Showing Category: Knowledge Base
How do I share a pathway with someone that doesn’t have Pathway Studio?
This can be done by right-clicking on the pathway image and selecting “Save Pathway as HTML” The resultant file and directory can be zipped and...
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 use MedScan to read a document I have on my local drive?
You can use MedScan to extract relationships for an individual file or from all files found in a directory. Files can be html or text or *.pdf documents (note:...
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 (i.e. red arrow – Figure 1). Zoom in by moving the scroll bar...
How is the localization of a protein determined in the Layout by Localization option for viewing a pathway?
Pathway Studio utilizes the Gene Ontology cellular component to assign its cellular localization for the Layout by Localization visualization. Keep in...
How often is ResNet Mammalian updated?
Currently this is done at 3 monthly intervals. You can download each quarterly ResNet update from the Ariadne website: www.ariadnegenomics.com. Log...
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 often is the ResNet Plant database updated?
The ResNet Plant database is updated twice a year.
For more information about ResNet Plant 2.1 see the Technical Support Bulletin describing this database in...
How to Enable the Model Organism Cartridges in MedScan Reader 2.1 (or higher)
Previous to Pathway Studio 6.1, support for the knowledge recovery for model organisms, Drosophila, C.Elegans, and Yeast was “hardcoded” into the MedScan...
How to Resolve the "Unrecognized datasource" error in Pathway Studio 6, Desktop Edition
Description
When a user tries to access the Mammalian ResNet 6 database in Pathway Studio 6, Desktop edition, 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:
For Fisher's analysis, p-values are from Fisher exact test, no mutiple testing...
ResNet 6 database fails to open when Pathway Studio Desktop is installed from a network DVD drive
Description
When Pathway Studio 6, Desktop Edition, is installed from a network DVD or from a local/network folder with the installation DVD content, the...
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...
What Affymetrix chipsets are included in the Affyplant mapping file?
What are the definitions of the relationship types?
MolTransport: Indicates that the regulator changes the localization of the target. Describes events of molecular translocation, export, import or...
What are the full text journals included in ResNet 6.0?
What are the full text journals included in ResNet Plant 2.1?
1. Annals of Botany2. Crop Science3. Journal of Experimental Botany4. New Phytologist5. Plant Cell6. Plant, Cell and...
What are the user roles in Pathway Studio Enterprise?
In a Pathway Studio Enterprise database, user accounts can be set up with one or more user roles. User roles are not cumulative and must be granted separately....
What do I do if the import of a RNEF file fails with the "illegal XML character" error?
When an input RNEF file contains a character non-compliant with XML standard, its import into Pathway Studio Desktop database fails with...
What does “Expand the content of functional classes and complexes in target gene sets” in the Fisher’s Exact Test and Gene Set Enrichment Analysis mean?
In both analyses: Find Pathways/Groups Enriched with Entities (the Fisher’s Exact Test) and Gene Set Enrichment Analysis, the algorithms identify when the...
