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 Explore.
Diagrams show...
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 Explore
There are different options to access the literature and the number of references supporting a relation in Pathway Studio Explore:1. From the Graphical View,...
How do I find the overlap between two groups?
1. Select the first group by navigating to the folder where the group resides. (Figure 1).
2. Copy to clipboard all the members of the first group. There is...
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 the result of a database query by performing the following steps:1. Open a New Group window by selecting “New Group” in the Home tab2. Select...
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 Explore.
To save the...
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 Explore:
For Fisher's analysis, p-values are from Fisher exact test, no mutiple...
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 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 Explore?
1. Several tissue profiling microarray experiments with different normal human tissue samples have been selected from GEO database. For the purpose of more...
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...
