Partek Pathway provides a visualization tool for pathway enrichment spreadsheets utilizing the KEGG database. This tutorial will illustrate:
Note: the workflow described below is enabled in Partek Genomics Suite version 7.0 software. Please fill out the form on Our support page to request this version or use the Help > Check for Updates command to check whether you have the latest released version. The screenshots shown within this tutorial may vary across platforms and across different versions of Partek Genomics Suite.
The pathway enrichment analysis illustrated in this user guide uses the miRNA Expression and Integration with Gene Expression data set. This data set is also used in our miRNA data analysis tutorial.
Download and save the zipped project folder in an accessible location on your computer. The project folder for the tutorial will be created in the same location the zipped project folder is stored.
Import the project using the zipped project importer in Partek Genomics Suite.
Select File from the main toolbar
Select Import
Select Zipped Project...
Choose the zipped project folder, miRNA_tutorial_data
The project will open with three spreadsheets:
1. Affy_miR_BrainHeart_intensities,
2. Affy_HuGeneST_BrainHeart_GeneIntensities,
3. ANOVAResults gene.
If you need additional assistance, please visit our support page to submit a help ticket or find phone numbers for regional support.
Before performing pathway enrichment, we need to create a gene list from the ANOVA results.
Select Gene Expression from the workflows drop-down menu
Select the ANOVAResults gene spreadsheet
Select Create Gene List from the Analysis section of the Gene Expression workflow
Select Brain vs. Heart from the List Manager dialog (Figure 1) leaving the other options as defaults
Select Create
Figure 1. Configuring the list manager dialog
A new list of 420 genes will be created as a child spreadsheet of 1 (ANOVAResults gene).
Select Close to exit the List Manager dialog
Select the new gene list, Brain vs. Heart
Select Pathway Analysis from the Biological Interpretation section of the Gene Expression workflow
Select Next > to continue with Pathway Enrichment
Pathway Enrichment is the only option available for a gene list. To learn more about the other option, Pathway ANOVA, see the Gene Ontology ANOVA tutorial, which follows the same procedure as Pathway ANOVA.
Select Next > to continue with the Brain vs. Heart spreadsheet
Select Next > to continue with default settings for Fisher's Exact test
Select Next > to continue with Homo sapiens and 4. Gene Symbol as parameters
Partek Pathway will now open. If this is your first time using Partek Pathway on the selected species, Partek Pathway will automatically download the KEGG information needed for the analysis. Once the pathway enrichment calculation has been performed, a new spreadsheet, Pathway-Enrichment.txt, will be added as a child spreadsheet of Brain vs. Heart and Partek Pathway will launch (Figure 2).
Figure 2. Partek Pathway displaying the most significantly enriched pathway from the gene list
The pathway currently displayed has the highest enrichment score. Both Partek Genomics Suite and Partek Pathway offer options for analyzing the results of pathway enrichment analysis. The next two sections of the user guide will show the options for analyzing the results of pathway enrichment in each program.
If you need additional assistance, please visit our support page to submit a help ticket or find phone numbers for regional support.
Pathway enrichment generates a results spreadsheet, Pathway-Enrichment.txt, visible in both Partek Genomics Suite (Figure 1) and in Partek Pathway.
Figure 1. The pathway enrichment spreadsheet is visible in both Partek Genomics Suite (shown here) and Partek Pathway
The spreadsheet includes 13 columns with information for each pathway represented in the source gene list.
1. Pathway Name - the name of the KEGG pathway
2. Database - the source database for the pathway annotation
3. Enrichment score - the negative natural log of the enrichment p-value derived from the contingency table (Fisher's Exact test) or the Chi-squared test
4. Enrichment p-value - the enrichment p-value derived from the contingency table (Fisher's Exact test) or the Chi-squared test
5. % genes in pathway that are present - the percentage of genes from the pathway that are present in the source gene list
6. Tissue score, 7. Replicate score, 8. Brain vs. Heart score - for each factor, interaction, and contrast in the ANVOA results spreadsheet, a separate score is calculated. This is derived form the negative log (base 10) of the average p-value for genes within the pathway for each factor. A high score indicates that the genes that fall into the pathway have a low p-value for the given factor.
9. # genes in list, in pathway - number of genes from the list in the pathway
10. # genes not in list, in pathway - number of genes from the pathway, not in the list
11. # genes in list, not in pathway - number of genes in list, not in the pathway
12. # genes, not in list, not in pathway - number of genes not in the pathway or the list that are included in KEGG database pathways for the species
13. Pathway ID - KEGG pathway ID
In Partek Genomics Suite, we can view several new options that are available for each pathway (row) in the Pathway-Enrichment.txt spreadsheet.
Right-click the row header of any row in the Pathway-Enrichment.txt spreadsheet (Figure 2)
Figure 2. The Pathway-Enrichment.txt spreadsheet in Partek Genomics Suite
The new options include:
Export genes in pathway, which creates a child spreadsheet of Pathway-Enrichment.txt that contains all the genes from the selected pathway(s) (Figure 3). This new spreadsheet includes gene symbols and their pathway.
Figure 3. Spreadsheet with all genes in pathway. Includes gene symbols and pathway.
Export genes in list and in pathway, which creates a child spreadsheet of Pathway-Enrichment.txt that contains the genes from your list that are present in the selected pathway(s) (Figure 4). This new spreadsheet includes gene symbols and their pathway.
Figure 4. Spreadsheet with genes only in list and pathway. Includes gene symbols and pathway.
Create Gene List, which creates a new child spreadsheet of the ANOVA results spreadsheet that contains the genes from your list that are present in the selected pathway(s) (Figure 5). This new spreadsheet includes all information for each gene from the ANOVA results spreadsheet. However, this list does not indicate the pathway of each gene.
Figure 5. Spreadsheet with genes in list and pathway. Includes all information from ANOVA results for each gene.
Show Pathway, which opens the selected pathway map in Partek Pathway.
If you need additional assistance, please visit our support page to submit a help ticket or find phone numbers for regional support.
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.
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)
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.
If you need additional assistance, please visit our support page to submit a help ticket or find phone numbers for regional support.
Select () to activate Selection Mode
Selecting () activates Navigation Mode. This enables navigation on large pathway diagrams by left-clicking and dragging to move the view.
Select () to open the search panel
Select () to search
Select () to minimize the Search panel
Select () in the upper left-hand corner of the Partek Pathway window
