Difference between revisions of "MSigDB v2.5 Release Notes"
Jump to navigation
Jump to search
| (31 intermediate revisions by 3 users not shown) | |||
| Line 1: | Line 1: | ||
| − | + | [http://www.broadinstitute.org/gsea/ GSEA Home] | | |
| + | [http://www.broadinstitute.org/gsea/downloads.jsp Downloads] | | ||
| + | [http://www.broadinstitute.org/gsea/msigdb/ Molecular Signatures Database] | | ||
| + | [http://www.broadinstitute.org/cancer/software/gsea/wiki/index.php/Main_Page Documentation] | | ||
| + | [http://www.broadinstitute.org/gsea/contact.jsp Contact]<br /> | ||
| + | <br /> | ||
| + | <p>This page describes the changes made to the gene set collections for Release 2.5 of the Molecular Signatures Database (MSigDB).</p> | ||
| + | <p><br /> | ||
| + | </p> | ||
| + | <h3>C1: Positional gene sets</h3> | ||
| + | No changes were made. <br /> | ||
| + | For a description of this collection, see the [http://www.broad.mit.edu/gsea/msigdb/collections.jsp Browse Collections] page.<br /> | ||
| + | | ||
| + | <h3>C2: Curated gene sets (+205)</h3> | ||
| + | Gene sets from two sources were added to the C2 collection:<br /> | ||
| + | <ul> | ||
| + | <li><strong>CGP</strong>: chemical and genetic perturbations (+5 gene sets). Gene sets by Bild et al. (Nature 439, 353 – 357, 2006) based on microarray analysis of expression profiles of key oncogenes in a model system where expression of these oncogenes transformed otherwise quiescent cells.</li> | ||
| + | <li><strong>CP</strong>: canonical pathways (+200 gene sets). Gene sets from the KEGG PATHWAY (http://www.genome.jp/kegg/) database of molecular interaction and reaction networks for metabolism, various cellular processes, and human diseases.</li> | ||
| + | </ul> | ||
| + | In addition, links to GenMAPP have been fixed. Specifically, broken links have been corrected in the External links section of the gene set page for any gene set derived from GenMAPP.<br /> | ||
| + | | ||
| + | |||
| + | <h3>C3: Motif gene sets</h3> | ||
| + | No changes were made.<br /> | ||
| + | For a description of this collection, see the [http://www.broad.mit.edu/gsea/msigdb/collections.jsp Browse Collections] page.<br /> | ||
| + | | ||
| + | <h3>C4: Computational gene sets (+456)</h3> | ||
| + | C4 now contains two subcollections:<br /> | ||
| + | <ul> | ||
| + | <li><strong>CGN</strong>: cancer gene neighborhoods (+0 gene sets). Gene sets defined by expression neighborhoods centered on 380 cancer-associated genes (Brentani, Caballero et al. 2003). This is the C4 collection from the previous MSigDB release.</li> | ||
| + | <li><strong>CM: </strong>cancer modules (+456 gene sets). Gene sets <em>identical </em>to the modules described in Segal et al. (Nature Genetics 36, 1090 – 1098, 2004). Gene sets in this subcollection are made of transcriptionally coregulated genes that share a common function and have been found significantly deregulated in tumors. Starting with a list of 2,849 gene sets from a variety of resources such as Gene Ontology, KEGG and others, the authors extracted 456 statistically significant regulatory modules from a large collection of published microarray data spanning 22 tumor types. This is an entirely new subcollection. </li> | ||
| + | </ul> | ||
| + | | ||
| + | <h3>C5: GO gene sets (+1454)</h3> | ||
| + | <p> Gene sets in this new collection are derived from the controlled vocabulary of the Gene Ontology (GO) project: The Gene Ontology Consortium. Gene Ontology: tool for the unification of biology. Nature Genet. (2000) 25: 25-29 (http://www.geneontology.org/). The gene sets are named by GO term and contain genes annotated by that term.</p> | ||
| + | <p>This collection is divided into three subcollections:</p> | ||
| + | <ul> | ||
| + | <li><strong>CC</strong>: GO Cellular component (+233 gene sets). Gene sets derived from the Cellular Component Ontology.</li> | ||
| + | <li><strong>MF</strong>: GO Molecular function (+396 gene sets). Gene sets derived from the Molecular Function Ontology.</li> | ||
| + | <li><strong>BP</strong>: GO Biological process (+825 gene sets). Gene sets derived from the Biological Process Ontology.</li> | ||
| + | </ul> | ||
| + | <p> <strong>GSEA users</strong>: Gene set enrichment analysis identifies gene sets consisting of co-regulated genes; GO gene sets are based on ontologies and do not generally consist of co-regulated genes.</p> | ||
| + | | ||
| + | <h3>For more information</h3> | ||
| + | For complete descriptions of all collections or to download the updated gene sets, go to the [http://www.broad.mit.edu/gsea/msigdb/collections.jsp Browse Collections] page. | ||
Latest revision as of 02:37, 25 September 2016
GSEA Home |
Downloads |
Molecular Signatures Database |
Documentation |
Contact
This page describes the changes made to the gene set collections for Release 2.5 of the Molecular Signatures Database (MSigDB).
Contents
C1: Positional gene sets
No changes were made.
For a description of this collection, see the Browse Collections page.
C2: Curated gene sets (+205)
Gene sets from two sources were added to the C2 collection:
- CGP: chemical and genetic perturbations (+5 gene sets). Gene sets by Bild et al. (Nature 439, 353 – 357, 2006) based on microarray analysis of expression profiles of key oncogenes in a model system where expression of these oncogenes transformed otherwise quiescent cells.
- CP: canonical pathways (+200 gene sets). Gene sets from the KEGG PATHWAY (http://www.genome.jp/kegg/) database of molecular interaction and reaction networks for metabolism, various cellular processes, and human diseases.
In addition, links to GenMAPP have been fixed. Specifically, broken links have been corrected in the External links section of the gene set page for any gene set derived from GenMAPP.
C3: Motif gene sets
No changes were made.
For a description of this collection, see the Browse Collections page.
C4: Computational gene sets (+456)
C4 now contains two subcollections:
- CGN: cancer gene neighborhoods (+0 gene sets). Gene sets defined by expression neighborhoods centered on 380 cancer-associated genes (Brentani, Caballero et al. 2003). This is the C4 collection from the previous MSigDB release.
- CM: cancer modules (+456 gene sets). Gene sets identical to the modules described in Segal et al. (Nature Genetics 36, 1090 – 1098, 2004). Gene sets in this subcollection are made of transcriptionally coregulated genes that share a common function and have been found significantly deregulated in tumors. Starting with a list of 2,849 gene sets from a variety of resources such as Gene Ontology, KEGG and others, the authors extracted 456 statistically significant regulatory modules from a large collection of published microarray data spanning 22 tumor types. This is an entirely new subcollection.
C5: GO gene sets (+1454)
Gene sets in this new collection are derived from the controlled vocabulary of the Gene Ontology (GO) project: The Gene Ontology Consortium. Gene Ontology: tool for the unification of biology. Nature Genet. (2000) 25: 25-29 (http://www.geneontology.org/). The gene sets are named by GO term and contain genes annotated by that term.
This collection is divided into three subcollections:
- CC: GO Cellular component (+233 gene sets). Gene sets derived from the Cellular Component Ontology.
- MF: GO Molecular function (+396 gene sets). Gene sets derived from the Molecular Function Ontology.
- BP: GO Biological process (+825 gene sets). Gene sets derived from the Biological Process Ontology.
GSEA users: Gene set enrichment analysis identifies gene sets consisting of co-regulated genes; GO gene sets are based on ontologies and do not generally consist of co-regulated genes.
For more information
For complete descriptions of all collections or to download the updated gene sets, go to the Browse Collections page.
