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Each gene set in the MSigDB (Molecular Signature Database) is fully described by a gene set card. From this web site, use the&nbsp; [http://gsea.broad.mit.edu:8080/cancer/msigdb/ MSigDB page] to find a gene set. Click the gene set name to display its gene set card. Alternatively, from within the GSEA application, use the [http://www.broad.mit.edu/cancer/software/gsea/doc/GSEAUserGuideFrame.html?Browse_MSigDB_Page Browse MSigDB page] to browse gene sets and display gene set cards. <br />
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[[image:gene_set_card.gif]] **update** this is an edit<br />
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[[image:msigdb_local.gif]]<br />
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Each gene set card contains the following information:<br />
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<strong> Brief description</strong>: A brief description of the gene. This is the description that appears on the Browse MSigDB page of the GSEA application.<br />
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<strong> Full description or abstract</strong>: A more complete description of the gene set. For example, for gene sets linked to a PubMed entry, this field shows the abstract of that entry.<br />
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<strong>Collection</strong>: The collection that contains the gene set: Positional (C1), Curated (C2), Motif (C3), or Computed (C4). See the [http://gsea.broad.mit.edu:8080/cancer/msigdb/aboutCollections.jsp MSigDB Collections page] for a description of each collection.<br />
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<strong>Source publication</strong>: When available, a link to the source publication followed by a list of its authors. <br />
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<strong> Related gene sets</strong>: Other gene sets (if any) from this publication. Other gene sets (if any) from publications by one or more of these authors.<br />
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<strong>External links</strong>: When available, links to external websites that contain more information about the gene set.<br />
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<strong>Organism</strong>: The organism that the experiment was conducted in (generic for canonical pathways and ontologies).<br />
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<strong> Contributed by</strong>: Name of the person (or external database; for example, KEGG) who collected the gene set.<br />
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<strong> Source platform</strong>: Microarray platform that was used for expression profiling (for example, Affymetrix HU6800). Gene_Symbol is used if the gene set was not tied to a specific experiment (for example, for ontologies or a gene set from a review article).<br />
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<strong> Download gene set</strong>: Links to download the gene set in different formats: grp (group), text, gmt, or gmx. For descriptions of each format, see [[Data_formats|Data Formats]].<br />
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<strong>Annotate by computing overlaps</strong>: Displays the overlap (if any) between this gene set and the gene sets in the selected collection.<br />
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<strong>Compendia expression profiles</strong>: Displays a heat map showing how the genes in this gene set are expressed in the selected expression dataset.<br />
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<strong>Advanced query</strong>: Copies the genes in this gene set to the annotations page, where you can modify and/or further explore the gene set.<br />
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<strong>Gene families</strong>: Displays a functional overview of this gene set by  categorizing its members into a small number of gene families, where each gene family describes a collection of proteins that share a common  feature such as homology or biochemical activity.<br />
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<strong>Show x genes</strong>: Specifies the number (<strong>x</strong>) of genes in this gene set. Click the Show (Hide) link show (hide) to list each gene (HUGO gene symbols) followed by links to external websites for gene-centric information.  <br />
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Old Documentation Home page<br />
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<a href="http://www.broad.mit.edu/gsea/">GSEA Home</a> |  <a href="../../software/software_index.html">Software</a> | <a href="../../msigdb/msigdb_index.html">MSigDB</a> | Documentation | <a href="../../resources/resources_index.html">Resources</a>  <br />
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<table cellspacing="1" cellpadding="1" border="0" align="" summary="" style="width: 689px; height: 84px;">
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        <tr>
            <td><font size="4">[http://www.broad.mit.edu/cancer/software/gsea/doc/GSEAUserGuideFrame.htm User Guide]</font></td>
            <td><font size="4">[[Release_Notes|GSEA Release Notes]]</font></td>
            <td><font size="4">[[Gsea_Algorithm|GSEA Algorithm]]</font></td>
        </tr>
        <tr>
            <td><font size="4">[http://www.broad.mit.edu/cancer/software/gsea/doc/desktop_tutorial.html Tutorial]</font></td>
            <td><font size="4"><font size="4">[[Release_Notes|MSigDB Release Notes]]<br />
            </font></font></td>
            <td><font size="4">[http://www.broad.mit.edu/cancer/software/gsea/resources/datasets_index.html Example Datasets]</font></td>
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            <td><font size="4">[[FAQ]]</font></td>
            <td><font size="4">[[Gene_set_card_guide|Guide to Gene Set Cards]]</font></td>
            <td><font size="4">[[Gsea_papers|GSEA Papers]]</font></td>
        </tr>
    </tbody>
</table>
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<font size="3">To cite GSEA, please reference Subramanian, Tamayo, et al. ([http://www.pnas.org/cgi/content/abstract/102/43/15545 2005, PNAS 102, 15545-15550]).<br />
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<font size="4"><font size="3">If you have questions or comments, contact us: [mailto:gsea@broad.mit.edu gsea@broad.mit.edu].<br />
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