Showing Category: Experimental Data Analysis
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.
Diagrams show the...
Does Pathway Studio support import for Affymetrix GeneChip HG_U95Av1 and MU_72v1?
Yes. Pathway Studio does support import for these withdrawn chips, however Ariadne does not have access to the .CDF files, required to analyze these...
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
There are different options to access the literature and the number of references supporting a relation in Pathway Studio:1. From the graphical view, put your...
How do I find the overlap between two groups?
Select the first group by navigating to the folder where the group resides. (Figure 1).
Open the file to see the tabular view of all the entities in the...
How do I find the subset of genes in an ontology group that identified in a GSEA analysis or a Fisher’s Exact test that are included in my experimental data list?
To find the overlap between the members of a group and the proteins in an experimental data set, do the following:
1. ...
How do I import a list of proteins?
In the database pane, select Import. From the drop-down menu select “Gene List”. The following dialog box appears (Figure 1).
Identifies such...
How do I save the list of proteins/entities that are the results of my database search?
You can save a group of entities identified from a database query by the following steps: open a New Group window by selecting “New Group” in the database...
How do I save the results of Gene Set Enrichment Analysis, Sub-Network Enrichment Analysis or Find Pathway/Groups Enriched with Selected Entities?
For each of these analysis, the results are displayed in the list pane. This table of results is not saved in Pathway Studio.
To save the results of any...
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.
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...
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 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 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 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 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 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,...
