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 visit the download center of the support section.
How to Resolve the "Unrecognized datasource" error in Pathway Studio 7, Desktop Edition
Description
When a user tries to access the ResNet 7 database in Pathway Studio 7, the following message is displayed:
Unrecognized...
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 7 database fails to open when Pathway Studio Desktop is installed from a network DVD drive
Description
When Pathway Studio 7, 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?
Binding: Physical interaction between molecules.Chemical Reaction: Symbolizes either enzyme catalyzed or spontaneous chemical reaction, i.e....
What are the full text journals included in ResNet 7.0?
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...
What format(s) of experiment data can I upload into PS7 for analysis?
You can upload tab-delimited files, MS Excel files, Affymetrix .cel files or .chp files and GEO dataset SOFT files using the importer.
When importing...
What Illumina beadchip mapping files are available?
Human Ref-8_V3Human WG-6_V3Human Ref-8_V2Human WG-6_V2
Mouse Ref-8_V2Mouse WG-6_V2Mouse Ref-8_V1.1Mouse WG-6_V1.1
RatRef-12_V1
What is Ariadne Ontology?
Ariadne has prepared an organization of genes for use in interpretation of experimental data, simplification of pathway diagrams, and summarization of analysis...
What is Gene Ontology?
Gene Ontology is a controlled vocabulary (ontology) that describe gene products in terms of their associated:
biological processes;cellular...
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...
