Difference between revisions of "Gene Set Pages"
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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 [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> | Each gene set in the MSigDB (Molecular Signature Database) is fully described by a gene set page. From this web site, use the [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> | ||
<p>Each gene set page contains the following information:</p> | <p>Each gene set page contains the following information:</p> | ||
| + | |||
<h2>Gene Set Annotations</h2> | <h2>Gene Set Annotations</h2> | ||
| − | < | + | <dl> |
| − | Gene set name in the database. Gene sets can have their names changed after reviewing or to correct potential errors. | + | <dt>Standard name |
| − | + | <dd>Gene set name in the database. Gene sets can have their names changed after reviewing or to correct potential errors. | |
| − | < | + | <dt>Systematic name |
| − | This serves to uniquely identify a gene set in MSigDB. Unlike standard names, systematic name never changes. | + | <dd>This serves to uniquely identify a gene set in MSigDB. Unlike standard names, systematic name never changes. |
| − | + | <dt> Brief description | |
| − | < | + | <dd>A one sentence description of the gene set to convey "at a glance" information about gene sets. |
| − | 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. | This description appears on the Browse MSigDB page of the GSEA application. | ||
| − | + | <dt> Full description or abstract | |
| − | < | + | <dd>An extensive annotation of the gene set. For gene sets curated from publications, this field contains publication's abstract. |
| − | An extensive annotation of the gene set. For gene sets curated from publications, this field contains publication's abstract. | + | <dt>Collection |
| − | + | <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. | |
| − | < | + | <dt>Source publication |
| − | 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. | + | <dd>When available, a link to the source publication followed by a list of its authors. |
| − | + | <dt>Exact source | |
| − | < | + | <dd>For gene sets curated from publications, this field indicates the exact source of a gene set in the publication (e.g., Table 1). |
| − | When available, a link to the source publication followed by a list of its authors. | + | <dt> Related gene sets |
| − | + | <dd>Other gene sets (if any) from the same publication or from publications shared with at least one of the authors. | |
| − | < | + | <dt>External links |
| − | For gene sets curated from publications, this field indicates the exact source of a gene set in the publication (e.g., Table 1). | + | <dd>When available, links to external websites with additional information about the gene set. |
| − | + | <dt>Organism | |
| − | < | + | <dd>The organism that the experiment was conducted in. |
| − | Other gene sets (if any) from the same publication or from publications shared with at least one of the authors. | + | <dt> Contributed by |
| − | + | <dd>Name of the person, institution, or external database (such as Reactome) who contributed the gene set. | |
| − | < | + | <dt> Source platform |
| − | When available, links to external websites with additional information about the gene set. | + | <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. |
| − | + | <dt>Dataset references | |
| − | < | + | <dd>GEO or ArrayExpress links for associated microarray data where appropriate. |
| − | The organism that the experiment was conducted in. | + | </dl> |
| − | |||
| − | < | ||
| − | Name of the person, institution, or external database (such as Reactome) who contributed the gene set. | ||
| − | |||
| − | < | ||
| − | 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. | ||
| − | |||
| − | < | ||
| − | GEO or ArrayExpress links for associated microarray data where appropriate. | ||
<h2>Gene set actions</h2> | <h2>Gene set actions</h2> | ||
| − | + | <dl> | |
| − | < | + | <dt> 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|Data Formats]]. | + | <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]]. |
| − | + | <dt>Annotate by computing overlaps | |
| − | < | + | <dd>Displays the overlap (if any) between this gene set and the gene sets in the selected collection. |
| − | Displays the overlap (if any) between this gene set and the gene sets in the selected collection. | + | <dt>Compendia expression profiles |
| − | + | <dd>Produce a heat map showing how genes in this gene set are expressed in the selected compendium dataset. | |
| − | < | + | <dt>Advanced query |
| − | Produce a heat map showing how genes in this gene set are expressed in the selected compendium dataset. | + | <dd>Copies the genes in this gene set to the annotations page, where you can modify and/or further explore the gene set. |
| − | + | <dt>Gene families | |
| − | < | + | <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. |
| − | Copies the genes in this gene set to the annotations page, where you can modify and/or further explore the gene set. | + | </dl> |
| − | |||
| − | < | ||
| − | 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. | ||
<h2>Inspecting gene set members</h2> | <h2>Inspecting gene set members</h2> | ||
| − | < | + | <dl> |
| − | Toggle the Show (Hide) link show (hide) gene set members followed by links to external websites for gene-centric information. | + | <dt>Show members |
| + | <dd>Toggle the Show (Hide) link show (hide) gene set members followed by links to external websites for gene-centric information. | ||
| + | </dl> | ||
<h2>Other</h2> | <h2>Other</h2> | ||
| − | + | <dl> | |
| − | < | + | <dt>Version history |
| − | Lists the history of this gene set (when it was introduced and any modifications) where available. | + | <dd>Lists the history of this gene set (when it was introduced and any modifications) where available. |
| + | </dl> | ||
Revision as of 18:36, 16 October 2012
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<a href="http://www.broadinstitute.org/gsea/contact.jsp">Contact</a>
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.
Inspecting 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.
