# Analyzing pathway enrichment in Partek Pathway

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

![](/files/r6jP2O7nM5UxpyovKdqu)

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.

![](/files/XpYVULFhzwkjEjhT0Ahm)

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.

![](/files/iWtTEWTQui1nKhZ1E7ro)

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.

![](/files/XFS4XUW1bLJ1LriXjnj8)

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).

![](/files/xCuPD7kdfK3LzzXdCNAs)

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.

![](/files/xPLQojTeTLyDGlA0IC3J)

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.

![](/files/BNmJBh8SSvExZWnY7bff)

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](/files/RZxTi8f9BqNoQWD2S0to)) to activate Selection Mode
* Right-click *GABAB* (Figure 8)

![](/files/oEIB2KQXp799RjqxUB8N)

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 (![](/files/3iN5ghnme2cwsdUvrdUY)) 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 (![](/files/bernociUeCQJ37a4dhvT)) to open the search panel
* Type **NSF** in the search box
* Select (![](/files/N4pqeHhlBCkUKPyko9Au)) to search

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

![](/files/ZyQATY0o23NpdpDzO4br)

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 (![](/files/9LGUFgOQNnYrs8oTE6YS)) to minimize the *Search* panel

![](/files/fASSZIzHDLi4fGXpsnTT)

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).

![](/files/pABjLIegqI4Vso76hobU)

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).

![](/files/02BsQegBoXbOmjcpc2Ok)

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 (![](/files/eZNdXzINF4TZPU4F4vWL)) in the upper left-hand corner of the Partek Pathway window

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

![](/files/fUMQZDLGLNLrdQA9u1xW)

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)

![](/files/DsmaSssriLznNkBKkKoS)

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.


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