Msigdb browser

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Use the Browse MSigDB page to explore the gene sets and to export the gene sets of interest to gene set files that can be used with the gene set enrichment analysis. To display the gene sets on the Browse MSigDB page, click the Load database button:

Use the fields at the top of the page to filter the gene sets displayed in the table:

        The filter field is a text filter. As you enter text in the field, GSEA updates the list of gene sets to show only those that match that text. To change the text search options, click on the magnifying glass, as shown below:

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The filter shown above uses the default options All, Case insensitive, and Match anywhere to display all gene sets that have the characters “ca” anywhere in any column. To display gene sets whose names begin with the lowercase characters “ca”, click the NAME, Case sensitive, and Match from start options.

        The QuickFilterPane filters gene sets based on the values in four key columns. When you select a value for a column in the QuickFilterPane, GSEA updates the list of gene sets to show only those that have the selected value in that column. For example, to display only Human gene sets, select Human  from the Organism column in the QuickFilterPane.

The Deep Search Options provide more advanced search options. When you select one of these options, GSEA prompts you for the search criteria and a name for the search results. GSEA performs the search and displays the results in a new tab in the MSigDB page identified by the name you supplied. For example, the figure below shows gene sets that contain the MEST gene. To view the initial MSigDB page, click the tab on the left; to view your search results, click the tab on the right. (The two tabs are circled for clarity.)

        Search by keyword prompts you for a keyword and a name for the search results. GSEA finds all gene sets that contain the keyword in **abstract or MeSH** -- is this only for pubMed?

        Find Sets that overlap with my set prompts you for a gene set and a name for the search results. All genes in the gene sets should be specified as HUGO gene symbols. You can select a gene set that you already created in memory or enter the genes for gene set:

         GeneSets(grp), which lists ** these are always in mem lists created by GSEA?**

         Text Entry, which allows you to create a gene set by entering the genes for that gene set; the gene set is created in memory and deleted when you exit from GSEA

        Find sets that contain this gene prompts you for a gene (case insensitive HUGO gene symbol) and a name for the search results. GSEA finds all gene sets that contain the specified gene.

To export gene sets from the MSigDB to a gene set file that can be used with GSEA:

1.      Select one or more of the gene sets in the table on the MSigDB page. To select multiple gene sets, use SHIFT-Click or CTRL-click.

2.      Click Export as GeneSetMatrix.

3.      Select the target chip; that is, the feature identifiers that you want to use in the gene set file. Typically, you want to select Gene Symbol.

4.      Select the file format for the gene set file. Typically, you want to select gmt.

5.      Enter a name for the gene set file.

6.      Click OK.

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