How can I set the same style for multiple entities on a pathway?
1. First set the style for only one of your entities of interest.- Select one entity
- Click on the button ‘style’ located in the main visualization toolbar...
How confident am I in the accuracy of a relationship?
Usually the number of references which are associated with this relationship gives an indication of the accuracy of the relationship.
As a rough guide,...
How do I export a pathway?
Select the file for export and select Export. A menu box appears with 3 export options. The first two options export the file as a *.gpp file that can...
How do I export an image of my pathway?
There are four options for exporting an image of your pathway:
- Copy Picture to clipboard…: the picture is copied to your clipboard and can be...
How do I find the intersection between the entities of a group and a pathway?
You can select the members of a pathway that overlap with a group by performing the following steps:
1. Right-click on the group icon in the explorer...
How do I find the intersection between two lists of groups?
Follow these steps to find the intersection between two lists of groups:
1. Open both list of groups in the list pane (ex. the results of a GSEA...
How do I find the overlap between two groups?
1. Select the first group by navigating to the folder where the group resides. (Figure 1).
2. Copy to clipboard all the members of the first group. There is...
How do I find the overlap between two pathways?
First, ensure both pathways are in the same folder. Select both pathways (hold the Ctrl button down while successively selecting both with the mouse). Next,...
How do I import a list of proteins?
In the database pane, select Import. From the drop-down menu select “Gene List”. The following dialog box appears (Figure 1).
Identifies such...
How do I make a publication quality (high resolution) image of a pathway?
There is two options to obtain a publication quality image of a pathway:
Option 1:1. Open your pathway2. Place your mouse pointer in a white area of the...
How do I save the list of proteins/entities that are the results of my database search?
You can save the result of a database query by performing the following steps:1. Open a New Group window by selecting “New Group” in the Home tab2. Select...
How do I save the results of Gene Set Enrichment Analysis, Sub-Network Enrichment Analysis or Find Pathway/Groups Enriched with Selected Entities?
For each of these analysis, the results are displayed in the list pane. This table of results is not saved in Pathway Studio Explore.
To save the...
How do I share a pathway with someone that doesn’t have Pathway Studio?
You can create a HTML image file of your pathway using the option 'Save Pathway as HTML…'
You can access to this option in two different ways:
- click on...
How do I sort the experimental data according to p-values, names or fold-change?
Open the experiment in the experiment folder. Click on the appropriate header cell with the LEFT mouse button to perform the desired sorting function.
How do I zoom in or out on a pathway?
The Zoom function scrollbar can be found at the top right hand side above the graphic pane (Figure 1). Zoom in by moving the scroll bar from the - to +...
How is the localization of a protein determined in the Layout by Localization option for viewing a pathway?
Pathway Studio Explore utilizes the Gene Ontology cellular component to assign its cellular localization for the Layout by Localization visualization. ...
How often is the Gene Ontology updated?
Gene Ontology and Entrez Gene IDs are updated when major ResNet updates are released. Currently that is approximately once a year.
How to Resolve the "Unrecognized datasource" error in Pathway Studio Explore?
Description
When a user tries to access the ResNet Explore database in Pathway Studio Explore, the following message is...
Is multiple testing correction performed on the calculated p-values?
There are multiple p-values reported in the analysis tools in Pathway Studio Explore:
For Fisher's analysis, p-values are from Fisher exact test, no mutiple...
What Affymetrix Chipsets are included in the Affymammal mapping file?
Human Genome U95 Set Human Genome U133 Human Genome U133A Human Genome U133A 2.0 Human Genome U133 Plus 2.0 Human Genome...
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