1. GSEA Tutorial – Overview |
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The GSEA Desktop Application Tutorial provides a brief overview of the main features of the GSEA application. It is organized in a series of slides which may be navigated by pressing “Next”, or you may jump to any section of interest using the links to the left. For more detailed information, see theDocumentation page. ![]() |
2. GSEA Tutorial – Ways to Run GSEA |
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You can run GSEA in multiple ways:
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3. GSEA Tutorial – Launching GSEA |
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To launch GSEA:
When GSEA starts, the main window appears. The main components of the user interface are:
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5. GSEA Tutorial – Loading the P53 Sample Data |
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The GSEA web site provides several sample datasets that correspond to results from the GSEA Subramanian & Tamayo PNAS 2005 paper. For the tutorial, you will use the P53 sample data. To download the P53 sample files:
To load the P53 data into GSEA:
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9. GSEA Tutorial – Viewing Program Progress and Results |
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Use the Processes panel at the lower left corner to view the status of analyses run in this session, including the currently running analysis: ![]()
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11. GSEA Tutorial – Running the Leading Edge Analysis |
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After running a gene set enrichment analysis, you can use the leading edge analysis to examine the genes in the leading edge subsets of selected enriched gene sets. Genes that appear in multiple subsets are more likely to be of interest than those that appear in only one. To run a leading edge analysis, click the Leading Edge Analysis icon on the GSEA main page. When GSEA displays the Leading Edge Analysis page:
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12. GSEA Tutorial – Browsing MSigDB Gene Sets |
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The power of the gene set enrichment analysis is a function of how well your gene sets represent meaningful coordinated or concordant gene expression behavior that reflects actual biological processes or states. You are welcome to use curated gene sets from the Molecular Signature Database (MSigDB), which is maintained by the GSEA team. You can browse the MSigDB from the Molecular Signatures Database page of the GSEA web site or the Browse MSigDB page of the GSEA application. To browse the MSigDB from the GSEA application:
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GSEA exports the gene set files to your default output folder (Help>Show GSEA Output Folder). The gene set files are tab-delimited ASCII text files that can be viewed in Excel or NotePad. |
16. GSEA Tutorial – Creating Data Files for GSEA |
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The gene set enrichment analysis requires four files: an expression dataset file, phenotype labels file, gene sets file, and chip annotations file. All four files are tab-delimited ASCII text files that can be created and edited using Excel or any text editor.
For descriptions of all of the GSEA file formats, see Data Formats. For more information about creating the data files, see Preparing Data Files for GSEA in the GSEA User Guide. |
17. GSEA Tutorial – Examples from Published GSEA Results |
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The GSEA web site provides the datasets that correspond to results from the GSEA Subramanian & Tamayo PNAS 2005 paper:
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18. GSEA Tutorial – Getting Help for GSEA |
As you begin to use GSEA, you can get help in several ways:
Thanks for taking the time for this Quick Tour of GSEA. If you have questions, comments or suggestions, we’d like to hear them: gsea@broadinstitute.org. |
Main Page
GSEA Home | Downloads | Molecular Signatures Database | Documentation | Contact
Use the navigation bar on the left to display documentation on GSEA software, MSigDB database or GSEA/MSigDB web site. If you have comments or questions not answered by the FAQ or the User Guide, contact us: gsea@broadinstitute.org.
- When contacting our team with questions about java GSEA programs, please send the following information:
- your computer’s operation system
- version of java which you used to run GSEA
- detailed log transcript from the GSEA session in questionto view the log, click [+] at the bottom of main screen of GSEA java desktop application, copy the text to a separate file and attach it to your request
Where to start
If you are new to GSEA, see the Tutorial for a brief overview of the software. If you have a question, see the FAQ or the User Guide. The User Guide describes how to prepare data files, load data files, run the gene set enrichment analysis, and interpret the results. It also includes instructions for running GSEA from the command line and a Quick Reference section, which describes each window of the GSEA desktop application.
MSigDB gene sets
Current release of the Molecular Signatures Database (v5.0 MSigDB) contains 10,348 gene sets for use with GSEA. The best source of information about the gene sets is the MSigDB web site. In addition, an overview of MSigDB gene set collections can be found here
Please note that gene sets can change or become deprecated in subsequent releases of MSigDB. It is thus important to indicate version of MSigDB to fully reference gene sets used in your study.
Software
We provide the following software implementations of the GSEA method:
- Java desktop application — Easy-to-use graphical interface that can be run from the Downloads page. The User Guide fully describes this application (referred to as GSEA or GSEA-P).
- Java jar file — Command line interface that can be downloaded from the Downloads page. See Command Line Running GSEA from the Command Line in the User Guide for details. This might be useful for analyzing several datasets sequentially, analyzing large datasets, or running analyses on a compute cluster.
- R-GSEA — R implementation of GSEA that can be downloaded from the Downloads page. This implementation is intended for experienced computational biologists who want to tweak and play with algorithm. The R-GSEA Readme provides brief instructions and support is limited. Please note that this implementation has not been actively maintained since 2005.
- Java source code — Source code and JavaDoc for the Java jar file can be downloaded from the Downloads page. Further information can be foundhere and in the Release Notes.
Thank you for your interest in GSEA,
The GSEA Team