See the video tutorial: Getting Started
Note that this video tutorial was created with GenePattern 3.2
This brief tutorial introduces you to GenePattern by providing step-by-step instructions for running an analysis and viewing the results. In less than 10 minutes you'll run your first analysis and review the results.
Note that this hands on tutorial was created with GenePattern 3.6
To start GenePattern:
GenePattern displays its home page.
|Click the GenePattern icon to return to this home page at any time.|
|The upper right corner shows your user name.|
|The navigation bar provides access to other pages.|
|The Modules & Pipelines panel lists the analyses that you can run. Enter the first few characters of a module or pipeline name in the search box to locate that analysis. Click the all radio button to list the analyses alphabetically.|
|The center pane is the main display pane, which GenePattern uses to display information and to prompt you for input. Notice the protocols listed here.|
|The Recent Jobs panel lists the most recent analyses that you have run and their results files. The Uploads panel lists files that you have copied to the GenePattern server. When you start GenePattern for the first time, these panels are empty.|
As an example, you will run the ComparativeMarkerSelection analysis. This analysis finds the genes in a dataset file that are most closely correlated with the two classes of samples in that dataset. You will run the analysis on an example dataset, all_aml_train.res, that contains gene expression data from Golub and Slonim et al. (1999). In that paper, the authors used clustering and prediction algorithms to find genes that distinguish between two subtypes of leukemia, ALL and AML. The dataset consists of 38 bone marrow samples (27 ALL, 11 AML) obtained from acute leukemia patients.
To run the ComparativeMarkerSelection analysis:
GenePattern displays the ComparativeMarkerSelection parameters.
To examine the results of the ComparativeMarkerSelection analysis, run the ComparativeMarkerSelectionViewer:
GenePattern displays the ComparativeMarkerSelectionViewer parameters. The comparative marker selection filename parameter is automatically set to the all_aml_train.comp.marker.odf results file.
Viewers run on your desktop PC, not on the GenePattern server. The first time you run a viewer on your desktop, a security message similar to the following may appear.
On the home page, the Recent Jobs pane shows the analysis jobs that you have run on the GenePattern server and the associated analysis results files. Click the job name or number for an analysis to redisplay the Job Status page for that job.
To exit from GenePattern:
The following documents provide more information about GenePattern:
|Concepts||Introduces GenePattern: its primary objects (modules, pipelines, suites) and its client-server architecture. Other GenePattern documentation assumes that you are familiar with this information.|
|Video Tutorials||Lists the GenePattern training videos.|
|Tutorial||Provides a 40 minute hands-on tour of GenePattern.|
|User Guide||Fully describes GenePattern.|
|Modules||Lists the modules and pipelines available from the Broad Institute, with links to their documentation.|
|File Formats||Describes all file formats and provides instructions for creating input files for GenePattern.|
|Release Notes||Describes new features and known issues in the current release.|
|Frequently Asked Questions||Answers commonly asked questions about GenePattern.|
We welcome your feedback. If you have suggestions, comments, or questions that are not answered by the documentation, contact the GenePattern help desk (firstname.lastname@example.org).