?alt=media)

Figure 11. The Pathway Detail panel

* Select **KEGG\_Gene** to open the list of genes in the pathway

Selecting a gene in the list will highlight it in the pathway diagram (Figure 12).

![](https://1384254481-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FJVEESmJAPppJ3ijFq5aR%2Fuploads%2Fgit-blob-1336306aff011e3efc65750d52d4a6264fdeeae4%2F2017-08-22%2011_05_04-Partek%20Pathway%20-%20Synaptic%20vesicle%20cycle.png?alt=media)

Figure 12. Selecting a gene in a pathway diagram using the Pathway Detail panel

Another way to select and view a pathway is browsing the Pathway Libraries.

* Select (![](https://1384254481-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FJVEESmJAPppJ3ijFq5aR%2Fuploads%2Fgit-blob-52de76237113aec5314e9594f093b047499d369a%2Fimage2017-8-22%2011_9_50.png?alt=media)) in the upper left-hand corner of the Partek Pathway window

The *Pathway Libraries* dialog will open (Figure 13).

![](https://1384254481-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FJVEESmJAPppJ3ijFq5aR%2Fuploads%2Fgit-blob-9706aa2a867f2a3e38702a220f479fa27339b192%2F2017-08-22%2011_12_26-Pathway%20Libraries.png?alt=media)

Figure 13. Downloading and browsing pathway libraries

In the upper section of the dialog, you can view available KEGG libraries and download them by selecting the *Download Library* link. Selecting a pathway opens it in the lower section of the dialog.

In the lower section of the dialog, you can view a list of all the pathways in the selected pathway library. You can also open any pathway from the selected library in the *Pathway Diagram* panel.

* Select **Adherens Junction**
* Select **View Pathway** to open the pathway diagram

We can use the *Project Elements* panel to close an open pathway diagram or list.

* Right-click **Adherens Junction** in the *Project Elements* panel
* Select Delete from the pop-up menu to close the diagram (Figure 14)

![](https://1384254481-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FJVEESmJAPppJ3ijFq5aR%2Fuploads%2Fgit-blob-bfd9179a731cf828ddc5b6e48cb65a779b926c90%2F2017-08-22%2011_29_44-.png?alt=media)

Figure 14. Closing a pathway diagram

The *Search* panel and *Pathway Libraries* can also be used to open pathway diagrams for pathways without any open gene or pathway lists.

## 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.