Difference between revisions of "Gene Set Pages"
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| − | <p | + | <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, click [http://wwwdev.broad.mit.edu/gsea/msigdb/cards_index.html here]. Or, from within the GSEA application, use the Browse MSigDB page to browse the gene sets and to display their gene set cards.</p> |
| − | <p | + | <p style="" class="MsoNormal">Each gene set card contains the following information:</p> |
| − | <p | + | <p style="" class="MsoNormal"><strong style="">Standard name</strong>: Gene set name.</p> |
| − | <p | + | <p style="" class="MsoNormal"><strong style="">Systematic name</strong>: Internal identifier for the gene set, which consists of three parts:<br /></p> |
| − | <p | + | <p style="" class="MsoNormal"> </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 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> |
| − | <p | + | <p style="" class="MsoNormal"><strong style="">Category</strong>: The category of the gene set, as defined above. </p> |
| − | <p | + | <p style="" class="MsoNormal"><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 14:37, 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. Or, from within the GSEA application, use the Browse MSigDB page to browse the gene sets and to display their 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.
