Quick Start

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.

Start the Web Client

To start the GenePattern Web Client:

1. Open a web browser, such a Mozilla Firefox, Internet Explorer, or Safari.


2. Enter the URL of the public GenePattern server: http://genepattern.broad.mit.edu/gp/.


3. Enter your user name and password and then click Sign In.
   If you do not have a GenePattern account, select Click to register.

   The Web Client start page appears.

   

• The Modules & Pipelines panel lists the analyses that you can run. By default, the analyses are organized by functional category.


• The center panel, which displays the welcome message, is the main display panel for the Web Client. The Web Client uses this panel to display information and to prompt you for input.


• The Recent Jobs panel lists the most recent analyses that you have run and their generated analysis results files. When you first start the Web Client, this panel is empty.


• The navigation bar provides access to other Web Client pages.

Run an Analysis

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:

1. In the Modules & Pipelines panel, under Gene List Selection, click ComparativeMarkerSelection.

   The analysis and its parameters appear in the center panel.

   



2. For the input file parameter, click the Specify URL radio button and enter the following URL: ftp://ftp.broad.mit.edu/pub/genepattern/datasets/all_aml/all_aml_train.res.


3. For the cls file parameter, click the Specify URL radio button and enter the following URL: ftp://ftp.broad.mit.edu/pub/genepattern/datasets/all_aml/all_aml_train.cls.

   



4. Click Run to start the analysis. The Web Client sends the analysis job to the GenePattern server and displays the ComparativeMarkerSelection Status page. After a few seconds, the GenePattern server finishes the analysis job and displays the results on the Status page.

   



5. Click Return to Modules & Pipelines Start to return to the Web Client start page.

View the Analysis Results

When you return to the Web Client start page, the Recent Jobs pane shows the ComparativeMarkerSelection analysis job that you ran on the GenePattern server and the associated analysis results files. To examine the results of the ComparativeMarkerSelection analysis results, use the ComparativeMarkerSelectionViewer module.

To run the ComparativeMarkerSelectionViewer:

1. In the Recent Jobs pane, click the icon next to the all_aml_train.comp.marker.odf results file. This displays a menu of the commands you can use to work with the file. (You may need to scroll your browser window to see the icon.)


2. Click the ComparativeMarkerSelectionViewer command.

   The ComparativeMarkerSelectionViewer and its parameters appear in the center pane. The comparative marker selection filename parameter is automatically set to the all_aml_train.comp.marker.odf results file.

   



3. For the dataset filename parameter, click the Specify URL radio button and enter the following URL: ftp://ftp.broad.mit.edu/pub/genepattern/datasets/all_aml/all_aml_train.res.

   This is the dataset file that you analyzed using the ComparativeMarkerSelection module.



4. Click Run to start the viewer.

   Viewers run on your desktop PC, not on the GenePattern server. The first time you run a viewer on your desktop, the following security message may appear.

   



5. If the security message appears, click Run to continue. The ComparativeMarkerSelectionViewer appears:

   



6. In the ComparativeMarkerSelectionViewer:
   • The Score column shows the value of the metric used to correlate gene expression and phenotype. A high score indicates correlation with the first phenotype (upregulated in ALL) and a low score indicates correlation with the second phenotype (upregulated in AML).
   
   
   • The middle columns, FDR through FWER, provide different ways to measure the significance of the score. The lower the value the more significant the result. For example, you might choose to measure significance using the false discovery rate (FDR) and set a significance cutoff of FDR < .05. Using this measure, you would focus on genes with the lowest and highest scores, where the measure of significance for the score was an FDR < .05.
   
   
7. To close the ComparativeMarkerSelectionViewer, select File>Exit.


8. In the Web Client, click Return to Modules & Pipelines Start to return to the Web Client start page.

   Notice that the ComparativeMarkerSelectionViewer analysis does not appear in the Recent Jobs pane. This is because the ComparativeMarkerSelectionViewer ran on your local PC, not on the GenePattern server.

Exit from the Web Client

When you are finished working with GenePattern, exit from the GenePattern Web Client:

1. Click Sign Out in the top right corner of the title bar.


2. Close the web browser window.

Learn More about GenePattern

The following documents provide more information 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 (gp-help@broad.mit.edu).