Can I create a duplicate/copy of an entity?
Yes, you can clone an entity in a pathway. To perform this, first the entity must have multiple relations. Entity cloning makes a visual copy of...
Can I display the trend of my intensity data for individual probes on the graphical view?
Yes, you can display your intensity data in a diagram view when you have imported intensity or log-intensity data into Pathway Studio Explore.
Diagrams show...
Can I select all the relationships for one specific entity in a complex pathway graph?
You can easily select all the relationships for one entity by performing the following steps:
1. In the pathway view select the entity of...
Can I view two pathways at the same time?
Yes, you can view two (or more) pathways at the same time. Simply select: Cascade Document Windows or Tile Document Windows from the Windows menu above...
Do relations to a functional class in a pathway include known relations to the proteins contained in the functional class?
Functional classes are a recognized type of entity within Pathway Studio Explore. Relations to the functional class are specifically for the functional...
How are Gene Set Enrichement Analysis and Sub-Network Enrichement Analysis calculated?
Sub-Network Enrichment Analysis (SNEA)
The following steps describe the computational steps performed in SNEA.
1.) Preparation of Sub-NetworksSNEA...
How are the Functional Classes colorized with experimental data when they contain more than one measured gene/protein?
A Functional Class can contain multiple proteins. By default, the color of this entity will be the color of the gene/protein that has the lowest p-value, if...
How can I access the literature and the number of references supporting a relation in Pathway Studio Explore
There are different options to access the literature and the number of references supporting a relation in Pathway Studio Explore:1. From the Graphical View,...
How can I add proteins to a functional class?
You can add proteins to an existing functional class or a newly created functional class by doing the following:
1. Open a new pathway and add to the pathway...
How can I attribute a specific shape to all miRNA in the ResNet Explore database?
In ResNet Explore database, miRNA belongs to the protein entity category. By default, the miRNA shape is an ellipse, the generic protein shape in ResNet....
How can I back up my data in Pathway Studio Explore?
There is two options to back up your data stored in the ResNet Explore database:
Option1 (recommended)
Backing up pathways and groups that you created...
How can I change the font size for the entities on a pathway?
By default the font size for the entities on a pathway is set in order that the text fit the smallest entity. To change the font size for the all the...
How can I change the style of an entity on a pathway?
Font, shape and color of an entity can be modified.1. Select your entity.
2. Click on the button ‘style’ located in the main visualization toolbar from...
How can I combine canonical pathways to build a model pathway for my research of interest?
Pathway Studio includes canonical metabolic and signaling pathways that have been curated by our scientists. You can edit, expand, and modify these...
How can I customize metabolic pathways (to look similar to Ariadne metabolic pathways)?
You can customize the layout of these pathways (Figure 1 - Ariadne Metabolic Pathway Example) you have built by performing the following steps:
Step 1 –...
How can I export a list of entities that I have selected in a pathway?
There is two options to export selected entities from a pathway:
Export a selection to Excel from the Entity Table View
1. Select the desired entities in...
How can I migrate Pathway Studio Explore to another PC?
The migration procedure is comprised of two major stages – transferring the user data and transferring the license.
1. Migrating...
How can I permanently delete a relation or entity from the ResNet database?
When you delete a relation or entity from a pathway view, it is only removed from that specific pathway but still remains in the ResNet database.
To...
How can I see the connectivity of an entity in ResNet or in a specific pathway?
There are many places in the interface where you can see information about the connectivity of an entity including:
1. Right click on an entity in a...
How can I set the same size for entities on a pathway?
1. Select all the entities you want to resize on your pathway.- All selected entities will have a blue halo around them.- One of these entities is...
