Difference between revisions of "Gene Set Pages"
Jump to navigation
Jump to search
| Line 1: | Line 1: | ||
| − | + | <p class="MsoListContinue"> </p> | |
| − | <p class=" | + | <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/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 style="" class="MsoNormal"><strong style="">Standard name</strong>: Gene set name.</p> | |
| − | + | <p style="" class="MsoNormal"><strong style="">Systematic name</strong>: Internal identifier for the gene set, which consists of three parts:</p> | |
| − | |||
| − | |||
| − | < | ||
| − | |||
| − | |||
| − | <p | ||
| − | |||
| − | |||
| − | |||
| − | |||
| − | < | ||
| − | <p | ||
| − | |||
| − | |||
| − | |||
<ul> | <ul> | ||
| − | <li><!--[if !supportLists]--><span style=" | + | <li><!--[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).</li> |
| − | <li | + | <li style="" class="MsoNormal">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.</li> |
| − | + | <li><!--[if !supportLists]--><span style="" />Number: a unique number with the category:subcategory classification.</li> | |
| − | |||
| − | <li><!--[if !supportLists]-- | ||
| − | |||
</ul> | </ul> | ||
| − | <p class=" | + | <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 class=" | + | <p style="" class="MsoNormal"><strong style="">Category</strong>: </p> |
| + | <p style="" class="MsoNormal"><strong style="">Sub-category</strong>: </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="">External links</strong>: When available, links to external websites that contain more information about the gene set.</p> | ||
| + | <p class="MsoNormal"><strong style="">Keywords & MeSH headings</strong>: Keywords derived from MeSH [[http://www.nlm.nih.gov/mesh/MBrowser.html National Library of Medicine]] and/or manually entered.</p> | ||
| + | <p class="MsoNormal"><strong style="">Organism</strong>: The organism that the experiment was conducted in (<em>generic</em> for canonical pathways and ontologies).</p> | ||
| + | <p class="MsoNormal"><strong style="">Contributed by</strong>: Name of the person (or external database; for example, KEGG) who collected the gene set.</p> | ||
| + | <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> | ||
| + | <p class="MsoNormal"><strong style="">Download</strong>: Links to download the gene set in different formats:</p> | ||
| + | <ul> | ||
| + | <li><!--[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]-->grp: lists the genes in the gene set in plain text format</li> | ||
| + | <li><!--[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]-->xml: gene set definition formatted with structure annotation </li> | ||
| + | <li><!--[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]-->map: lists the genes in the gene set with details of the mapping between the originally reported accessions and their HUGO gene symbols</li> | ||
| + | </ul> | ||
| + | <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> | ||
Revision as of 13:29, 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:
Sub-category:
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.
