Difference between revisions of "Gene Set Pages"

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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> | [[Main_Page|Documentation]] | <a href="../../resources/resources_index.html">Resources</a>  <br />
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[http://www.broadinstitute.org/gsea/ GSEA Home] |
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<br />
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[http://www.broadinstitute.org/gsea/downloads.jsp Downloads] |
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<p class="MsoListContinue">  </p>
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[http://www.broadinstitute.org/gsea/msigdb/ Molecular Signatures Database] |  
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<p style="" class="MsoNormal">Each gene set in the MSigDB (Molecular Signature Database) is fully described by a gene set card. To review the gene set cards:<br />
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[http://www.broadinstitute.org/cancer/software/gsea/wiki/index.php/Main_Page Documentation] |
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</p>
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[http://www.broadinstitute.org/gsea/contact.jsp Contact]
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<ol>
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<br>
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    <li>Click GeneSetCards at the top of this page. The web page displays gene set categories.<br />
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<p>
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    </li>
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Each gene set in the MSigDB (Molecular Signature Database) is fully described by a gene set page. From this web site, use the&nbsp; [http://www.broadinstitute.org/gsea/msigdb/ MSigDB page] to find a gene set. Click the gene set name to display its gene set page. Alternatively, from within the GSEA application, use the [http://www.broadinstitute.org/gsea/doc/GSEAUserGuideFrame.html?Browse_MSigDB_Page Browse MSigDB page] to browse gene sets and display gene set pages. </p>
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    <li>Click the double arrow next to a category to display the gene sets in that category.</li>
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<p>Each gene set page contains the following information:</p>
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    <li>Click a gene set name to display its gene set card.</li>
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</ol>
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<h2>Gene Set Annotations</h2>
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Alternatively, from within the GSEA application, use the Browse MSigDB page to browse gene sets and display gene set cards. For more information, see the [http://www.broad.mit.edu/cancer/software/gsea/doc/GSEAUserGuideFrame.html?Browse_MSigDB_Page Browse MSigDB Page] of the <span style="font-style: italic;">GSEA User Guide</span>.<br />
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<dl>
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<br />
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<dt>Standard name
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[[image:gene_set_card.gif]]
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<dd>Gene set name in the database. Gene sets can have their names changed after reviewing or to correct potential errors.
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<p style="" class="MsoNormal">Each gene set card contains the following information:</p>
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<dt>Systematic name
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<p style="" class="MsoNormal"><strong style="">Standard name</strong>: Gene set name.</p>
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<dd>This serves to uniquely identify a gene set in MSigDB. Unlike standard names, systematic name never changes.
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<p style="" class="MsoNormal"><strong style="">LSID</strong>: Internal identifier for the gene set.</p>
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<dt> Brief description
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<!--[if !supportLists]--><!--[endif]-->      <!--[if !supportLists]-->
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<dd>A one sentence description of the gene set to convey "at a glance" information about gene sets.
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<p style="" class="MsoNormal"><strong style="">Brief description</strong>: A brief description of the gene. This is the description that appears on the Browse MSigDB page of the GSEA application. </p>
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This description appears on the Browse MSigDB page of the GSEA application.
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<p style="" class="MsoNormal"><strong style="">Category</strong>: The category of the gene set: Positional (C1), Curated (C2), Motif (C3), or Computed (C4). </p>
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<dt> Full description or abstract
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<p class="MsoNormal"><strong style="">Sub-category</strong>: The subcategory of the gene set: <br />
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<dd>An extensive annotation of the gene set. For gene sets curated from publications, this field contains publication's abstract.
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</p>
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<dt>Collection
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<ul>
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<dd>The collection that contains the gene set: Positional (C1), Curated (C2), Motif (C3), Computed (C4), GO (C5) or Oncogenic signatures (C6). In appropriate cases, this will also include the sub-collection hierarchy that contains the gene set. See the [http://www.broadinstitute.org/gsea/msigdb/collections.jsp MSigDB Collections page] for detailed descriptions of each collection.
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    <li>for C1, always Cytogenic; <br />
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<dt>Source publication
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    </li>
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<dd>When available, a link to the source publication followed by a list of its authors.  
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    <li>for C2, Animal Model, Clinical, Experimental pertuberation, Expert curation, Misc, Ontology, Pathway database, or Review paper; <br />
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<dt>Exact source
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    </li>
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<dd>For gene sets curated from publications, this field indicates the exact source of a gene set in the publication (e.g., Table 1).
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    <li>for C3, Representative motifs or Transfac; and <br />
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<dt> Related gene sets
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    </li>
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<dd>Other gene sets (if any) from the same publication or from publications shared with at least one of the authors.
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    <li>for C4, always Neighborhood.</li>
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<dt>External links
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</ul>
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<dd>When available, links to external websites with additional information about the gene set.
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<p class="MsoNormal"><span style="font-weight: bold;"><strong style="">Full description or Abstract</strong>:</span> 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.</p>
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<dt>Organism
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<p class="MsoNormal"><strong style="">Publication URL</strong>: When available, a link to the source publication. For example, for gene sets linked to a PubMed entry, this is a link to the Entrez record of the source publication. </p>
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<dd>The organism that the experiment was conducted in.
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<p class="MsoNormal"><strong style="">External links</strong>: When available, links to external websites that contain more information about the gene set.</p>
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<dt> Contributed by
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<p class="MsoNormal"><strong style="">Keywords &amp; MeSH headings</strong>: Keywords derived from MeSH [http://www.nlm.nih.gov/mesh/MBrowser.html National Library of Medicine] and/or manually entered.</p>
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<dd>Name of the person, institution, or external database (such as Reactome) who contributed the gene set.
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<p class="MsoNormal"><strong style="">Organism</strong>: The organism that the experiment was conducted in (<em>generic</em> for canonical pathways and ontologies).</p>
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<dt> Source platform
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<p class="MsoNormal"><strong style="">Contributed by</strong>: Name of the person (or external database; for example, KEGG) who collected the gene set.</p>
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<dd>This field indicates kind of original members as they appeared in the gene set source. For microarray data, this often indicates microarray platform when original members are probe set IDs or other kind of platform specific identifiers. SEQ_ACCESSION indicates NCBI GenBank accession numbers.
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<p class="MsoNormal"><strong style="">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).</p>
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<dt>Dataset references
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<p class="MsoNormal"><strong style="">Download</strong>: Links to download the gene set in different formats:<br />
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<dd>GEO or ArrayExpress links for associated microarray data where appropriate.
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</p>
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</dl>
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<p class="MsoNormal"> </p>
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<ul>
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<h2>Gene Set Actions</h2>
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    <li><!--[if !supportLists]--><span style="">grp: lists the genes in the gene set in plain text format</span></li>
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<dl>
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    <li><!--[if !supportLists]--><span style=""><!--[endif]-->xml: gene set definition formatted with structure annotation </span></li>
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<dt> Download gene set
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    <li><!--[if !supportLists]--><span style="">map: lists the genes in the gene set with details of the mapping between the originally reported accessions and their HUGO gene symbols</span></li>
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<dd>Links to download the gene set in different formats: GRP (group), TXT, GMT, GMX, or XML. For descriptions of each format, see [[Data_formats|Data Formats]].
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</ul>
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<dt>Annotate by computing overlaps
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<p class="MsoNormal"><strong style="">Genes</strong>: Displays the number of genes (HUGO gene symbols) and accessions (native accessions) in this gene set; if each native accession mapped to a unique HUGO gene symbol, these values are identical. Click the Toggle View link to show/hide the genes in the gene set along with their descriptions and links to external websites for gene-centric information. </p>
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<dd>Displays the overlap (if any) between this gene set and the gene sets in the selected collection.
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<dt>Compendia expression profiles
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<dd>Produce a heat map showing how genes in this gene set are expressed in the selected compendium dataset.
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<dt>Advanced query
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<dd>Copies the genes in this gene set to the annotations page, where you can modify and/or further explore the gene set.
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<dt>Gene families
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<dd>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.
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</dl>
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<h2>Gene Set Members</h2>
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<dl>
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<dt>Show members
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<dd>Toggle the Show (Hide) link show (hide) gene set members followed by links to external websites for gene-centric information.
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</dl>
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<h2>Other</h2>
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<dl>
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<dt>Version history
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<dd>Lists the history of this gene set (when it was introduced and any modifications) where available.
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</dl>

Latest revision as of 02:20, 25 September 2016

GSEA Home | Downloads | Molecular Signatures Database | Documentation | Contact

Each gene set in the MSigDB (Molecular Signature Database) is fully described by a gene set page. From this web site, use the  MSigDB page to find a gene set. Click the gene set name to display its gene set page. Alternatively, from within the GSEA application, use the Browse MSigDB page to browse gene sets and display gene set pages.

Each gene set page contains the following information:

Gene Set Annotations

Standard name
Gene set name in the database. Gene sets can have their names changed after reviewing or to correct potential errors.
Systematic name
This serves to uniquely identify a gene set in MSigDB. Unlike standard names, systematic name never changes.
Brief description
A one sentence description of the gene set to convey "at a glance" information about gene sets. This description appears on the Browse MSigDB page of the GSEA application.
Full description or abstract
An extensive annotation of the gene set. For gene sets curated from publications, this field contains publication's abstract.
Collection
The collection that contains the gene set: Positional (C1), Curated (C2), Motif (C3), Computed (C4), GO (C5) or Oncogenic signatures (C6). In appropriate cases, this will also include the sub-collection hierarchy that contains the gene set. See the MSigDB Collections page for detailed descriptions of each collection.
Source publication
When available, a link to the source publication followed by a list of its authors.
Exact source
For gene sets curated from publications, this field indicates the exact source of a gene set in the publication (e.g., Table 1).
Related gene sets
Other gene sets (if any) from the same publication or from publications shared with at least one of the authors.
External links
When available, links to external websites with additional information about the gene set.
Organism
The organism that the experiment was conducted in.
Contributed by
Name of the person, institution, or external database (such as Reactome) who contributed the gene set.
Source platform
This field indicates kind of original members as they appeared in the gene set source. For microarray data, this often indicates microarray platform when original members are probe set IDs or other kind of platform specific identifiers. SEQ_ACCESSION indicates NCBI GenBank accession numbers.
Dataset references
GEO or ArrayExpress links for associated microarray data where appropriate.

Gene Set Actions

Download gene set
Links to download the gene set in different formats: GRP (group), TXT, GMT, GMX, or XML. For descriptions of each format, see Data Formats.
Annotate by computing overlaps
Displays the overlap (if any) between this gene set and the gene sets in the selected collection.
Compendia expression profiles
Produce a heat map showing how genes in this gene set are expressed in the selected compendium dataset.
Advanced query
Copies the genes in this gene set to the annotations page, where you can modify and/or further explore the gene set.
Gene families
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.

Gene Set Members

Show members
Toggle the Show (Hide) link show (hide) gene set members followed by links to external websites for gene-centric information.

Other

Version history
Lists the history of this gene set (when it was introduced and any modifications) where available.
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