Difference between revisions of "Gene Set Pages"

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<h1><a name="_Toc127331832">Content</a></h1>
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[http://www.broadinstitute.org/gsea/ GSEA Home] |
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<p class="MsoNormal">The introduction to each section that has subsections, should provide hyperlinks to the subsections. </p>
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[http://www.broadinstitute.org/gsea/downloads.jsp Downloads] |
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<p class="MsoNormal">This section describes how to work with project directories in GenePattern:</p>
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[http://www.broadinstitute.org/gsea/msigdb/ Molecular Signatures Database] |
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<p class="MsoListBullet"><!--[if !supportLists]--><span style="font-family: Symbol;"><span style="">&middot;<span style="font-family: &quot;Times New Roman&quot;; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><!--[endif]--><a href="#_Opening_a_Project_Directory">Projects Pane</a></p>
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[http://www.broadinstitute.org/cancer/software/gsea/wiki/index.php/Main_Page Documentation] |
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<p class="MsoListBullet"><!--[if !supportLists]--><span style="font-family: Symbol;"><span style="">&middot;<span style="font-family: &quot;Times New Roman&quot;; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><!--[endif]--><a href="#_Opening_a_Project_Directory_1">Opening a Project Directory</a></p>
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[http://www.broadinstitute.org/gsea/contact.jsp Contact]
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<h2><a name="_Toc127331833"></a><a name="_Opening_a_Project_Directory"></a><a name="_Projects_Pane"></a><span style="">Projects Pane</span></h2>
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<br>
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<p class="MsoNormal">Blah, blah, blah.</p>
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<p>
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<h2><a name="_Toc127331834"></a><a name="_Opening_a_Project_Directory_1"></a><span style="">Opening a Project Directory</span></h2>
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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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<p class="MsoNormal">Blah, blah, blah.</p>
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<p>Each gene set page contains the following information:</p>
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<br />
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<p class="MsoNormal">&nbsp;</p>
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<h2>Gene Set Annotations</h2>
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<br />
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<dl>
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<p class="MsoNormal">&nbsp;</p>
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<dt>Standard name
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<br />
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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 class="MsoNormal">&nbsp;</p>
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<dt>Systematic name
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<br />
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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 class="MsoNormal">&nbsp;</p>
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<dt> Brief description
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<p class="MsoNormal">  </p>
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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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<h1><a name="_Toc127331829">Text Formats</a></h1>
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This description appears on the Browse MSigDB page of the GSEA application.
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<p class="MsoNormal">Within paragraph text, we use a number of character formats:</p>
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<dt> Full description or abstract
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<ul>
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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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    <li><!--[if !supportLists]--><span style="font-family: Symbol;"><span style="">&middot;<span style="font-family: &quot;Times New Roman&quot;; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><!--[endif]-->Hyperlinks: <span class="MsoHyperlink">hyperlink</span></li>
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<dt>Collection
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    <li><!--[if !supportLists]--><span class="brcode"><span style="font-size: 10pt; font-family: Symbol;"><span style="">&middot;<span style="font-family: &quot;Times New Roman&quot;; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span></span><!--[endif]-->Code and file names: <span class="brcode"><span style="font-size: 10pt;">br_code<o:p></o:p></span></span></li>
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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><!--[if !supportLists]--><span class="brGUI"><span style="font-family: Symbol; font-style: normal;"><span style="">&middot;<span style="font-family: &quot;Times New Roman&quot;; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span></span><!--[endif]-->For GUI items, like menus and buttons: <span class="brGUI">br_GUI</span><span class="brGUI"><span style="font-style: normal;"><o:p></o:p></span></span></li>
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<dt>Source publication
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    <li><!--[if !supportLists]--><span style="font-family: Symbol;"><span style="">&middot;<span style="font-family: &quot;Times New Roman&quot;; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><!--[endif]-->For menus, we use angle brackets, which need to be preserved: <span class="brGUI">File&gt;Open</span>. </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><!--[if !supportLists]--><span class="brvariable"><span style="font-family: Symbol; font-style: normal; text-decoration: none;"><span style="">&middot;<span style="font-family: &quot;Times New Roman&quot;; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span></span><!--[endif]-->For variables (this looks the same as GUI, but might in the future): <span class="brvariable">br_variable</span><span class="brvariable"><span style="font-style: normal;"><o:p></o:p></span></span></li>
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<dt>Exact source
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    <li><!--[if !supportLists]--><span style="font-family: Symbol;"><span style="">&middot;<span style="font-family: &quot;Times New Roman&quot;; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><!--[endif]-->For various reasons, most formats can be bold. So bold needs to be preserved.</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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</ul>
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<dt> Related gene sets
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<p class="MsoListContinue">Normal formats: <st1:city w:st="on"><st1:place w:st="on">Normal</st1:place></st1:city>, <span class="brcode"><span style="font-size: 10pt;">br_code, </span></span><span class="brGUI">br_GUI, </span><span class="brvariable">br_variable<o:p></o:p></span></p>
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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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<p class="MsoListContinue">Bold formats: <st1:city w:st="on"><st1:place w:st="on"><strong style="">Normal</strong></st1:place></st1:city><strong style="">, </strong><span class="brcode"><strong style=""><span style="font-size: 10pt;">br_code, </span></strong></span><span class="brGUI"><strong>br_GUI, </strong></span><span class="brvariable"><strong>br_variable</strong><o:p></o:p></span></p>
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<dt>External links
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<dd>When available, links to external websites with additional information about the gene set.
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<dt>Organism
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<dd>The organism that the experiment was conducted in.
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<dt> Contributed by
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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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<dt> Source platform
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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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<dt>Dataset references
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<dd>GEO or ArrayExpress links for associated microarray data where appropriate.
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</dl>
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<h2>Gene Set Actions</h2>
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<dl>
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<dt> Download gene set
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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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<dt>Annotate by computing overlaps
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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.
Retrieved from "https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=Gene_Set_Pages&oldid=4014"