Analyzing pathway enrichment in Partek Pathway

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

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.

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.

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.

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).

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.

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.

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.

Right-click GABAB (Figure 8)

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

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

Type NSF in the search box

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

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).

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).

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).

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.

The Pathway Libraries dialog will open (Figure 13).

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.