Difference between revisions of "Gene Set Pages"
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| − | <p | + | <p class="MsoNormal" style="">Each gene set in the MSigDB (Molecular Signature Database) is fully described by a gene set card. To review the gene set cards:<br /></p> |
| − | <p | + | <ol> |
| − | <p | + | <li>Click [http://wwwdev.broad.mit.edu/gsea/msigdb/cards_index.html here]. <br /></li> |
| − | <p | + | <li>Click the double arrow next to a category to display the gene sets in that category.</li> |
| − | <p | + | <li>Click a gene set to display its gene set card.</li> |
| + | </ol> | ||
| + | Alternatively, from within the GSEA application, use the Browse MSigDB page ([[msigdb_browser]]) to browse gene sets and display gene set cards. | ||
| + | <p class="MsoNormal" style="">Each gene set card contains the following information:</p> | ||
| + | <p class="MsoNormal" style=""><strong style="">Standard name</strong>: Gene set name.</p> | ||
| + | <p class="MsoNormal" style=""><strong style="">Systematic name</strong>: Internal identifier for the gene set, which consists of three parts:<br /></p> | ||
| + | <p class="MsoNormal" style=""> </p> | ||
<p class="MsoListBullet2"><!--[if !supportLists]--><span style="">▪<span style="font-family: "Times New Roman"; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;"> </span></span><!--[endif]-->Category: Positional (C1), Curated (C2), Motif (C3), or Computed (C4).</p> | <p class="MsoListBullet2"><!--[if !supportLists]--><span style="">▪<span style="font-family: "Times New Roman"; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;"> </span></span><!--[endif]-->Category: Positional (C1), Curated (C2), Motif (C3), or Computed (C4).</p> | ||
<span style="">▪<span style="font-family: "Times New Roman"; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;"> </span></span>Subcategory: for C1, always Cytogenic; for C2, Animal Model, Clinical, Experimental pertuberation, Expert curation, Misc, Ontology, Pathway database, or Review paper; for C3, Representative motifs or Transfac; and for C4, always Neighborhood. | <span style="">▪<span style="font-family: "Times New Roman"; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;"> </span></span>Subcategory: for C1, always Cytogenic; for C2, Animal Model, Clinical, Experimental pertuberation, Expert curation, Misc, Ontology, Pathway database, or Review paper; for C3, Representative motifs or Transfac; and for C4, always Neighborhood. | ||
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| − | <p | + | <p class="MsoNormal" style=""><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> |
| − | <p | + | <p class="MsoNormal" style=""><strong style="">Category</strong>: The category of the gene set, as defined above. </p> |
| − | <p | + | <p class="MsoNormal" style=""><strong style="">Sub-category</strong>: The subcategory of the gene set, as defined above.</p> |
<p class="MsoNormal"><strong style="">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.</p> | <p class="MsoNormal"><strong style="">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.</p> | ||
<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> | <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> | ||
Revision as of 15:00, 24 March 2006
Each gene set in the MSigDB (Molecular Signature Database) is fully described by a gene set card. To review the gene set cards:
- Click here.
- Click the double arrow next to a category to display the gene sets in that category.
- Click a gene set to display its gene set card.
Alternatively, from within the GSEA application, use the Browse MSigDB page (msigdb_browser) to browse gene sets and display gene set cards.
Each gene set card contains the following information:
Standard name: Gene set name.
Systematic name: Internal identifier for the gene set, which consists of three parts:
▪ Category: Positional (C1), Curated (C2), Motif (C3), or Computed (C4).
▪ Subcategory: for C1, always Cytogenic; for C2, Animal Model, Clinical, Experimental pertuberation, Expert curation, Misc, Ontology, Pathway database, or Review paper; for C3, Representative motifs or Transfac; and for C4, always Neighborhood.
▪ Number: a unique number with the category:subcategory classification.
Brief description: A brief description of the gene. This is the description that appears on the Browse MSigDB page of the GSEA application.
Category: The category of the gene set, as defined above.
Sub-category: The subcategory of the gene set, as defined above.
Full description or Abstract: 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.
Publication URL: 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.
External links: When available, links to external websites that contain more information about the gene set.
Keywords & MeSH headings: Keywords derived from MeSH National Library of Medicine and/or manually entered.
Organism: The organism that the experiment was conducted in (generic for canonical pathways and ontologies).
Contributed by: Name of the person (or external database; for example, KEGG) who collected the gene set.
Source platform: 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).
Download: Links to download the gene set in different formats:
▪ grp: lists the genes in the gene set in plain text format
▪ xml: gene set definition formatted with structure annotation
▪ map: lists the genes in the gene set with details of the mapping between the originally reported accessions and their HUGO gene symbols
Genes: 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.
