What format(s) of experiment data can I upload into PS6 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...
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.
What is the source of the data in the AveragedTissues experiment found in the Experiment folder in ResNet 6?
1. Several tissue profiling microarray experiments with different normal human tissue samples have been selected from GEO database. For the purpose of more...
What is the source of the relationships in the ResNet Mammal databases?
ResNet 6 Mammalian includes molecular interactions, extracted by Ariadne’s MedScan (Natural Language Processing) technology, from over 17 million PubMed...
What is the source of the relationships in the ResNet Plant 2.1 database?
MedScan Dictionaries (Plant 2.1) are populated with all the gene symbols and aliases from Arabidopsis. When MedScan processes documents and encounters a...
What is the source of the signaling pathways in the ResNet Plant 2.1 database?
Ariadne has prepared and curated 17 signaling pathways that are included with Plant 2.1 database. The signaling process in plants is not as well...
What species are supported in the ResNet Plant 2.1 database?
Protein annotation is available for ten plant species (Arabidopsis, barley, corn, potato, rice, sorghum, soybean, tobacco, tomato, and wheat ), however most...
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...
What types of experimental data values can be imported into Pathway Studio?
1.) What are the basic types of numeric data supported for import by Pathway Studio
Pathway Studio supports import of signal intensity data,...
When I search for a term in Pathway Studio 6, I get a lot of records I don't expect. Is there a way to improve the search results?
By default, when you search in the left hand search dialog in Pathway Studio 6, the results include exact matches on the search term along with full-text...
Where can I find the Pathway Studio End-User License Agreement?
If you have the Pathway Studio Desktop or Pathway Studio PC Client installed, you can find the Pathway Studio End-User License Agreement here:
C:\Program...
Why can't I activate my Pathway Studio installation on my Vista computer even when using the Administrator account?
In Vista, programs are usually run with restricted privileges, even when using the administrator's account.
To run Pathway Studio with elevated privileges, do...
Why do I get different number of entities when querying the local ResNet database versus when querying the server ResNet database?
This is because the server database limits results to 1,000 entities for a regular user and 3,000 entities for a power user. If the number of entities...
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...
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...
Why does MedScan reader highlight some entities in the marked up text view but then does not list those same entities in the resultant Entity List in the Current Digest Pane (in the upper right)?
MedScan Reader will mark up all the entities that are recognized in the specific MedScan dictionary that is currently being used. The dictionary contains...
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