Difference between revisions of "MSigDB v2023.1.Mm Release Notes"
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<h2>M2:CGP</h2> | <h2>M2:CGP</h2> | ||
| − | + | 3 Gene sets contributed by MSigDB users have been added to M2:CGP | |
<ul> | <ul> | ||
| − | <li><span class="plainlinks">[https://gsea-msigdb.org/gsea/msigdb/mouse/geneset/]</span></li> | + | <li><span class="plainlinks">[https://gsea-msigdb.org/gsea/msigdb/mouse/geneset/SAUL_SEN_MAYO SAUL_SEN_MAYO]</span></li> |
| + | <li><span class="plainlinks">[https://gsea-msigdb.org/gsea/msigdb/mouse/geneset/MA_RAT_AGING_UP MA_RAT_AGING_UP]</span></li> | ||
| + | <li><span class="plainlinks">[https://gsea-msigdb.org/gsea/msigdb/mouse/geneset/MA_RAT_AGING_DN MA_RAT_AGING_DN]</span></li> | ||
</ul> | </ul> | ||
<br> | <br> | ||
| Line 32: | Line 34: | ||
<ul> | <ul> | ||
| − | <li>Reactome gene sets have been updated to reflect the state of the Reactome pathway architecture as of '''Reactome v83''' (+ | + | <li>Reactome gene sets have been updated to reflect the state of the Reactome pathway architecture as of '''Reactome v83''' (+2 gene sets).</li> |
<li>As previously described in the [[MSigDB_v7.0_Release_Notes#C2:CP:Reactome_-_Major_overhaul | Reactome release notes for MSigDB 7.0]], in order to limit redundancy between gene sets within the Reactome sub-collection we applied a filtering procedure based on Jaccard coefficients and distance from the top level of the Reactome event hierarchy.</li> | <li>As previously described in the [[MSigDB_v7.0_Release_Notes#C2:CP:Reactome_-_Major_overhaul | Reactome release notes for MSigDB 7.0]], in order to limit redundancy between gene sets within the Reactome sub-collection we applied a filtering procedure based on Jaccard coefficients and distance from the top level of the Reactome event hierarchy.</li> | ||
</ul> | </ul> | ||
| Line 40: | Line 42: | ||
<h2>M3:GTRD</h2> | <h2>M3:GTRD</h2> | ||
| − | <p>GTRD data was updated to the 21.12 release.</p> | + | <p>GTRD data was updated to the 21.12 release (+7 gene sets).</p> |
<h2>M5:GO (Gene Ontology)</h2> | <h2>M5:GO (Gene Ontology)</h2> | ||
| Line 47: | Line 49: | ||
<p>This collection is divided into three sub-collections:</p> | <p>This collection is divided into three sub-collections:</p> | ||
<ul> | <ul> | ||
| − | <li><strong>BP</strong>: GO Biological process (+ | + | <li><strong>BP</strong>: GO Biological process (+67 gene sets). Gene sets derived from the Biological Process Ontology, which are prefixed with "GOBP_".</li> |
| − | <li><strong>CC</strong>: GO Cellular component ( | + | <li><strong>CC</strong>: GO Cellular component (-11 gene sets). Gene sets derived from the Cellular Component Ontology, which are prefixed with "GOCC_".</li> |
| − | <li><strong>MF</strong>: GO Molecular function (+ | + | <li><strong>MF</strong>: GO Molecular function (+57 gene sets). Gene sets derived from the Molecular Function Ontology, which are prefixed with "GOMF_"..</li> |
</ul> | </ul> | ||
| Line 56: | Line 58: | ||
<h2>M8 cell type signature gene sets</h2> | <h2>M8 cell type signature gene sets</h2> | ||
| − | <p>Added gene sets describing uterine cell type identity signatures from <span class="plainlinks">[https://pubmed.ncbi.nlm.nih.gov/35669188/ Zhang, et al. 2022 Digital Cell Atlas of Mouse Uterus: From Regenerative Stage to Maturational Stage.]</span> | + | <p>Added gene sets describing uterine cell type identity signatures from <span class="plainlinks">[https://pubmed.ncbi.nlm.nih.gov/35669188/ Zhang, et al. 2022 Digital Cell Atlas of Mouse Uterus: From Regenerative Stage to Maturational Stage.]</span> (+18 gene sets)</p> |
<h2>CHIP file updates</h2> | <h2>CHIP file updates</h2> | ||
| Line 63: | Line 65: | ||
<li>Gene orthology annotations for mapping human and rat genes to their best match mouse orthologs have been updated to <span class="plainlinks">[https://www.alliancegenome.org/ Alliance of Genome Resources]</span> orthology database release 5.3.0 (2022-10-28)</li> | <li>Gene orthology annotations for mapping human and rat genes to their best match mouse orthologs have been updated to <span class="plainlinks">[https://www.alliancegenome.org/ Alliance of Genome Resources]</span> orthology database release 5.3.0 (2022-10-28)</li> | ||
</ul> | </ul> | ||
| + | |||
| + | <h2>SQLite Database</h2> | ||
| + | <p>With this release we have created a new SQLite database for the fully annotated gene sets in both the Human (2023.1.Hs) and the Mouse (2023.1.Ms) resources. Each ships as a single-file database usable with any compliant SQLite client. This new format brings the MSigDB contents and metadata with all of the searchability and manipulative power of a full relational database. See our [[MSigDB_SQLite_Database|documentation]] for more details on the contents and usage.</p> | ||
| + | <p>Note that we will continue producing the XML file for now, but it should be considered deprecated with the intention to eventually be entirely removed in a future release.</p> | ||
Latest revision as of 16:19, 6 April 2023
GSEA Home | Downloads | Molecular Signatures Database | Documentation | Contact
Contents
Important Notices
This page describes updates made to the Molecular Signatures Database Mouse Collections for release 2023.1 (MSigDB 2023.1.Mm).
In order to access the MSigBD mouse collections through the GSEA UI, the GSEA 4.3.0 or newer is required.
MSigDB v2023.1 is based on gene annotation data from Ensembl Release 109 (Feb 2023).
Updates to Mouse Collections (MSigDB v2023.1.Mm)
M1: positional gene sets
As previously noted in the MSigDB_v2022.1.Mm_Release_Notes the underlying data for the M1 collection remains based on the cytogenetic band annotations provided in the Ensembl 102 release, corresponding to the GRCm38 assembly as cytogentic band annotations for GRCm39 remain unavailable, however gene identifiers have been updated.
M2:CGP
3 Gene sets contributed by MSigDB users have been added to M2:CGP
M2:CP:Reactome
- Reactome gene sets have been updated to reflect the state of the Reactome pathway architecture as of Reactome v83 (+2 gene sets).
- As previously described in the Reactome release notes for MSigDB 7.0, in order to limit redundancy between gene sets within the Reactome sub-collection we applied a filtering procedure based on Jaccard coefficients and distance from the top level of the Reactome event hierarchy.
M2:CP:WikiPathways
WikiPathways gene sets have been updated to the February 10, 2023 release (+XX gene sets).
M3:GTRD
GTRD data was updated to the 21.12 release (+7 gene sets).
M5:GO (Gene Ontology)
Gene sets in these sub-collections 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). The gene sets are named by GO term and contain genes annotated by that term. This collection has been updated to the most recent GO annotations as present in the GO-basic obo file released on 2023-01-01 and NCBI gene2go annotations downloaded on 2023-02-10.
This collection is divided into three sub-collections:
- BP: GO Biological process (+67 gene sets). Gene sets derived from the Biological Process Ontology, which are prefixed with "GOBP_".
- CC: GO Cellular component (-11 gene sets). Gene sets derived from the Cellular Component Ontology, which are prefixed with "GOCC_".
- MF: GO Molecular function (+57 gene sets). Gene sets derived from the Molecular Function Ontology, which are prefixed with "GOMF_"..
These updates were generated in accordance with the procedure described in the GO release notes for MSigDB 7.0.
M8 cell type signature gene sets
Added gene sets describing uterine cell type identity signatures from Zhang, et al. 2022 Digital Cell Atlas of Mouse Uterus: From Regenerative Stage to Maturational Stage. (+18 gene sets)
CHIP file updates
- MSigDB 2023.1.Mm gene annotations and gene mapping CHIP files have been updated to data from Ensembl 109.
- Gene orthology annotations for mapping human and rat genes to their best match mouse orthologs have been updated to Alliance of Genome Resources orthology database release 5.3.0 (2022-10-28)
SQLite Database
With this release we have created a new SQLite database for the fully annotated gene sets in both the Human (2023.1.Hs) and the Mouse (2023.1.Ms) resources. Each ships as a single-file database usable with any compliant SQLite client. This new format brings the MSigDB contents and metadata with all of the searchability and manipulative power of a full relational database. See our documentation for more details on the contents and usage.
Note that we will continue producing the XML file for now, but it should be considered deprecated with the intention to eventually be entirely removed in a future release.
