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What are the definitions of the relationship types?

Binding:  Physical interaction between molecules.Chemical Reaction:  Symbolizes either enzyme catalyzed or spontaneous chemical reaction, i.e....

10/03/2008 Category: Working with Pathways

What are the full text journals included in ResNet 7 Explore?

1.    Am J Respir Cell Mol Biol2.    Am J Transplantation3.    ATVB 4.    Biology of...

09/03/2008 Category: ResNet Databases and Ontologies

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 Explore database fails with...

06/08/2009 Category: Working with Pathways

What is Ariadne Ontology?

Ariadne has prepared an organization of genes/miRNAs for use in interpretation of experimental data, simplification of pathway diagrams, and summarization of...

09/03/2008 Category: ResNet Databases and Ontologies

What is Gene Ontology?

Gene Ontology is a controlled vocabulary (ontology) that describe gene products in terms of their associated:

biological processes;cellular...

06/25/2008 Category: ResNet Databases and Ontologies

What is the difference between the Fisher's Exact Test and Gene Set Enrichment Analysis?

Fisher’s Exact Test (Find Pathways/Groups Enriched with Selected Entities)

Fisher's exact test is a statistical test used to determine if there are nonrandom...

11/26/2008 Category: Experimental Data Analysis

What is the source of the cellular processes in ResNet?

The cellular process categories and associated aliases come directly from the Gene Ontology without further annotation or curation by Ariadne.

06/15/2009 Category: Working with Pathways, ResNet Databases and Ontologies

What is the source of the data in the AveragedTissues experiment found in the Experiment folder in ResNet Explore?

1. Several tissue profiling microarray experiments with different normal human tissue samples have been selected from GEO database. For the purpose of more...

06/19/2009 Category: Experimental Data Analysis

What should I do when the computer has prompted me to reboot several times during Pathway Studio Explore installation?

Description:

The message reads “The computer restart is pending. To continue the installation, please restart your computer and run the installer...

03/24/2010 Category: Installation and Maintenance

What steps can I take to reduce the size of a large network?

When you are mining the ResNet database to build interesting networks, you may find, from time to time, that the resultant network you have created has a large...

07/16/2009 Category: Working with Pathways

Where can I find the Pathway Studio Explore End-User License Agreement?

If you have the Pathway Studio Explore installed, you can find the Pathway Studio End-User License Agreement here:

C:\Program Files\Ariadne Genomics\EZ...

01/24/2009 Category: Installation and Maintenance

Why do I see two arrow heads for a relation I have created?

The relation arrow includes in “intermediate point” which then allows for the instances of three way (or more) connectivity (such as rendering a metabolic...

04/01/2009 Category: Working with Pathways

Why do some proteins have three different Entrez Gene IDs?

ResNet contains information for human, mouse and rat proteins.  When an Entrez GeneID exists in each species for a protein, all three IDs will be listed...

08/05/2008 Category: ResNet Databases and Ontologies, Experimental Data Analysis

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