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Information is included in this section for connecting to GenePattern from caIntegrator. Directions for launching specific GenePattern tools from caIntegrator are included as well, but you may want to refer to additional GenePattern documentation
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You have two options for using GenePattern from caIntegrator:
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Option 1 – Use the web-interface of any available GenePattern instances. To use the public instance from Broad, first register for an account. In caIntegrator, enter the URL for connecting: http://genepattern.broadinstitute.org/gp/services/Analysis,
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then enter your user ID and password. - Option 2 – Use GenePattern on the grid.
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GenePattern Modules
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| {multi-excerpt-include: To launch the analyses described in this section, you must have a registered GenePattern account. For more information, see http://genepattern.broadinstitute.org/gp/pages/login.jsf Wiki Markup |
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- To configure the link for accessing GenePattern from caIntegrator, open the appropriate page as described in Analyzing Data with GenePattern.
- Select the study whose data you want to analyze in the upper right portion of the caIntegrator page.
- Click GenePattern Analysis in the left sidebar of caIntegrator. This opens the GenePattern Analysis Status page.
- Make sure GenePattern Modules is selected in the drop down list. Click New Analysis Job.
In the GenePattern Analysis dialog box, shown in the following figure, specify connection information and click Connect. Fields are described in the table following the figure.
Field
Description
Server URL
{multi-excerpt-include: Enter any GenePattern publicly available URL, such as http://genepattern.broadinstitute.org/gp/pages/login.jsf
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.GenePattern Username
Enter your GenePattern user name.
GenePattern Password
Enter your GenePattern password.
- After logging in with the GenePattern profile, the dialog box, shown in the following figure, expands to include fields for defining the GenePattern analysis.
Enter information for the following fields. Fields with a red asterisk are required.
Field
Description
Job Name*
Enter a unique name for the analysis
Analysis Method
Select any method from the drop down list. Click Analysis Method Documentation for descriptions of the different analysis methods.
Data
All genomic data is selected by default. Select from the list any list that has been created for this study.
cls
Select any annotation field.
The CLS file format defines phenotype (class or template) labels and associates each sample in the expression data with a label. It uses spaces or tabs to separate the fields. The CLS file format differs somewhat depending on whether you are defining categorical or continuous phenotypes:
Categorical labels define discrete phenotypes; for example, normal vs tumor).
Continuous phenotypes are used for time series experiments or to define the profile of a gene of interest (gene neighbors).Info title Note Most GenePattern modules are intended for use with categorical phenotypes. Therefore, unless the module documentation explicitly states otherwise, a CLS file should define categorical labels.
prediction.results.file
Enter the name of this file which is part of the output from a GenePattern module.
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Click Perform Analysis. Based on the analysis method you select, you may be asked to add more information for the analysis. For more information, refer to the GenePattern Help site: http://www.broadinstitute.org/cancer/software/genepattern/tutorial/gp_concepts
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Once the analysis is launched, caIntegrator returns to the GenePattern Analysis Status page where you can monitor the status of your current study, which is listed in the Analysis Method column. You can also view information about other GP analyses that have been run on this study. An example displays in the following figure.
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For more information, see GenePattern
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To perform a CMS analysis, follow these steps:
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You can configure GenePattern grid parameters for preprocessing the dataset in addition to PCA module parameters. For more information, see the GenePattern website
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To perform a PCA analysis, follow these steps:
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The GISTIC Module is a GenePattern tool that identifies regions of the genome that are significantly amplified or deleted across a set of samples. For more information, see GenePattern Module documentation
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To perform a GISTIC-supported analysis, follow these steps:
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Additionally, upon completion of a successful GISTIC anaylsis, caIntegrator automatically displays the two gene lists that it generates in the Gene List Picker so that you can use them in a caIntegrator query or plot calculation. The lists are visible only to your userID. For more information, see Choosing Genes. The genes will also display in Saved Copy Number Analyses in the left sidebar. See #Editing Editing a GISTIC Analysis.
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If samples from a copy number source are deleted, the GISTIC job in which they are appear is also deleted. |
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