https://software.broadinstitute.org/cancer/software/gsea/wiki/api.php?action=feedcontributions&user=Acastanza&feedformat=atom GeneSetEnrichmentAnalysisWiki - User contributions [en] 2024-03-29T12:34:51Z User contributions MediaWiki 1.34.4 https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=Release_Notes&diff=4562 Release Notes 2023-10-20T19:55:20Z <p>Acastanza: </p> <hr /> <div>[http://www.broadinstitute.org/gsea/ GSEA Home] |<br /> [http://www.broadinstitute.org/gsea/downloads.jsp Downloads] | <br /> [http://www.broadinstitute.org/gsea/msigdb/ Molecular Signatures Database] | <br /> [http://www.broadinstitute.org/cancer/software/gsea/wiki/index.php/Main_Page Documentation] |<br /> [http://www.broadinstitute.org/gsea/contact.jsp Contact]<br /> &lt;br&gt;<br /> <br /> &lt;h3&gt;&lt;font color=&quot;#3366ff&quot;&gt;GSEA Software Release Notes&lt;/font&gt;&lt;/h3&gt;<br /> &lt;table width=&quot;700&quot; cellspacing=&quot;1&quot; cellpadding=&quot;1&quot; border=&quot;0&quot; align=&quot;&quot; height=&quot;78&quot; summary=&quot;&quot;&gt;<br /> &lt;tr&gt;<br /> &lt;td&gt;&lt;strong&gt;Date&lt;/strong&gt;&lt;/td&gt;<br /> &lt;td&gt;&lt;strong&gt;Release&lt;/strong&gt;&lt;/td&gt;<br /> &lt;td&gt;&lt;strong&gt;Description&lt;/strong&gt;&lt;/td&gt;<br /> &lt;td&gt;&lt;strong&gt;Release Notes&lt;/strong&gt;&lt;/td&gt;<br /> &lt;/tr&gt;<br /> &lt;tr&gt;<br /> &lt;td&gt;Sep 2022&lt;/td&gt;<br /> &lt;td&gt;4.3.&lt;em&gt;x&lt;/em&gt;*&lt;br /&gt;<br /> &lt;/td&gt;<br /> &lt;td&gt;Support for the new Mouse MSigDB database and versioning scheme changes.<br /> &lt;/td&gt;<br /> &lt;td&gt;[[GSEA_v4.3.x_Release_Notes|wiki]]&lt;/td&gt;<br /> &lt;/tr&gt;<br /> &lt;tr&gt;<br /> &lt;td&gt;Dec 2021 - Jan 2022&lt;/td&gt;<br /> &lt;td&gt;4.2.&lt;em&gt;x&lt;/em&gt;&lt;br /&gt;<br /> &lt;/td&gt;<br /> &lt;td&gt;New metric (Spearman) and new collapse mode (Absolute Max), better handling of missing values and many other fixes. Updated to latest Log4J jars to avoid concerns of vulnerabilities in earlier Log4J versions.&lt;br /&gt;<br /> &lt;/td&gt;<br /> &lt;td&gt;[[GSEA_v4.2.x_Release_Notes|wiki]]&lt;/td&gt;<br /> &lt;/tr&gt;<br /> &lt;tr&gt;<br /> &lt;td&gt;Jul 2020&lt;/td&gt;<br /> &lt;td&gt;4.1.&lt;em&gt;x&lt;/em&gt;&lt;br /&gt;<br /> &lt;/td&gt;<br /> &lt;td&gt;Improved support for macOS Catalina, updated and improved Enrichment Reports, and numerous bug fixes&lt;br /&gt;<br /> &lt;/td&gt;<br /> &lt;td&gt;[[GSEA_v4.1.x_Release_Notes|wiki]]&lt;/td&gt;<br /> &lt;/tr&gt;<br /> &lt;tr&gt;<br /> &lt;td&gt;Aug 2019 - Nov 2019&lt;/td&gt;<br /> &lt;td&gt;4.0.&lt;em&gt;x&lt;/em&gt;&lt;br /&gt;<br /> &lt;/td&gt;<br /> &lt;td&gt;Updates for MSigDB 7.0, Java 11 compatibility, and better performance&lt;br /&gt;<br /> &lt;/td&gt;<br /> &lt;td&gt;[[GSEA_v4.0.x_Release_Notes|wiki]]&lt;/td&gt;<br /> &lt;/tr&gt;<br /> &lt;tr&gt;<br /> &lt;td&gt;Jul 2017&lt;/td&gt;<br /> &lt;td&gt;3.0&lt;br /&gt;<br /> &lt;/td&gt;<br /> &lt;td&gt;Open source release, with numerous improvements and bug fixes&lt;br /&gt;<br /> &lt;/td&gt;<br /> &lt;td&gt;[[GSEA_v3.0_Release_Notes|wiki]]&lt;/td&gt;<br /> &lt;/tr&gt;<br /> &lt;tr&gt;<br /> &lt;td&gt;Mar 2015 - Apr 2017&lt;/td&gt;<br /> &lt;td&gt;2.2.x&lt;br /&gt;<br /> &lt;/td&gt;<br /> &lt;td&gt;&amp;nbsp;&lt;br /&gt;<br /> &lt;/td&gt;<br /> &lt;td&gt;[[GSEA_v2.2.x_Release_Notes|wiki]]&lt;/td&gt;<br /> &lt;/tr&gt;<br /> &lt;tr&gt;<br /> &lt;td&gt;Jun 2014&lt;/td&gt;<br /> &lt;td&gt;2.1.0&lt;/td&gt;<br /> &lt;td&gt;Added Enrichment Map visualization of GSEA results&lt;/td&gt;<br /> &lt;td&gt;[[GSEA_v2.1.0._Release_Notes|wiki]]&lt;/td&gt;<br /> &lt;/tr&gt;<br /> &lt;tr&gt;<br /> &lt;td&gt;Jan 2007 - Jan 2014&lt;/td&gt;<br /> &lt;td&gt;2.0.x&lt;br /&gt;<br /> &lt;/td&gt;<br /> &lt;td&gt;&amp;nbsp;&lt;br /&gt;<br /> &lt;/td&gt;<br /> &lt;td&gt;[[GSEA_v2.0.x_Release_Notes|wiki]]&lt;/td&gt;<br /> &lt;/tr&gt;<br /> &lt;tr&gt;<br /> &lt;td&gt;Mar 2005&lt;/td&gt;<br /> &lt;td&gt;1.0&lt;/td&gt;<br /> &lt;td&gt;Initial release&lt;/td&gt;<br /> &lt;td&gt;&amp;nbsp;&lt;/td&gt;<br /> &lt;/tr&gt;<br /> &lt;/table&gt;<br /> <br /> &lt;h3&gt;&lt;font color=&quot;#3366ff&quot;&gt;MSigDB Release Notes&lt;/font&gt;&lt;/h3&gt;<br /> &lt;table height=&quot;83&quot; width=&quot;637&quot; cellspacing=&quot;1&quot; cellpadding=&quot;1&quot; border=&quot;0&quot; align=&quot;&quot; summary=&quot;&quot;&gt;<br /> &lt;tr&gt;<br /> &lt;td&gt;&lt;strong&gt;Date&lt;/strong&gt;&lt;/td&gt;<br /> &lt;td&gt;&lt;strong&gt;Release&lt;/strong&gt;&lt;/td&gt;<br /> &lt;td&gt;&lt;strong&gt;Description&lt;/strong&gt;&lt;/td&gt;<br /> &lt;td&gt;&lt;strong&gt;Release Notes&lt;/strong&gt;&lt;/td&gt;<br /> &lt;/tr&gt;<br /> &lt;tr valign=&quot;top&gt;<br /> &lt;td&gt;Mar 2023&lt;/td&gt;<br /> &lt;td&gt;&amp;nbsp;2023.2.Hs*&lt;/td&gt;<br /> &lt;td&gt;Update to Ensembl 110 gene annotation data. Miscellaneous collection updates&lt;br&gt;<br /> &lt;td&gt;&lt;span class=&quot;plainlinks&quot;&gt;[https://docs.gsea-msigdb.org/#MSigDB/Release_Notes/MSigDB_2023.2.Hs/ New Docs Site]&lt;/span&gt;<br /> &lt;/td&gt;<br /> &lt;/tr&gt; <br /> &lt;tr valign=&quot;top&gt;<br /> &lt;td&gt;Mar 2023&lt;/td&gt;<br /> &lt;td&gt;&amp;nbsp;2023.2.Mm*&lt;/td&gt;<br /> &lt;td&gt;Update to Ensembl 110 gene annotation data. Miscellaneous collection updates&lt;br&gt;<br /> &lt;td&gt;&lt;span class=&quot;plainlinks&quot;&gt;[https://docs.gsea-msigdb.org/#MSigDB/Release_Notes/MSigDB_2023.2.Mm/ New Docs Site]&lt;/span&gt;<br /> &lt;/td&gt;<br /> &lt;/tr&gt; <br /> &lt;tr valign=&quot;top&gt;<br /> &lt;td&gt;Mar 2023&lt;/td&gt;<br /> &lt;td&gt;&amp;nbsp;2023.1.Hs*&lt;/td&gt;<br /> &lt;td&gt;Update to Ensembl 109 gene annotation data. Miscellaneous collection updates&lt;br&gt;<br /> &lt;td&gt;[[MSigDB_v2023.1.Hs_Release_Notes|wiki]]&lt;/td&gt;<br /> &lt;/tr&gt; <br /> &lt;tr valign=&quot;top&gt;<br /> &lt;td&gt;Mar 2023&lt;/td&gt;<br /> &lt;td&gt;&amp;nbsp;2023.1.Mm*&lt;/td&gt;<br /> &lt;td&gt;Update to Ensembl 109 gene annotation data. Miscellaneous collection updates&lt;br&gt;<br /> &lt;td&gt;[[MSigDB_v2023.1.Mm_Release_Notes|wiki]]&lt;/td&gt;<br /> &lt;/tr&gt; <br /> &lt;tr valign=&quot;top&gt;<br /> &lt;td&gt;Sep 2022&lt;/td&gt;<br /> &lt;td&gt;&amp;nbsp;2022.1.Hs&lt;/td&gt;<br /> &lt;td&gt;Human MSigDB under a new versioning scheme&lt;br&gt;<br /> &lt;td&gt;[[MSigDB_v2022.1.Hs_Release_Notes|wiki]]&lt;/td&gt;<br /> &lt;/tr&gt; <br /> &lt;tr valign=&quot;top&gt;<br /> &lt;td&gt;Sep 2022&lt;/td&gt;<br /> &lt;td&gt;&amp;nbsp;2022.1.Mm&lt;/td&gt;<br /> &lt;td&gt;Initial release of Mouse MSigDB&lt;br&gt;<br /> &lt;td&gt;[[MSigDB_v2022.1.Mm_Release_Notes|wiki]]&lt;/td&gt;<br /> &lt;/tr&gt; <br /> &lt;tr valign=&quot;top&gt;<br /> &lt;td&gt;Jan 2022&lt;/td&gt;<br /> &lt;td&gt;&amp;nbsp;7.5&lt;/td&gt;<br /> &lt;td&gt;&lt;br&gt;<br /> &lt;td&gt;[[MSigDB_v7.5_Release_Notes|wiki]]&lt;/td&gt;<br /> &lt;/tr&gt; <br /> &lt;tr valign=&quot;top&gt;<br /> &lt;td&gt;Mar 2021&lt;/td&gt;<br /> &lt;td&gt;&amp;nbsp;7.4&lt;/td&gt;<br /> &lt;td&gt;&lt;br&gt;<br /> &lt;td&gt;[[MSigDB_v7.4_Release_Notes|wiki]]&lt;/td&gt;<br /> &lt;/tr&gt; <br /> &lt;tr valign=&quot;top&gt;<br /> &lt;td&gt;Mar 2021&lt;/td&gt;<br /> &lt;td&gt;&amp;nbsp;7.3&lt;/td&gt;<br /> &lt;td&gt;C2:CP:WikiPathways +15; C2:CP:Reactome +15; C3:GTRD +175 (bugfix); C5:GO -88; C5:HPO +319; C7:VAX (new sub-collection); C8: +333&lt;br&gt;<br /> &lt;td&gt;[[MSigDB_v7.3_Release_Notes|wiki]]&lt;/td&gt;<br /> &lt;/tr&gt; <br /> &lt;tr valign=&quot;top&gt;<br /> &lt;td&gt;Sep 2020&lt;/td&gt;<br /> &lt;td&gt;&amp;nbsp;7.2&lt;/td&gt;<br /> &lt;td&gt;C2:CGP +60; C2:CP:WikiPathways (new sub-collection); C2:CP:Reactome +22; C3:GTRD -176; C5:GO +79, C5:HPO (new sub-collection); C8: +51 (promoted from supplementary)&lt;br&gt;<br /> &lt;td&gt;[[MSigDB_v7.2_Release_Notes|wiki]]&lt;/td&gt;<br /> &lt;/tr&gt; <br /> &lt;tr valign=&quot;top&gt;<br /> &lt;td&gt;Mar 2020&lt;/td&gt;<br /> &lt;td&gt;&amp;nbsp;7.1&lt;/td&gt;<br /> &lt;td&gt;C2 (+28); C3 (+2904); C5(+196)&lt;br&gt;<br /> &lt;td&gt;[[MSigDB_v7.1_Release_Notes|wiki]]&lt;/td&gt;<br /> &lt;/tr&gt; <br /> &lt;tr valign=&quot;top&gt;<br /> &lt;td&gt;Aug 2019&lt;/td&gt;<br /> &lt;td&gt;&amp;nbsp;7.0&lt;/td&gt;<br /> &lt;td&gt;C1 (-27); C2 (+738); C5 (+4079); &lt;br&gt;<br /> &lt;td&gt;[[MSigDB_v7.0_Release_Notes|wiki]]&lt;/td&gt;<br /> &lt;/tr&gt; <br /> &lt;tr valign=&quot;top&gt;<br /> &lt;td&gt;Jul 2018&lt;/td&gt;<br /> &lt;td&gt;&amp;nbsp;6.2&lt;/td&gt;<br /> &lt;td&gt;C2 (+24)&lt;br&gt;<br /> [[Mapping_between_v6.2_and_v6.1_gene_sets|Mapping between v6.2 and v6.1 gene sets]]&lt;/td&gt;<br /> &lt;td&gt;[[MSigDB_v6.2_Release_Notes|wiki]]&lt;/td&gt;<br /> &lt;/tr&gt; <br /> &lt;tr valign=&quot;top&gt;<br /> &lt;td&gt;Oct 2017&lt;/td&gt;<br /> &lt;td&gt;&amp;nbsp;6.1&lt;/td&gt;<br /> &lt;td&gt;C2 (+7)&lt;br&gt;<br /> [[Mapping_between_v6.1_and_v6.0_gene_sets|Mapping between v6.1 and v6.0 gene sets]]&lt;/td&gt;<br /> &lt;td&gt;[[MSigDB_v6.1_Release_Notes|wiki]]&lt;/td&gt;<br /> &lt;/tr&gt; <br /> &lt;tr valign=&quot;top&gt;<br /> &lt;td&gt;Apr 2017&lt;/td&gt;<br /> &lt;td&gt;&amp;nbsp;6.0&lt;/td&gt;<br /> &lt;td&gt;C2 (+2); C5 (-249)&lt;/td&gt;<br /> &lt;td&gt;[[MSigDB_v6.0_Release_Notes|wiki]]&lt;/td&gt;<br /> &lt;/tr&gt; <br /> &lt;tr valign=&quot;top&quot;&gt;<br /> &lt;td&gt;Oct 2016&lt;/td&gt;<br /> &lt;td&gt;&amp;nbsp;5.2&lt;/td&gt;<br /> &lt;td&gt;C2 (+4); C5 (+4,712)&lt;br&gt;<br /> [[Mapping_between_v5.2_and_v5.1_gene_sets|Mapping between v5.2 and v5.1 gene sets]]&lt;/td&gt;<br /> &lt;td&gt;[[MSigDB_v5.2_Release_Notes|wiki]]&lt;/td&gt;<br /> &lt;tr valign=&quot;top&gt;<br /> &lt;td&gt;Jan 2016&lt;/td&gt;<br /> &lt;td&gt;&amp;nbsp;5.1&lt;/td&gt;<br /> &lt;td&gt;C2 (+1); C7 (+2,962)&lt;/td&gt;<br /> &lt;td&gt; [[MSigDB_v5.1_Release_Notes|wiki]]&lt;/td&gt;<br /> &lt;/tr&gt;<br /> &lt;tr valign=&quot;top&quot;&gt;<br /> &lt;td&gt;Mar 2015&lt;/td&gt;<br /> &lt;td&gt;&amp;nbsp;5.0&lt;/td&gt;<br /> &lt;td&gt;H (+50); C2 (+3)&lt;br&gt;<br /> [[Mapping_between_v5.0_and_v4.0_gene_sets|Mapping between v5.0 and v4.0 gene sets]]&lt;/td&gt;<br /> &lt;td&gt;[[MSigDB_v5.0_Release_Notes|wiki]]&lt;/td&gt;<br /> &lt;/tr&gt;<br /> &lt;tr valign=&quot;top&quot;&gt;<br /> &lt;td&gt;May 2013&lt;/td&gt;<br /> &lt;td&gt;&amp;nbsp;4.0&lt;/td&gt;<br /> &lt;td&gt;C2 (-128); C7 (+1,910)&lt;/td&gt;<br /> &lt;td&gt;[[MSigDB_v4.0_Release_Notes|wiki]]&lt;/td&gt;<br /> &lt;/tr&gt;<br /> &lt;tr valign=&quot;top&quot;&gt;<br /> &lt;td&gt;Oct 2012&lt;/td&gt;<br /> &lt;td&gt;&amp;nbsp;3.1&lt;/td&gt;<br /> &lt;td&gt;C2 (+1,578); C4 (-23); C6 (+189)&lt;br&gt;<br /> [[Mapping_between_v3.1_and_v3.0_gene_sets|Mapping between v3.0 and v3.1 gene sets]]&lt;/td&gt;<br /> &lt;td&gt;[[MSigDB_v3.1_Release_Notes|wiki]]&lt;/td&gt;<br /> &lt;/tr&gt;<br /> &lt;tr valign=&quot;top&quot;&gt;<br /> &lt;td&gt;Sept 2010&lt;/td&gt;<br /> &lt;td&gt;&amp;nbsp;3.0&lt;/td&gt;<br /> &lt;td&gt;C1 (-60); C2 (+1,380); C3 (-1); C4 (-2) &lt;br&gt;<br /> [[Msigdb_mapping_v2.5_to_v3|Mapping between v2.5 and v3.0 gene sets]]&lt;/td&gt;<br /> &lt;td&gt;[[MSigDB_v3.0_Release_Notes|wiki]]&lt;/td&gt;<br /> &lt;/tr&gt;<br /> &lt;tr valign=&quot;top&quot;&gt;<br /> &lt;td&gt;April 2008&lt;/td&gt;<br /> &lt;td&gt;&amp;nbsp;2.5&lt;/td&gt;<br /> &lt;td&gt; C2 (+205); C4 (+456); C5 (+1454) &lt;br /&gt;<br /> &lt;/td&gt;<br /> &lt;td&gt;[[MSigDB_v2.5_Release_Notes|wiki]]&lt;/td&gt;<br /> &lt;/tr&gt;<br /> &lt;tr valign=&quot;top&quot;&gt;<br /> &lt;td&gt;Feb 2007&lt;/td&gt;<br /> &lt;td&gt;&amp;nbsp;2.1&lt;/td&gt;<br /> &lt;td&gt;Minor updates to MSigDB v2.0 annotations &lt;/td&gt;<br /> &lt;td&gt;&lt;br /&gt;<br /> &lt;/td&gt;<br /> &lt;/tr&gt;<br /> &lt;tr valign=&quot;top&quot;&gt;<br /> &lt;td&gt;Jan 2007&lt;/td&gt;<br /> &lt;td&gt;&amp;nbsp;2.0&lt;/td&gt;<br /> &lt;td&gt;C1 (updated); C2 (+269); C3 (+214) &lt;br /&gt;<br /> [[Msigdb_mapping_v1_to_v2|Mapping between v1 and v2 gene sets]]&lt;/td&gt;<br /> &lt;td&gt;[[Msigdb_may_2006_release_notes|wiki]]&lt;/td&gt;<br /> &lt;/tr&gt;<br /> &lt;tr valign=&quot;top&quot;&gt;<br /> &lt;td&gt;Nov 2005&lt;/td&gt;<br /> &lt;td&gt;&amp;nbsp;1.1&lt;/td&gt;<br /> &lt;td&gt;C1 (updated); C2 (+350); C3 (+566); C4&lt;br /&gt;<br /> &lt;/td&gt;<br /> &lt;td&gt;[http://www.broadinstitute.org/gsea/doc/msigdb_nov_2005_release_notes.pdf pdf]&lt;/td&gt;<br /> &lt;/tr&gt;<br /> &lt;tr valign=&quot;top&quot;&gt;<br /> &lt;td&gt;March 2005&lt;/td&gt;<br /> &lt;td&gt;&amp;nbsp;1.0&lt;/td&gt;<br /> &lt;td&gt;Initial release &lt;br /&gt;<br /> &lt;/td&gt;<br /> &lt;td&gt; [http://www.broadinstitute.org/gsea/doc/msigdb_march_2005_release_notes.pdf pdf]&lt;/td&gt;<br /> &lt;/tr&gt;<br /> &lt;/table&gt;<br /> &lt;h3&gt;&lt;font color=&quot;#3366ff&quot;&gt;Web site Release Notes&lt;/font&gt;&lt;/h3&gt;<br /> &lt;table height=&quot;78&quot; width=&quot;639&quot; cellspacing=&quot;1&quot; cellpadding=&quot;1&quot; border=&quot;0&quot; align=&quot;&quot; summary=&quot;&quot;&gt;<br /> &lt;tr&gt;<br /> &lt;td&gt;&lt;strong&gt;Date&lt;/strong&gt;&lt;/td&gt;<br /> &lt;td&gt;&lt;strong&gt;Release&lt;/strong&gt;&lt;/td&gt;<br /> &lt;td&gt;&lt;strong&gt;Description&lt;/strong&gt;&lt;/td&gt;<br /> &lt;td&gt;&lt;strong&gt;Release Notes&lt;/strong&gt;&lt;/td&gt;<br /> &lt;/tr&gt;<br /> &lt;tr&gt;<br /> &lt;td&gt;Aug 2019&lt;/td&gt;<br /> &lt;td&gt;6.4*&lt;/td&gt;<br /> &lt;td&gt;Upgrades to support v7.0 MSigDB.&lt;/td&gt;<br /> &lt;td&gt;[[Web site v6.4 Release Notes|wiki]]&lt;/td&gt;<br /> &lt;/tr&gt;<br /> &lt;tr&gt;<br /> &lt;td&gt;Apr 2017&lt;/td&gt;<br /> &lt;td&gt;6.0&lt;/td&gt;<br /> &lt;td&gt;Upgrades to support v6.0 MSigDB.&lt;/td&gt;<br /> &lt;td&gt;&lt;/td&gt;<br /> &lt;/tr&gt;<br /> &lt;tr&gt;<br /> &lt;td&gt;Mar 2015&lt;/td&gt;<br /> &lt;td&gt;5.0&lt;/td&gt;<br /> &lt;td&gt;Upgrades to support v5.0 MSigDB.&lt;/td&gt;<br /> &lt;td&gt;&lt;/td&gt;<br /> &lt;/tr&gt;<br /> &lt;tr&gt;<br /> &lt;td&gt;Jun 2014&lt;/td&gt;<br /> &lt;td&gt;4.05&lt;/td&gt;<br /> &lt;td&gt;Several minor updates&lt;/td&gt;<br /> &lt;td&gt;&lt;/td&gt;<br /> &lt;/tr&gt;<br /> &lt;tr&gt;<br /> &lt;td&gt;Apr 2013&lt;/td&gt;<br /> &lt;td&gt;3.87&lt;/td&gt;<br /> &lt;td&gt;Several bug fixes and new functionality.&lt;/td&gt;<br /> &lt;td&gt;[[Web site v3.87 Release Notes|wiki]]&lt;/td&gt;<br /> &lt;/tr&gt;<br /> &lt;tr&gt;<br /> &lt;td&gt;Oct 2012&lt;/td&gt;<br /> &lt;td&gt;3.84&lt;/td&gt;<br /> &lt;td&gt;Several updates and new functionality.&lt;/td&gt;<br /> &lt;td&gt;&lt;/td&gt;<br /> &lt;/tr&gt;<br /> &lt;tr&gt;<br /> &lt;td&gt;Jan 2011&lt;/td&gt;<br /> &lt;td&gt;3.5&lt;/td&gt;<br /> &lt;td&gt;Several bug fixes and some new functionality.&lt;/td&gt;<br /> &lt;td&gt;[[Web site v3.4 Release Notes|wiki]]&lt;br /&gt;<br /> &lt;/td&gt;<br /> &lt;/tr&gt;<br /> &lt;/table&gt;<br /> <br /> &lt;br /&gt;<br /> &lt;hr&gt;<br /> * Current release &lt;br /&gt;</div> Acastanza https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=MSigDB_Latest_Release_Notes&diff=4561 MSigDB Latest Release Notes 2023-10-20T19:52:43Z <p>Acastanza: </p> <hr /> <div>&lt;span class=&quot;plainlinks&quot;&gt;[https://docs.gsea-msigdb.org/#MSigDB/Release_Notes/MSigDB_2023.2.Hs/ MSigDB_v2023.2.Hs_Release_Notes]&lt;/span&gt;<br /> &lt;br&gt;<br /> &lt;span class=&quot;plainlinks&quot;&gt;[https://docs.gsea-msigdb.org/#MSigDB/Release_Notes/MSigDB_2023.2.Mm/ MSigDB_v2023.2.Mm_Release_Notes]&lt;/span&gt;</div> Acastanza https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=MSigDB_Latest_Release_Notes&diff=4560 MSigDB Latest Release Notes 2023-10-20T19:52:32Z <p>Acastanza: </p> <hr /> <div>&lt;span class=&quot;plainlinks&quot;&gt;[https://docs.gsea-msigdb.org/#MSigDB/Release_Notes/MSigDB_2023.2.Hs/ MSigDB_v2023.2.Hs_Release_Notes]&lt;/span&gt;<br /> &lt;span class=&quot;plainlinks&quot;&gt;[https://docs.gsea-msigdb.org/#MSigDB/Release_Notes/MSigDB_2023.2.Mm/ MSigDB_v2023.2.Mm_Release_Notes]&lt;/span&gt;</div> Acastanza https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=MSigDB_Latest_Release_Notes&diff=4559 MSigDB Latest Release Notes 2023-10-20T19:49:41Z <p>Acastanza: </p> <hr /> <div>[[MSigDB_v2023.2.Hs_Release_Notes]]<br /> <br /> [[MSigDB_v2023.2.Mm_Release_Notes]]</div> Acastanza https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=Version_check&diff=4558 Version check 2023-10-20T19:49:19Z <p>Acastanza: </p> <hr /> <div>TCGA_SampleSelection: 2023.2.Hs</div> Acastanza https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=MSigDB_v7.5.1_Release_Notes&diff=4557 MSigDB v7.5.1 Release Notes 2023-09-15T22:14:28Z <p>Acastanza: Fixed Missing Release Note for PRC2_EED_DN sets</p> <hr /> <div>&lt;span class=&quot;plainlinks&quot;&gt;<br /> [http://www.broadinstitute.org/gsea/ GSEA Home] |<br /> [http://www.broadinstitute.org/gsea/downloads.jsp Downloads] | <br /> [http://www.broadinstitute.org/gsea/msigdb/ Molecular Signatures Database] | <br /> [http://www.broadinstitute.org/cancer/software/gsea/wiki/index.php/Main_Page Documentation] |<br /> [http://www.broadinstitute.org/gsea/contact.jsp Contact]<br /> &lt;/span&gt;<br /> <br /> This page describes the changes made to the gene set collections for Release 7.5.x of the Molecular Signatures Database (MSigDB). This release contains updates to: C1, GO, HPO, and Reactome, as well as the addition of curated sets to C8 and user submitted sets to C2:CGP. This update incorporates the removal of clone based gene IDs introduced in Ensembl 104. <br /> <br /> <br /> &lt;b&gt;Note:&lt;/b&gt; Due to substantial changes introduced in MSigDB 7.0, using GSEA 4.0.0+ is recommended when utilizing MSigDB 7.0+ resources.&lt;br&gt;<br /> &lt;b&gt;Advisory&lt;/b&gt;: It is strongly recommended that users of MSigDB 7.5 '''always''' use the GSEA &quot;Collapse/Remap to gene symbols&quot; feature with the provided Symbol Remapping chip file if your dataset was generated with a transcriptome other than '''Ensembl v105/GENCODE v39'''.<br /> <br /> &lt;h1&gt;Specific Updates in the MSigDB 7.5.1 Patch Release&lt;/h1&gt;<br /> &lt;h3&gt;C2:CGP and C2:CP:WikiPathways&lt;/h3&gt;<br /> &lt;ul&gt;<br /> &lt;li&gt;SATOH_COLORECTAL_CANCER_MYC_DN contributed by Rintaro Saito, Institute for Advanced Biosciences, Keio University (+1 gene set) from [https://pubmed.ncbi.nlm.nih.gov/28847964 (PMID:28847964)] was inadvertently omitted from MSigDB 7.5, this has been corrected&lt;/li&gt;<br /> &lt;li&gt;In C2:CP:WikiPathways duplicate WP_ARYL_HYDROCARBON_RECEPTOR_PATHWAY gene sets have been disambiguated by using the specific WikiPathways ID number as a suffix; the two sets are now indicated as &lt;span class=&quot;plainlinks&quot;&gt;[https://www.gsea-msigdb.org/gsea/msigdb/cards/WP_ARYL_HYDROCARBON_RECEPTOR_PATHWAY_WP2586.html WP_ARYL_HYDROCARBON_RECEPTOR_PATHWAY_WP2586]&lt;/span&gt; and &lt;span class=&quot;plainlinks&quot;&gt;[https://www.gsea-msigdb.org/gsea/msigdb/cards/WP_ARYL_HYDROCARBON_RECEPTOR_PATHWAY_WP2873 WP_ARYL_HYDROCARBON_RECEPTOR_PATHWAY_WP2873]&lt;/span&gt;&lt;/li&gt;<br /> &lt;li&gt;In C2:CP:WikiPathways duplicate WP_HEDGEHOG_SIGNALING_PATHWAYgene sets have been disambiguated by using the specific WikiPathways ID number as a suffix; the two sets are now indicated as &lt;span class=&quot;plainlinks&quot;&gt;[https://www.gsea-msigdb.org/gsea/msigdb/cards/WP_HEDGEHOG_SIGNALING_PATHWAY_WP4249.html WP_HEDGEHOG_SIGNALING_PATHWAY_WP4249]&lt;/span&gt; and &lt;span class=&quot;plainlinks&quot;&gt;[https://www.gsea-msigdb.org/gsea/msigdb/cards/WP_HEDGEHOG_SIGNALING_PATHWAY_WP47 WP_HEDGEHOG_SIGNALING_PATHWAY_WP47]&lt;/span&gt;&lt;/li&gt;<br /> &lt;li&gt;MSigDB version numbers in CHIP files and other collection GMTs have also been incremented to MSigDB 7.5.1.<br /> &lt;/ul&gt;<br /> <br /> &lt;h3&gt;Known Issues&lt;/h3&gt;<br /> &lt;ul&gt;&lt;li&gt;The gene set descriptions in C1 incorrectly state that the gene positional information was taken from Ensembl 103. This is stated correctly in the &quot;Version history&quot; field to be from Ensembl 105&lt;/li&gt;&lt;/ul&gt;<br /> &lt;br&gt;<br /> &lt;h1&gt;MSigDB 7.5 Initial Release&lt;/h1&gt;<br /> <br /> &lt;h2&gt;Updates to Collections&lt;/h2&gt;<br /> <br /> &lt;h3&gt;C1&lt;/h3&gt;<br /> Updated human gene annotations to Ensembl 105 (+21 gene sets).<br /> &lt;h3&gt;C2:CGP&lt;/h3&gt;<br /> Gene sets contributed by the following individuals have been added to C2:CGP<br /> &lt;ul&gt;<br /> &lt;li&gt;NRF response gene sets contributed by Lara Ibrahim, The Scripps Research Institute (+6 gene sets) from [https://pubmed.ncbi.nlm.nih.gov/33096892/ (PMID:33096892)]&lt;/li&gt;<br /> &lt;li&gt;Gene sets describing the epithelial-mesenchymal transition (EMT) upon transforming growth factor beta (TGFb) stimulation contributed by Dharmesh D. Bhuva, Walter and Eliza Hall Institute of Medical Research (+6 gene sets) from [https://pubmed.ncbi.nlm.nih.gov/28119430 (PMID:28119430)]&lt;/li&gt;<br /> &lt;li&gt;SEAVEY_EPITHELIOID_HEMANGIOENDOTHELIOMA contributed by Caleb Seavey, Cleveland Clinic Foundation (+1 gene set) from [https://pubmed.ncbi.nlm.nih.gov/33766982 (PMID:33766982)]&lt;/li&gt;<br /> &lt;li&gt;SATOH_COLORECTAL_CANCER_MYC_UP contributed by Rintaro Saito, Institute for Advanced Biosciences, Keio University (+1 gene set) from [https://pubmed.ncbi.nlm.nih.gov/28847964 (PMID:28847964)]&lt;/li&gt;<br /> &lt;li&gt;GLASS_IGF2BP1_CLIP_TARGETS_KNOCKDOWN_DN contributed by Markus Gla&amp;szlig;, Martin Luther University Halle-Wittenberg (+1 gene set) from [https://pubmed.ncbi.nlm.nih.gov/33829040 (PMID:33829040)]&lt;/li&gt;<br /> <br /> &lt;/ul&gt;<br /> <br /> &lt;h3&gt;C2:CP:Reactome&lt;/h3&gt;<br /> <br /> &lt;ul&gt;<br /> &lt;li&gt;Reactome gene sets have been updated to reflect the state of the Reactome pathway architecture as of '''Reactome v78''' (+11 gene sets).&lt;/li&gt;<br /> &lt;li&gt;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.&lt;/li&gt;<br /> &lt;/ul&gt;<br /> <br /> &lt;h3&gt;C2:CP:WikiPathways&lt;/h3&gt;<br /> WikiPathways gene sets have been updated to the January 10, 2022 release (+47 gene sets).<br /> <br /> &lt;h3&gt;C3:TFT:GTRD&lt;/h3&gt;<br /> As a result of Ensembl gene annotations, 5 gene sets were removed from GTRD as they no fall below the the maximum number genes threshold (&lt;2000 genes). (-5)<br /> <br /> &lt;h3&gt;C5:GO (Gene Ontology)&lt;/h3&gt;<br /> &lt;p&gt; 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 (&lt;span class=&quot;plainlinks&quot;&gt;[http://www.geneontology.org Nature Genet 2000]&lt;/span&gt;). 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 2021-12-15 and NCBI gene2go annotations downloaded on 2022-01-03.&lt;/p&gt;<br /> &lt;p&gt;This collection is divided into three sub-collections:&lt;/p&gt;<br /> &lt;ul&gt;<br /> &lt;li&gt;&lt;strong&gt;BP&lt;/strong&gt;: GO Biological process (+177 gene sets). Gene sets derived from the Biological Process Ontology.&lt;/li&gt;<br /> &lt;li&gt;&lt;strong&gt;CC&lt;/strong&gt;: GO Cellular component (+10 gene sets). Gene sets derived from the Cellular Component Ontology.&lt;/li&gt;<br /> &lt;li&gt;&lt;strong&gt;MF&lt;/strong&gt;: GO Molecular function (+30 gene sets). Gene sets derived from the Molecular Function Ontology.&lt;/li&gt;<br /> &lt;/ul&gt;<br /> <br /> &lt;p&gt;These updates were generated in accordance with the procedure described in the [[MSigDB_v7.0_Release_Notes#C5_.28Gene_Ontology_collection.29_-_Major_overhaul | GO release notes for MSigDB 7.0.]]<br /> <br /> &lt;h3&gt;C5:HPO (Human Phenotype Ontology)&lt;/h3&gt;<br /> <br /> Gene sets in this sub-collection have been updated to reflect the 2021-10-10 release of the Human Phenotype Ontology database (+258 gene sets). This sub-collection has been redundancy filtered through a procedure comparable to that of the GO and Reactome sub-collections.<br /> <br /> &lt;h3&gt;C8: cell type signature gene sets&lt;/h3&gt;<br /> Added eye gene sets from &lt;span class=&quot;plainlinks&quot;&gt;[https://www.ncbi.nlm.nih.gov/labs/pmc/articles/PMC8478974/ Gautam and Hamashima et al. 2021. Multi-species single-cell transcriptomic analysis of ocular compartment regulons.]&lt;/span&gt; (+29 gene sets)<br /> <br /> &lt;h3&gt;Gene Set Corrections&lt;/h3&gt;<br /> &lt;ul&gt;<br /> &lt;li&gt;PRC2_EED_UP.V1_UP was renamed to PRC2_EED_DN.V1_UP to more accurately reflect the biological perturbation performed in the source study&lt;/li&gt;<br /> &lt;li&gt;PRC2_EED_UP.V1_DN was renamed to PRC2_EED_DN.V1_DN to more accurately reflect the biological perturbation performed in the source study&lt;/li&gt;<br /> &lt;/ul&gt;<br /> <br /> <br /> &lt;h3&gt;CHIP file updates&lt;/h3&gt;<br /> &lt;ul&gt;<br /> &lt;li&gt;MSigDB 7.5 gene annotations and gene mapping CHIP files have been updated to data from Ensembl 105.&lt;/li&gt;<br /> &lt;li&gt;MSigDB 7.5 includes new handling for deprecated Ensembl Gene IDs thanks to work by &lt;span class=&quot;plainlinks&quot;&gt;[https://github.com/dhimmel Daniel Himmelstein]&lt;/span&gt;. Briefly, historical IDs that map uniquely to one &quot;newest&quot; ensembl gene ID were extracted from the &quot;old_to_newest.tsv&quot; file from the respective Human, Mouse, and Rat repositories generated for Ensembl 105 &lt;span class=&quot;plainlinks&quot;&gt;[https://github.com/related-sciences/ensembl-genes (see: Github repository)]&lt;/span&gt; and then merged into the species specific Ensembl_Gene_ID chip file.&lt;/li&gt;<br /> &lt;li&gt;Gene orthology annotations for mapping mouse and rat genes to their best match human orthologs have been updated to &lt;span class=&quot;plainlinks&quot;&gt;[https://www.alliancegenome.org/ Alliance of Genome Resources]&lt;/span&gt; orthology database release 4.2.&lt;/li&gt;<br /> &lt;li&gt;&lt;b&gt;Warning:&lt;/b&gt; Rat Microarray derived annotations. Ensembl 105 brought a major update to the rat genome assembly transitioning from the deprecated Rnor_6.0 assembly to the modern mRatBN7.2 assembly. However, Ensembl has not yet released updated microarray probe mappings for the mRatBN7.2 assembly. In order to continue to provide CHIP files and internal mappings in MSigDB for experiments derived from these platforms, we have carried forward the historical Probe-to-Gene mappings from Ensembl 103/MSigDB v7.4 and remapped the target genes to the current assembly using the Ensembl_Gene_ID_MSigDB.v7.5 chip. However, until Ensembl releases updated probe to gene mappings derived directly from the mRatBN7.2 assembly the quality of MSigDB's rat microarray chip files may be impacted. Rat CHIP files affected by this have recieved the suffix the temporary suffix &lt;b&gt;_REMAPPED&lt;/b&gt; after the MSigDB version number.&lt;/li&gt;<br /> &lt;/ul&gt;</div> Acastanza https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=Version_check&diff=4556 Version check 2023-07-29T06:25:40Z <p>Acastanza: </p> <hr /> <div>TCGA_SampleSelection: 2023.1.Hs</div> Acastanza https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=MSigDB_Latest_Release_Notes&diff=4528 MSigDB Latest Release Notes 2023-03-04T00:21:08Z <p>Acastanza: </p> <hr /> <div>[[MSigDB_v2023.1.Hs_Release_Notes]]<br /> <br /> [[MSigDB_v2023.1.Mm_Release_Notes]]</div> Acastanza https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=Release_Notes&diff=4527 Release Notes 2023-03-04T00:20:41Z <p>Acastanza: </p> <hr /> <div>[http://www.broadinstitute.org/gsea/ GSEA Home] |<br /> [http://www.broadinstitute.org/gsea/downloads.jsp Downloads] | <br /> [http://www.broadinstitute.org/gsea/msigdb/ Molecular Signatures Database] | <br /> [http://www.broadinstitute.org/cancer/software/gsea/wiki/index.php/Main_Page Documentation] |<br /> [http://www.broadinstitute.org/gsea/contact.jsp Contact]<br /> &lt;br&gt;<br /> <br /> &lt;h3&gt;&lt;font color=&quot;#3366ff&quot;&gt;GSEA Software Release Notes&lt;/font&gt;&lt;/h3&gt;<br /> &lt;table width=&quot;700&quot; cellspacing=&quot;1&quot; cellpadding=&quot;1&quot; border=&quot;0&quot; align=&quot;&quot; height=&quot;78&quot; summary=&quot;&quot;&gt;<br /> &lt;tr&gt;<br /> &lt;td&gt;&lt;strong&gt;Date&lt;/strong&gt;&lt;/td&gt;<br /> &lt;td&gt;&lt;strong&gt;Release&lt;/strong&gt;&lt;/td&gt;<br /> &lt;td&gt;&lt;strong&gt;Description&lt;/strong&gt;&lt;/td&gt;<br /> &lt;td&gt;&lt;strong&gt;Release Notes&lt;/strong&gt;&lt;/td&gt;<br /> &lt;/tr&gt;<br /> &lt;tr&gt;<br /> &lt;td&gt;Sep 2022&lt;/td&gt;<br /> &lt;td&gt;4.3.&lt;em&gt;x&lt;/em&gt;*&lt;br /&gt;<br /> &lt;/td&gt;<br /> &lt;td&gt;Support for the new Mouse MSigDB database and versioning scheme changes.<br /> &lt;/td&gt;<br /> &lt;td&gt;[[GSEA_v4.3.x_Release_Notes|wiki]]&lt;/td&gt;<br /> &lt;/tr&gt;<br /> &lt;tr&gt;<br /> &lt;td&gt;Dec 2021 - Jan 2022&lt;/td&gt;<br /> &lt;td&gt;4.2.&lt;em&gt;x&lt;/em&gt;&lt;br /&gt;<br /> &lt;/td&gt;<br /> &lt;td&gt;New metric (Spearman) and new collapse mode (Absolute Max), better handling of missing values and many other fixes. Updated to latest Log4J jars to avoid concerns of vulnerabilities in earlier Log4J versions.&lt;br /&gt;<br /> &lt;/td&gt;<br /> &lt;td&gt;[[GSEA_v4.2.x_Release_Notes|wiki]]&lt;/td&gt;<br /> &lt;/tr&gt;<br /> &lt;tr&gt;<br /> &lt;td&gt;Jul 2020&lt;/td&gt;<br /> &lt;td&gt;4.1.&lt;em&gt;x&lt;/em&gt;&lt;br /&gt;<br /> &lt;/td&gt;<br /> &lt;td&gt;Improved support for macOS Catalina, updated and improved Enrichment Reports, and numerous bug fixes&lt;br /&gt;<br /> &lt;/td&gt;<br /> &lt;td&gt;[[GSEA_v4.1.x_Release_Notes|wiki]]&lt;/td&gt;<br /> &lt;/tr&gt;<br /> &lt;tr&gt;<br /> &lt;td&gt;Aug 2019 - Nov 2019&lt;/td&gt;<br /> &lt;td&gt;4.0.&lt;em&gt;x&lt;/em&gt;&lt;br /&gt;<br /> &lt;/td&gt;<br /> &lt;td&gt;Updates for MSigDB 7.0, Java 11 compatibility, and better performance&lt;br /&gt;<br /> &lt;/td&gt;<br /> &lt;td&gt;[[GSEA_v4.0.x_Release_Notes|wiki]]&lt;/td&gt;<br /> &lt;/tr&gt;<br /> &lt;tr&gt;<br /> &lt;td&gt;Jul 2017&lt;/td&gt;<br /> &lt;td&gt;3.0&lt;br /&gt;<br /> &lt;/td&gt;<br /> &lt;td&gt;Open source release, with numerous improvements and bug fixes&lt;br /&gt;<br /> &lt;/td&gt;<br /> &lt;td&gt;[[GSEA_v3.0_Release_Notes|wiki]]&lt;/td&gt;<br /> &lt;/tr&gt;<br /> &lt;tr&gt;<br /> &lt;td&gt;Mar 2015 - Apr 2017&lt;/td&gt;<br /> &lt;td&gt;2.2.x&lt;br /&gt;<br /> &lt;/td&gt;<br /> &lt;td&gt;&amp;nbsp;&lt;br /&gt;<br /> &lt;/td&gt;<br /> &lt;td&gt;[[GSEA_v2.2.x_Release_Notes|wiki]]&lt;/td&gt;<br /> &lt;/tr&gt;<br /> &lt;tr&gt;<br /> &lt;td&gt;Jun 2014&lt;/td&gt;<br /> &lt;td&gt;2.1.0&lt;/td&gt;<br /> &lt;td&gt;Added Enrichment Map visualization of GSEA results&lt;/td&gt;<br /> &lt;td&gt;[[GSEA_v2.1.0._Release_Notes|wiki]]&lt;/td&gt;<br /> &lt;/tr&gt;<br /> &lt;tr&gt;<br /> &lt;td&gt;Jan 2007 - Jan 2014&lt;/td&gt;<br /> &lt;td&gt;2.0.x&lt;br /&gt;<br /> &lt;/td&gt;<br /> &lt;td&gt;&amp;nbsp;&lt;br /&gt;<br /> &lt;/td&gt;<br /> &lt;td&gt;[[GSEA_v2.0.x_Release_Notes|wiki]]&lt;/td&gt;<br /> &lt;/tr&gt;<br /> &lt;tr&gt;<br /> &lt;td&gt;Mar 2005&lt;/td&gt;<br /> &lt;td&gt;1.0&lt;/td&gt;<br /> &lt;td&gt;Initial release&lt;/td&gt;<br /> &lt;td&gt;&amp;nbsp;&lt;/td&gt;<br /> &lt;/tr&gt;<br /> &lt;/table&gt;<br /> <br /> &lt;h3&gt;&lt;font color=&quot;#3366ff&quot;&gt;MSigDB Release Notes&lt;/font&gt;&lt;/h3&gt;<br /> &lt;table height=&quot;83&quot; width=&quot;637&quot; cellspacing=&quot;1&quot; cellpadding=&quot;1&quot; border=&quot;0&quot; align=&quot;&quot; summary=&quot;&quot;&gt;<br /> &lt;tr&gt;<br /> &lt;td&gt;&lt;strong&gt;Date&lt;/strong&gt;&lt;/td&gt;<br /> &lt;td&gt;&lt;strong&gt;Release&lt;/strong&gt;&lt;/td&gt;<br /> &lt;td&gt;&lt;strong&gt;Description&lt;/strong&gt;&lt;/td&gt;<br /> &lt;td&gt;&lt;strong&gt;Release Notes&lt;/strong&gt;&lt;/td&gt;<br /> &lt;/tr&gt;<br /> &lt;tr valign=&quot;top&gt;<br /> &lt;td&gt;Mar 2023&lt;/td&gt;<br /> &lt;td&gt;&amp;nbsp;2023.1.Hs*&lt;/td&gt;<br /> &lt;td&gt;Update to Ensembl 109 gene annotation data. Miscellaneous collection updates&lt;br&gt;<br /> &lt;td&gt;[[MSigDB_v2023.1.Hs_Release_Notes|wiki]]&lt;/td&gt;<br /> &lt;/tr&gt; <br /> &lt;tr valign=&quot;top&gt;<br /> &lt;td&gt;Mar 2023&lt;/td&gt;<br /> &lt;td&gt;&amp;nbsp;2023.1.Mm*&lt;/td&gt;<br /> &lt;td&gt;Update to Ensembl 109 gene annotation data. Miscellaneous collection updates&lt;br&gt;<br /> &lt;td&gt;[[MSigDB_v2023.1.Mm_Release_Notes|wiki]]&lt;/td&gt;<br /> &lt;/tr&gt; <br /> &lt;tr valign=&quot;top&gt;<br /> &lt;td&gt;Sep 2022&lt;/td&gt;<br /> &lt;td&gt;&amp;nbsp;2022.1.Hs&lt;/td&gt;<br /> &lt;td&gt;Human MSigDB under a new versioning scheme&lt;br&gt;<br /> &lt;td&gt;[[MSigDB_v2022.1.Hs_Release_Notes|wiki]]&lt;/td&gt;<br /> &lt;/tr&gt; <br /> &lt;tr valign=&quot;top&gt;<br /> &lt;td&gt;Sep 2022&lt;/td&gt;<br /> &lt;td&gt;&amp;nbsp;2022.1.Mm&lt;/td&gt;<br /> &lt;td&gt;Initial release of Mouse MSigDB&lt;br&gt;<br /> &lt;td&gt;[[MSigDB_v2022.1.Mm_Release_Notes|wiki]]&lt;/td&gt;<br /> &lt;/tr&gt; <br /> &lt;tr valign=&quot;top&gt;<br /> &lt;td&gt;Jan 2022&lt;/td&gt;<br /> &lt;td&gt;&amp;nbsp;7.5&lt;/td&gt;<br /> &lt;td&gt;&lt;br&gt;<br /> &lt;td&gt;[[MSigDB_v7.5_Release_Notes|wiki]]&lt;/td&gt;<br /> &lt;/tr&gt; <br /> &lt;tr valign=&quot;top&gt;<br /> &lt;td&gt;Mar 2021&lt;/td&gt;<br /> &lt;td&gt;&amp;nbsp;7.4&lt;/td&gt;<br /> &lt;td&gt;&lt;br&gt;<br /> &lt;td&gt;[[MSigDB_v7.4_Release_Notes|wiki]]&lt;/td&gt;<br /> &lt;/tr&gt; <br /> &lt;tr valign=&quot;top&gt;<br /> &lt;td&gt;Mar 2021&lt;/td&gt;<br /> &lt;td&gt;&amp;nbsp;7.3&lt;/td&gt;<br /> &lt;td&gt;C2:CP:WikiPathways +15; C2:CP:Reactome +15; C3:GTRD +175 (bugfix); C5:GO -88; C5:HPO +319; C7:VAX (new sub-collection); C8: +333&lt;br&gt;<br /> &lt;td&gt;[[MSigDB_v7.3_Release_Notes|wiki]]&lt;/td&gt;<br /> &lt;/tr&gt; <br /> &lt;tr valign=&quot;top&gt;<br /> &lt;td&gt;Sep 2020&lt;/td&gt;<br /> &lt;td&gt;&amp;nbsp;7.2&lt;/td&gt;<br /> &lt;td&gt;C2:CGP +60; C2:CP:WikiPathways (new sub-collection); C2:CP:Reactome +22; C3:GTRD -176; C5:GO +79, C5:HPO (new sub-collection); C8: +51 (promoted from supplementary)&lt;br&gt;<br /> &lt;td&gt;[[MSigDB_v7.2_Release_Notes|wiki]]&lt;/td&gt;<br /> &lt;/tr&gt; <br /> &lt;tr valign=&quot;top&gt;<br /> &lt;td&gt;Mar 2020&lt;/td&gt;<br /> &lt;td&gt;&amp;nbsp;7.1&lt;/td&gt;<br /> &lt;td&gt;C2 (+28); C3 (+2904); C5(+196)&lt;br&gt;<br /> &lt;td&gt;[[MSigDB_v7.1_Release_Notes|wiki]]&lt;/td&gt;<br /> &lt;/tr&gt; <br /> &lt;tr valign=&quot;top&gt;<br /> &lt;td&gt;Aug 2019&lt;/td&gt;<br /> &lt;td&gt;&amp;nbsp;7.0&lt;/td&gt;<br /> &lt;td&gt;C1 (-27); C2 (+738); C5 (+4079); &lt;br&gt;<br /> &lt;td&gt;[[MSigDB_v7.0_Release_Notes|wiki]]&lt;/td&gt;<br /> &lt;/tr&gt; <br /> &lt;tr valign=&quot;top&gt;<br /> &lt;td&gt;Jul 2018&lt;/td&gt;<br /> &lt;td&gt;&amp;nbsp;6.2&lt;/td&gt;<br /> &lt;td&gt;C2 (+24)&lt;br&gt;<br /> [[Mapping_between_v6.2_and_v6.1_gene_sets|Mapping between v6.2 and v6.1 gene sets]]&lt;/td&gt;<br /> &lt;td&gt;[[MSigDB_v6.2_Release_Notes|wiki]]&lt;/td&gt;<br /> &lt;/tr&gt; <br /> &lt;tr valign=&quot;top&gt;<br /> &lt;td&gt;Oct 2017&lt;/td&gt;<br /> &lt;td&gt;&amp;nbsp;6.1&lt;/td&gt;<br /> &lt;td&gt;C2 (+7)&lt;br&gt;<br /> [[Mapping_between_v6.1_and_v6.0_gene_sets|Mapping between v6.1 and v6.0 gene sets]]&lt;/td&gt;<br /> &lt;td&gt;[[MSigDB_v6.1_Release_Notes|wiki]]&lt;/td&gt;<br /> &lt;/tr&gt; <br /> &lt;tr valign=&quot;top&gt;<br /> &lt;td&gt;Apr 2017&lt;/td&gt;<br /> &lt;td&gt;&amp;nbsp;6.0&lt;/td&gt;<br /> &lt;td&gt;C2 (+2); C5 (-249)&lt;/td&gt;<br /> &lt;td&gt;[[MSigDB_v6.0_Release_Notes|wiki]]&lt;/td&gt;<br /> &lt;/tr&gt; <br /> &lt;tr valign=&quot;top&quot;&gt;<br /> &lt;td&gt;Oct 2016&lt;/td&gt;<br /> &lt;td&gt;&amp;nbsp;5.2&lt;/td&gt;<br /> &lt;td&gt;C2 (+4); C5 (+4,712)&lt;br&gt;<br /> [[Mapping_between_v5.2_and_v5.1_gene_sets|Mapping between v5.2 and v5.1 gene sets]]&lt;/td&gt;<br /> &lt;td&gt;[[MSigDB_v5.2_Release_Notes|wiki]]&lt;/td&gt;<br /> &lt;tr valign=&quot;top&gt;<br /> &lt;td&gt;Jan 2016&lt;/td&gt;<br /> &lt;td&gt;&amp;nbsp;5.1&lt;/td&gt;<br /> &lt;td&gt;C2 (+1); C7 (+2,962)&lt;/td&gt;<br /> &lt;td&gt; [[MSigDB_v5.1_Release_Notes|wiki]]&lt;/td&gt;<br /> &lt;/tr&gt;<br /> &lt;tr valign=&quot;top&quot;&gt;<br /> &lt;td&gt;Mar 2015&lt;/td&gt;<br /> &lt;td&gt;&amp;nbsp;5.0&lt;/td&gt;<br /> &lt;td&gt;H (+50); C2 (+3)&lt;br&gt;<br /> [[Mapping_between_v5.0_and_v4.0_gene_sets|Mapping between v5.0 and v4.0 gene sets]]&lt;/td&gt;<br /> &lt;td&gt;[[MSigDB_v5.0_Release_Notes|wiki]]&lt;/td&gt;<br /> &lt;/tr&gt;<br /> &lt;tr valign=&quot;top&quot;&gt;<br /> &lt;td&gt;May 2013&lt;/td&gt;<br /> &lt;td&gt;&amp;nbsp;4.0&lt;/td&gt;<br /> &lt;td&gt;C2 (-128); C7 (+1,910)&lt;/td&gt;<br /> &lt;td&gt;[[MSigDB_v4.0_Release_Notes|wiki]]&lt;/td&gt;<br /> &lt;/tr&gt;<br /> &lt;tr valign=&quot;top&quot;&gt;<br /> &lt;td&gt;Oct 2012&lt;/td&gt;<br /> &lt;td&gt;&amp;nbsp;3.1&lt;/td&gt;<br /> &lt;td&gt;C2 (+1,578); C4 (-23); C6 (+189)&lt;br&gt;<br /> [[Mapping_between_v3.1_and_v3.0_gene_sets|Mapping between v3.0 and v3.1 gene sets]]&lt;/td&gt;<br /> &lt;td&gt;[[MSigDB_v3.1_Release_Notes|wiki]]&lt;/td&gt;<br /> &lt;/tr&gt;<br /> &lt;tr valign=&quot;top&quot;&gt;<br /> &lt;td&gt;Sept 2010&lt;/td&gt;<br /> &lt;td&gt;&amp;nbsp;3.0&lt;/td&gt;<br /> &lt;td&gt;C1 (-60); C2 (+1,380); C3 (-1); C4 (-2) &lt;br&gt;<br /> [[Msigdb_mapping_v2.5_to_v3|Mapping between v2.5 and v3.0 gene sets]]&lt;/td&gt;<br /> &lt;td&gt;[[MSigDB_v3.0_Release_Notes|wiki]]&lt;/td&gt;<br /> &lt;/tr&gt;<br /> &lt;tr valign=&quot;top&quot;&gt;<br /> &lt;td&gt;April 2008&lt;/td&gt;<br /> &lt;td&gt;&amp;nbsp;2.5&lt;/td&gt;<br /> &lt;td&gt; C2 (+205); C4 (+456); C5 (+1454) &lt;br /&gt;<br /> &lt;/td&gt;<br /> &lt;td&gt;[[MSigDB_v2.5_Release_Notes|wiki]]&lt;/td&gt;<br /> &lt;/tr&gt;<br /> &lt;tr valign=&quot;top&quot;&gt;<br /> &lt;td&gt;Feb 2007&lt;/td&gt;<br /> &lt;td&gt;&amp;nbsp;2.1&lt;/td&gt;<br /> &lt;td&gt;Minor updates to MSigDB v2.0 annotations &lt;/td&gt;<br /> &lt;td&gt;&lt;br /&gt;<br /> &lt;/td&gt;<br /> &lt;/tr&gt;<br /> &lt;tr valign=&quot;top&quot;&gt;<br /> &lt;td&gt;Jan 2007&lt;/td&gt;<br /> &lt;td&gt;&amp;nbsp;2.0&lt;/td&gt;<br /> &lt;td&gt;C1 (updated); C2 (+269); C3 (+214) &lt;br /&gt;<br /> [[Msigdb_mapping_v1_to_v2|Mapping between v1 and v2 gene sets]]&lt;/td&gt;<br /> &lt;td&gt;[[Msigdb_may_2006_release_notes|wiki]]&lt;/td&gt;<br /> &lt;/tr&gt;<br /> &lt;tr valign=&quot;top&quot;&gt;<br /> &lt;td&gt;Nov 2005&lt;/td&gt;<br /> &lt;td&gt;&amp;nbsp;1.1&lt;/td&gt;<br /> &lt;td&gt;C1 (updated); C2 (+350); C3 (+566); C4&lt;br /&gt;<br /> &lt;/td&gt;<br /> &lt;td&gt;[http://www.broadinstitute.org/gsea/doc/msigdb_nov_2005_release_notes.pdf pdf]&lt;/td&gt;<br /> &lt;/tr&gt;<br /> &lt;tr valign=&quot;top&quot;&gt;<br /> &lt;td&gt;March 2005&lt;/td&gt;<br /> &lt;td&gt;&amp;nbsp;1.0&lt;/td&gt;<br /> &lt;td&gt;Initial release &lt;br /&gt;<br /> &lt;/td&gt;<br /> &lt;td&gt; [http://www.broadinstitute.org/gsea/doc/msigdb_march_2005_release_notes.pdf pdf]&lt;/td&gt;<br /> &lt;/tr&gt;<br /> &lt;/table&gt;<br /> &lt;h3&gt;&lt;font color=&quot;#3366ff&quot;&gt;Web site Release Notes&lt;/font&gt;&lt;/h3&gt;<br /> &lt;table height=&quot;78&quot; width=&quot;639&quot; cellspacing=&quot;1&quot; cellpadding=&quot;1&quot; border=&quot;0&quot; align=&quot;&quot; summary=&quot;&quot;&gt;<br /> &lt;tr&gt;<br /> &lt;td&gt;&lt;strong&gt;Date&lt;/strong&gt;&lt;/td&gt;<br /> &lt;td&gt;&lt;strong&gt;Release&lt;/strong&gt;&lt;/td&gt;<br /> &lt;td&gt;&lt;strong&gt;Description&lt;/strong&gt;&lt;/td&gt;<br /> &lt;td&gt;&lt;strong&gt;Release Notes&lt;/strong&gt;&lt;/td&gt;<br /> &lt;/tr&gt;<br /> &lt;tr&gt;<br /> &lt;td&gt;Aug 2019&lt;/td&gt;<br /> &lt;td&gt;6.4*&lt;/td&gt;<br /> &lt;td&gt;Upgrades to support v7.0 MSigDB.&lt;/td&gt;<br /> &lt;td&gt;[[Web site v6.4 Release Notes|wiki]]&lt;/td&gt;<br /> &lt;/tr&gt;<br /> &lt;tr&gt;<br /> &lt;td&gt;Apr 2017&lt;/td&gt;<br /> &lt;td&gt;6.0&lt;/td&gt;<br /> &lt;td&gt;Upgrades to support v6.0 MSigDB.&lt;/td&gt;<br /> &lt;td&gt;&lt;/td&gt;<br /> &lt;/tr&gt;<br /> &lt;tr&gt;<br /> &lt;td&gt;Mar 2015&lt;/td&gt;<br /> &lt;td&gt;5.0&lt;/td&gt;<br /> &lt;td&gt;Upgrades to support v5.0 MSigDB.&lt;/td&gt;<br /> &lt;td&gt;&lt;/td&gt;<br /> &lt;/tr&gt;<br /> &lt;tr&gt;<br /> &lt;td&gt;Jun 2014&lt;/td&gt;<br /> &lt;td&gt;4.05&lt;/td&gt;<br /> &lt;td&gt;Several minor updates&lt;/td&gt;<br /> &lt;td&gt;&lt;/td&gt;<br /> &lt;/tr&gt;<br /> &lt;tr&gt;<br /> &lt;td&gt;Apr 2013&lt;/td&gt;<br /> &lt;td&gt;3.87&lt;/td&gt;<br /> &lt;td&gt;Several bug fixes and new functionality.&lt;/td&gt;<br /> &lt;td&gt;[[Web site v3.87 Release Notes|wiki]]&lt;/td&gt;<br /> &lt;/tr&gt;<br /> &lt;tr&gt;<br /> &lt;td&gt;Oct 2012&lt;/td&gt;<br /> &lt;td&gt;3.84&lt;/td&gt;<br /> &lt;td&gt;Several updates and new functionality.&lt;/td&gt;<br /> &lt;td&gt;&lt;/td&gt;<br /> &lt;/tr&gt;<br /> &lt;tr&gt;<br /> &lt;td&gt;Jan 2011&lt;/td&gt;<br /> &lt;td&gt;3.5&lt;/td&gt;<br /> &lt;td&gt;Several bug fixes and some new functionality.&lt;/td&gt;<br /> &lt;td&gt;[[Web site v3.4 Release Notes|wiki]]&lt;br /&gt;<br /> &lt;/td&gt;<br /> &lt;/tr&gt;<br /> &lt;/table&gt;<br /> <br /> &lt;br /&gt;<br /> &lt;hr&gt;<br /> * Current release &lt;br /&gt;</div> Acastanza https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=Main_Page&diff=4526 Main Page 2023-03-04T00:18:32Z <p>Acastanza: </p> <hr /> <div>[http://www.broadinstitute.org/gsea/ GSEA Home] |<br /> [http://www.broadinstitute.org/gsea/downloads.jsp Downloads] | <br /> [http://www.broadinstitute.org/gsea/msigdb/ Molecular Signatures Database] | <br /> [http://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Main_Page Documentation] |<br /> [http://www.broadinstitute.org/gsea/contact.jsp Contact]<br /> &lt;br&gt;<br /> &lt;p&gt; Use the navigation bar on the left to display documentation on GSEA software, MSigDB database or GSEA/MSigDB web site. If you have comments or questions not answered by the [[FAQ]] or the [http://www.broadinstitute.org/gsea/doc/GSEAUserGuideFrame.html User Guide], contact us at [https://groups.google.com/group/gsea-help groups.google.com/group/gsea-help].&lt;/p&gt;<br /> <br /> &lt;ul&gt; When contacting our team with questions about java GSEA programs, please send the following information:<br /> &lt;li&gt; your computer's operation system<br /> &lt;li&gt; version of java which you used to run GSEA<br /> &lt;li&gt; detailed log transcript from the GSEA session in question<br /> &lt;p&gt; to view the log, click [+] at the bottom of main screen of GSEA java desktop application, copy the text to a separate file and attach it to your request &lt;/p&gt;<br /> &lt;/ul&gt;<br /> <br /> &lt;h2&gt;Where to start&lt;/h2&gt;<br /> &lt;p&gt; If you are new to GSEA, see the [http://www.broadinstitute.org/gsea/doc/desktop_tutorial.jsp Tutorial] for a brief overview of the software. <br /> If you have a question, see the [[FAQ]] or the [http://www.broadinstitute.org/gsea/doc/GSEAUserGuideFrame.html User Guide]. The User Guide describes how to prepare data files, load data files, run the gene set enrichment analysis, and interpret the results. It also includes instructions for running GSEA from the command line and a Quick Reference section, which describes each window of the GSEA desktop application. &lt;br /&gt;<br /> &lt;/p&gt;<br /> &lt;h3&gt;Getting started with RNA-seq and GSEA&lt;/h3&gt;<br /> The GSEA method was originally developed for analysis of microarray data. In order to best adapt this method for RNA-sequencing data sets the GSEA team has developed a [[Using_RNA-seq_Datasets_with_GSEA|collection of guidelines and suggestions which describe how to properly handle these data.]]<br /> &lt;h2&gt;MSigDB gene sets&lt;/h2&gt;<br /> &lt;p&gt; Current release of the Molecular Signatures Database is divided into two parts, the MSigDB Human Collections, and the MSigDB Mouse collections. Release notes for the current version of the Human collections are available here: ([[MSigDB_v2023.1.Hs_Release_Notes|MSigDB v2023.1.Hs]]) and the release notes for the current version of the Mouse collections are available here: ([[MSigDB_v2023.1.Mm_Release_Notes|MSigDB v2023.1.Mm]]). For information about MSigDB and the gene sets, see the [http://www.broadinstitute.org/gsea/msigdb MSigDB web site]. &lt;/p&gt;<br /> &lt;p&gt; Please note that gene sets can change or become deprecated in subsequent releases of MSigDB. It is thus important to indicate the version of MSigDB to fully reference gene sets used in your study. &lt;/p&gt;<br /> <br /> &lt;h2&gt;Software&lt;/h2&gt;<br /> &lt;p&gt;We provide the following software implementations of the GSEA method:<br /> &lt;ul&gt;<br /> &lt;li&gt;Java desktop application -- Easy-to-use graphical interface that can be run from the [http://www.broadinstitute.org/gsea/downloads.jsp Downloads] page. The [http://www.broadinstitute.org/gsea/doc/GSEAUserGuideFrame.html User Guide] fully describes this application in detail.<br /> &lt;/li&gt;<br /> &lt;li&gt;Java jar file -- Command line interface that can be downloaded from the [http://www.broadinstitute.org/gsea/downloads.jsp Downloads] page. See [http://software.broadinstitute.org/gsea/doc/GSEAUserGuideTEXT.htm#_Running_GSEA_from Running GSEA from the Command Line] in the &lt;i&gt;User Guide&lt;/i&gt; for details. This might be useful for analyzing several datasets sequentially, analyzing large datasets, or running analyses on a compute cluster.&lt;/li&gt;<br /> &lt;li&gt;R-GSEA -- R implementation of GSEA that can be downloaded from the [http://www.broadinstitute.org/gsea/downloads_archive.jsp Archived Downloads] page. This implementation is intended for experienced computational biologists who may want to explore the underlying algorithm. The [[R-GSEA_Readme|R-GSEA Readme]] provides brief instructions and support is limited. Please note that this implementation is not actively maintained or supported.&lt;/li&gt;<br /> &lt;/ul&gt;<br /> &lt;/p&gt;<br /> &lt;p&gt;Thank you for your interest in GSEA,&lt;br&gt;<br /> The GSEA Team&lt;/p&gt;</div> Acastanza https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=MSigDB_v2023.1.Mm_Release_Notes&diff=4525 MSigDB v2023.1.Mm Release Notes 2023-03-03T22:35:05Z <p>Acastanza: </p> <hr /> <div>&lt;span class=&quot;plainlinks&quot;&gt;<br /> [http://www.broadinstitute.org/gsea/ GSEA Home] |<br /> [http://www.broadinstitute.org/gsea/downloads.jsp Downloads] | <br /> [http://www.broadinstitute.org/gsea/msigdb/ Molecular Signatures Database] | <br /> [http://www.broadinstitute.org/cancer/software/gsea/wiki/index.php/Main_Page Documentation] |<br /> [http://www.broadinstitute.org/gsea/contact.jsp Contact]<br /> &lt;/span&gt;<br /> <br /> &lt;h1&gt;Important Notices&lt;/h1&gt;<br /> <br /> This page describes updates made to the Molecular Signatures Database Mouse Collections for release 2023.1 (MSigDB 2023.1.Mm).<br /> <br /> '''In order to access the MSigBD mouse collections through the GSEA UI, the GSEA 4.3.0 or newer is required.'''<br /> <br /> MSigDB v2023.1 is based on gene annotation data from Ensembl Release 109 (Feb 2023).<br /> <br /> <br /> &lt;h1&gt;Updates to Mouse Collections (MSigDB v2023.1.Mm)&lt;/h1&gt;<br /> <br /> &lt;h2&gt;M1: positional gene sets&lt;/h2&gt;<br /> 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.<br /> <br /> &lt;h2&gt;M2:CGP&lt;/h2&gt;<br /> <br /> 3 Gene sets contributed by MSigDB users have been added to M2:CGP<br /> &lt;ul&gt;<br /> &lt;li&gt;&lt;span class=&quot;plainlinks&quot;&gt;[https://gsea-msigdb.org/gsea/msigdb/mouse/geneset/SAUL_SEN_MAYO SAUL_SEN_MAYO]&lt;/span&gt;&lt;/li&gt;<br /> &lt;li&gt;&lt;span class=&quot;plainlinks&quot;&gt;[https://gsea-msigdb.org/gsea/msigdb/mouse/geneset/MA_RAT_AGING_UP MA_RAT_AGING_UP]&lt;/span&gt;&lt;/li&gt;<br /> &lt;li&gt;&lt;span class=&quot;plainlinks&quot;&gt;[https://gsea-msigdb.org/gsea/msigdb/mouse/geneset/MA_RAT_AGING_DN MA_RAT_AGING_DN]&lt;/span&gt;&lt;/li&gt;<br /> &lt;/ul&gt;<br /> &lt;br&gt;<br /> <br /> &lt;h2&gt;M2:CP:Reactome&lt;/h2&gt;<br /> <br /> &lt;ul&gt;<br /> &lt;li&gt;Reactome gene sets have been updated to reflect the state of the Reactome pathway architecture as of '''Reactome v83''' (+2 gene sets).&lt;/li&gt;<br /> &lt;li&gt;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.&lt;/li&gt;<br /> &lt;/ul&gt;<br /> <br /> &lt;h2&gt;M2:CP:WikiPathways&lt;/h2&gt;<br /> WikiPathways gene sets have been updated to the February 10, 2023 release (+XX gene sets).<br /> <br /> &lt;h2&gt;M3:GTRD&lt;/h2&gt;<br /> &lt;p&gt;GTRD data was updated to the 21.12 release (+7 gene sets).&lt;/p&gt;<br /> <br /> &lt;h2&gt;M5:GO (Gene Ontology)&lt;/h2&gt;<br /> &lt;p&gt; 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 (&lt;span class=&quot;plainlinks&quot;&gt;[http://www.geneontology.org Nature Genet 2000]&lt;/span&gt;). 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.&lt;/p&gt;<br /> <br /> &lt;p&gt;This collection is divided into three sub-collections:&lt;/p&gt;<br /> &lt;ul&gt;<br /> &lt;li&gt;&lt;strong&gt;BP&lt;/strong&gt;: GO Biological process (+67 gene sets). Gene sets derived from the Biological Process Ontology, which are prefixed with &quot;GOBP_&quot;.&lt;/li&gt;<br /> &lt;li&gt;&lt;strong&gt;CC&lt;/strong&gt;: GO Cellular component (-11 gene sets). Gene sets derived from the Cellular Component Ontology, which are prefixed with &quot;GOCC_&quot;.&lt;/li&gt;<br /> &lt;li&gt;&lt;strong&gt;MF&lt;/strong&gt;: GO Molecular function (+57 gene sets). Gene sets derived from the Molecular Function Ontology, which are prefixed with &quot;GOMF_&quot;..&lt;/li&gt;<br /> &lt;/ul&gt;<br /> <br /> &lt;p&gt;These updates were generated in accordance with the procedure described in the [[MSigDB_v7.0_Release_Notes#C5_.28Gene_Ontology_collection.29_-_Major_overhaul | GO release notes for MSigDB 7.0.]]&lt;/p&gt;<br /> <br /> <br /> &lt;h2&gt;M8 cell type signature gene sets&lt;/h2&gt;<br /> &lt;p&gt;Added gene sets describing uterine cell type identity signatures from &lt;span class=&quot;plainlinks&quot;&gt;[https://pubmed.ncbi.nlm.nih.gov/35669188/ Zhang, et al. 2022 Digital Cell Atlas of Mouse Uterus: From Regenerative Stage to Maturational Stage.]&lt;/span&gt; (+18 gene sets)&lt;/p&gt;<br /> <br /> &lt;h2&gt;CHIP file updates&lt;/h2&gt;<br /> &lt;ul&gt;<br /> &lt;li&gt;MSigDB 2023.1.Mm gene annotations and gene mapping CHIP files have been updated to data from Ensembl 109.&lt;/li&gt;<br /> &lt;li&gt;Gene orthology annotations for mapping human and rat genes to their best match mouse orthologs have been updated to &lt;span class=&quot;plainlinks&quot;&gt;[https://www.alliancegenome.org/ Alliance of Genome Resources]&lt;/span&gt; orthology database release 5.3.0 (2022-10-28)&lt;/li&gt;<br /> &lt;/ul&gt;</div> Acastanza https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=MSigDB_v2023.1.Hs_Release_Notes&diff=4524 MSigDB v2023.1.Hs Release Notes 2023-03-03T22:34:52Z <p>Acastanza: </p> <hr /> <div>&lt;span class=&quot;plainlinks&quot;&gt;<br /> [http://www.broadinstitute.org/gsea/ GSEA Home] |<br /> [http://www.broadinstitute.org/gsea/downloads.jsp Downloads] | <br /> [http://www.broadinstitute.org/gsea/msigdb/ Molecular Signatures Database] | <br /> [http://www.broadinstitute.org/cancer/software/gsea/wiki/index.php/Main_Page Documentation] |<br /> [http://www.broadinstitute.org/gsea/contact.jsp Contact]<br /> &lt;/span&gt;<br /> <br /> &lt;h1&gt;Important Notices&lt;/h1&gt;<br /> <br /> This page describes updates made to the Molecular Signatures Database Human Collections for release 2023.1 (MSigDB 2023.1.Hs).<br /> <br /> '''In order to access the MSigBD mouse collections through the GSEA UI, the GSEA 4.3.0 or newer is required.'''<br /> <br /> MSigDB v2023.1 is based on gene annotation data from Ensembl Release 109 (Feb 2023).<br /> <br /> <br /> &lt;h1&gt;Updates to Human Collections (MSigDB v2023.1.Hs)&lt;/h1&gt;<br /> <br /> &lt;h2&gt;C1: positional gene sets&lt;/h2&gt;<br /> Updated human gene annotations to Ensembl 109 (+1 gene set).<br /> &lt;h2&gt;C2:CGP&lt;/h2&gt;<br /> <br /> 6 Gene sets contributed by MSigDB users have been added to C2:CGP<br /> &lt;ul&gt;<br /> &lt;li&gt;&lt;span class=&quot;plainlinks&quot;&gt;[https://gsea-msigdb.org/gsea/msigdb/human/geneset/SAUL_SEN_MAYO SAUL_SEN_MAYO]&lt;/span&gt;&lt;/li&gt;<br /> &lt;li&gt;&lt;span class=&quot;plainlinks&quot;&gt;[https://gsea-msigdb.org/gsea/msigdb/human/geneset/MA_RAT_AGING_UP MA_RAT_AGING_UP]&lt;/span&gt;&lt;/li&gt;<br /> &lt;li&gt;&lt;span class=&quot;plainlinks&quot;&gt;[https://gsea-msigdb.org/gsea/msigdb/human/geneset/MA_RAT_AGING_DN MA_RAT_AGING_DN]&lt;/span&gt;&lt;/li&gt;<br /> &lt;li&gt;&lt;span class=&quot;plainlinks&quot;&gt;[https://gsea-msigdb.org/gsea/msigdb/human/geneset/NOURUZI_NEPC_ASCL1_TARGETS NOURUZI_NEPC_ASCL1_TARGETS]&lt;/span&gt;&lt;/li&gt;<br /> &lt;li&gt;&lt;span class=&quot;plainlinks&quot;&gt;[https://gsea-msigdb.org/gsea/msigdb/human/geneset/KOHN_EMT_EPITHELIAL KOHN_EMT_EPITHELIAL]&lt;/span&gt;&lt;/li&gt;<br /> &lt;li&gt;&lt;span class=&quot;plainlinks&quot;&gt;[https://gsea-msigdb.org/gsea/msigdb/human/geneset/KOHN_EMT_MESENCHYMAL KOHN_EMT_MESENCHYMAL]&lt;/span&gt;&lt;/li&gt;<br /> &lt;/ul&gt;<br /> &lt;br&gt;<br /> <br /> &lt;h2&gt;C2:CP:Reactome&lt;/h2&gt;<br /> <br /> &lt;ul&gt;<br /> &lt;li&gt;Reactome gene sets have been updated to reflect the state of the Reactome pathway architecture as of '''Reactome v83''' (+19 gene sets).&lt;/li&gt;<br /> &lt;li&gt;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.&lt;/li&gt;<br /> &lt;/ul&gt;<br /> <br /> &lt;h2&gt;C2:CP:WikiPathways&lt;/h2&gt;<br /> WikiPathways gene sets have been updated to the February 10, 2023 release (+21 gene sets).<br /> <br /> &lt;h2&gt;C3:TFT:GTRD&lt;/h2&gt;<br /> &lt;p&gt;GTRD data was updated to the 21.12 release. (-12 gene sets)&lt;/p&gt;<br /> <br /> &lt;h2&gt;C5:GO (Gene Ontology)&lt;/h2&gt;<br /> &lt;p&gt; 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 (&lt;span class=&quot;plainlinks&quot;&gt;[http://www.geneontology.org Nature Genet 2000]&lt;/span&gt;). 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.&lt;/p&gt;<br /> <br /> &lt;p&gt;This collection is divided into three sub-collections:&lt;/p&gt;<br /> &lt;ul&gt;<br /> &lt;li&gt;&lt;strong&gt;BP&lt;/strong&gt;: GO Biological process (-12 gene sets). Gene sets derived from the Biological Process Ontology, which are prefixed with &quot;GOBP_&quot;.&lt;/li&gt;<br /> &lt;li&gt;&lt;strong&gt;CC&lt;/strong&gt;: GO Cellular component (-26 gene sets). Gene sets derived from the Cellular Component Ontology, which are prefixed with &quot;GOCC_&quot;.&lt;/li&gt;<br /> &lt;li&gt;&lt;strong&gt;MF&lt;/strong&gt;: GO Molecular function (+9 gene sets). Gene sets derived from the Molecular Function Ontology, which are prefixed with &quot;GOMF_&quot;..&lt;/li&gt;<br /> &lt;/ul&gt;<br /> <br /> &lt;p&gt;These updates were generated in accordance with the procedure described in the [[MSigDB_v7.0_Release_Notes#C5_.28Gene_Ontology_collection.29_-_Major_overhaul | GO release notes for MSigDB 7.0.]]&lt;/p&gt;<br /> <br /> &lt;h2&gt;C5:HPO (Human Phenotype Ontology)&lt;/h2&gt;<br /> <br /> Gene sets in this sub-collection have been updated to reflect the 2023-01-27 release of the Human Phenotype Ontology database (+263 gene sets). This sub-collection has been redundancy filtered through a procedure comparable to that of the GO and Reactome sub-collections.<br /> <br /> &lt;h2&gt;C8 cell type signature gene sets&lt;/h2&gt;<br /> &lt;p&gt;Added gene sets describing lung cell type identity signatures from &lt;span class=&quot;plainlinks&quot;&gt;[https://pubmed.ncbi.nlm.nih.gov/36493756/ He P., Lim K., et al. 2022 A human fetal lung cell atlas uncovers proximal-distal gradients of differentiation and key regulators of epithelial fates.]&lt;/span&gt; &lt;span class=&quot;plainlinks&quot;&gt;(https://lungcellatlas.org)&lt;/span&gt; (+126 gene sets)&lt;/p&gt;<br /> <br /> &lt;h2&gt;CHIP file updates&lt;/h2&gt;<br /> &lt;ul&gt;<br /> &lt;li&gt;MSigDB 2023.1.Hs gene annotations and gene mapping CHIP files have been updated to data from Ensembl 109.&lt;/li&gt;<br /> &lt;li&gt;Gene orthology annotations for mapping mouse and rat genes to their best match human orthologs have been updated to &lt;span class=&quot;plainlinks&quot;&gt;[https://www.alliancegenome.org/ Alliance of Genome Resources]&lt;/span&gt; orthology database release 5.3.0 (2022-10-28)&lt;/li&gt;<br /> &lt;/ul&gt;</div> Acastanza https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=MSigDB_v2023.1.Mm_Release_Notes&diff=4523 MSigDB v2023.1.Mm Release Notes 2023-03-03T17:42:44Z <p>Acastanza: Added collection count changes</p> <hr /> <div>&lt;span class=&quot;plainlinks&quot;&gt;<br /> [http://www.broadinstitute.org/gsea/ GSEA Home] |<br /> [http://www.broadinstitute.org/gsea/downloads.jsp Downloads] | <br /> [http://www.broadinstitute.org/gsea/msigdb/ Molecular Signatures Database] | <br /> [http://www.broadinstitute.org/cancer/software/gsea/wiki/index.php/Main_Page Documentation] |<br /> [http://www.broadinstitute.org/gsea/contact.jsp Contact]<br /> &lt;/span&gt;<br /> <br /> &lt;h1&gt;Important Notices&lt;/h1&gt;<br /> <br /> This page describes updates made to the Molecular Signatures Database Mouse Collections for release 2023.1 (MSigDB 2023.1.Mm).<br /> <br /> '''In order to access the MSigBD mouse collections through the GSEA UI, the GSEA 4.3.0 or newer is required.'''<br /> <br /> MSigDB v2023.1 is based on gene annotation data from Ensembl Release 109 (Feb 2023).<br /> <br /> <br /> &lt;h1&gt;Updates to Mouse Collections (MSigDB v2023.1.Mm)&lt;/h1&gt;<br /> <br /> &lt;h2&gt;M1: positional gene sets&lt;/h2&gt;<br /> 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.<br /> <br /> &lt;h2&gt;M2:CGP&lt;/h2&gt;<br /> <br /> 3 Gene sets contributed by MSigDB users have been added to M2:CGP<br /> &lt;ul&gt;<br /> &lt;li&gt;&lt;span class=&quot;plainlinks&quot;&gt;[https://gsea-msigdb.org/gsea/msigdb/mouse/geneset/]&lt;/span&gt;&lt;/li&gt;<br /> &lt;/ul&gt;<br /> &lt;br&gt;<br /> <br /> &lt;h2&gt;M2:CP:Reactome&lt;/h2&gt;<br /> <br /> &lt;ul&gt;<br /> &lt;li&gt;Reactome gene sets have been updated to reflect the state of the Reactome pathway architecture as of '''Reactome v83''' (+2 gene sets).&lt;/li&gt;<br /> &lt;li&gt;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.&lt;/li&gt;<br /> &lt;/ul&gt;<br /> <br /> &lt;h2&gt;M2:CP:WikiPathways&lt;/h2&gt;<br /> WikiPathways gene sets have been updated to the February 10, 2023 release (+XX gene sets).<br /> <br /> &lt;h2&gt;M3:GTRD&lt;/h2&gt;<br /> &lt;p&gt;GTRD data was updated to the 21.12 release (+7 gene sets).&lt;/p&gt;<br /> <br /> &lt;h2&gt;M5:GO (Gene Ontology)&lt;/h2&gt;<br /> &lt;p&gt; 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 (&lt;span class=&quot;plainlinks&quot;&gt;[http://www.geneontology.org Nature Genet 2000]&lt;/span&gt;). 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.&lt;/p&gt;<br /> <br /> &lt;p&gt;This collection is divided into three sub-collections:&lt;/p&gt;<br /> &lt;ul&gt;<br /> &lt;li&gt;&lt;strong&gt;BP&lt;/strong&gt;: GO Biological process (+67 gene sets). Gene sets derived from the Biological Process Ontology, which are prefixed with &quot;GOBP_&quot;.&lt;/li&gt;<br /> &lt;li&gt;&lt;strong&gt;CC&lt;/strong&gt;: GO Cellular component (-11 gene sets). Gene sets derived from the Cellular Component Ontology, which are prefixed with &quot;GOCC_&quot;.&lt;/li&gt;<br /> &lt;li&gt;&lt;strong&gt;MF&lt;/strong&gt;: GO Molecular function (+57 gene sets). Gene sets derived from the Molecular Function Ontology, which are prefixed with &quot;GOMF_&quot;..&lt;/li&gt;<br /> &lt;/ul&gt;<br /> <br /> &lt;p&gt;These updates were generated in accordance with the procedure described in the [[MSigDB_v7.0_Release_Notes#C5_.28Gene_Ontology_collection.29_-_Major_overhaul | GO release notes for MSigDB 7.0.]]&lt;/p&gt;<br /> <br /> <br /> &lt;h2&gt;M8 cell type signature gene sets&lt;/h2&gt;<br /> &lt;p&gt;Added gene sets describing uterine cell type identity signatures from &lt;span class=&quot;plainlinks&quot;&gt;[https://pubmed.ncbi.nlm.nih.gov/35669188/ Zhang, et al. 2022 Digital Cell Atlas of Mouse Uterus: From Regenerative Stage to Maturational Stage.]&lt;/span&gt; (+18 gene sets)&lt;/p&gt;<br /> <br /> &lt;h2&gt;CHIP file updates&lt;/h2&gt;<br /> &lt;ul&gt;<br /> &lt;li&gt;MSigDB 2023.1.Mm gene annotations and gene mapping CHIP files have been updated to data from Ensembl 109.&lt;/li&gt;<br /> &lt;li&gt;Gene orthology annotations for mapping human and rat genes to their best match mouse orthologs have been updated to &lt;span class=&quot;plainlinks&quot;&gt;[https://www.alliancegenome.org/ Alliance of Genome Resources]&lt;/span&gt; orthology database release 5.3.0 (2022-10-28)&lt;/li&gt;<br /> &lt;/ul&gt;</div> Acastanza https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=MSigDB_v2023.1.Hs_Release_Notes&diff=4522 MSigDB v2023.1.Hs Release Notes 2023-03-03T17:41:06Z <p>Acastanza: Added collection count changes</p> <hr /> <div>&lt;span class=&quot;plainlinks&quot;&gt;<br /> [http://www.broadinstitute.org/gsea/ GSEA Home] |<br /> [http://www.broadinstitute.org/gsea/downloads.jsp Downloads] | <br /> [http://www.broadinstitute.org/gsea/msigdb/ Molecular Signatures Database] | <br /> [http://www.broadinstitute.org/cancer/software/gsea/wiki/index.php/Main_Page Documentation] |<br /> [http://www.broadinstitute.org/gsea/contact.jsp Contact]<br /> &lt;/span&gt;<br /> <br /> &lt;h1&gt;Important Notices&lt;/h1&gt;<br /> <br /> This page describes updates made to the Molecular Signatures Database Human Collections for release 2023.1 (MSigDB 2023.1.Hs).<br /> <br /> '''In order to access the MSigBD mouse collections through the GSEA UI, the GSEA 4.3.0 or newer is required.'''<br /> <br /> MSigDB v2023.1 is based on gene annotation data from Ensembl Release 109 (Feb 2023).<br /> <br /> <br /> &lt;h1&gt;Updates to Human Collections (MSigDB v2023.1.Hs)&lt;/h1&gt;<br /> <br /> &lt;h2&gt;C1: positional gene sets&lt;/h2&gt;<br /> Updated human gene annotations to Ensembl 109 (+1 gene set).<br /> &lt;h2&gt;C2:CGP&lt;/h2&gt;<br /> <br /> 6 Gene sets contributed by MSigDB users have been added to C2:CGP<br /> &lt;ul&gt;<br /> &lt;li&gt;&lt;span class=&quot;plainlinks&quot;&gt;[https://gsea-msigdb.org/gsea/msigdb/human/geneset/]&lt;/span&gt;&lt;/li&gt;<br /> &lt;/ul&gt;<br /> &lt;br&gt;<br /> <br /> &lt;h2&gt;C2:CP:Reactome&lt;/h2&gt;<br /> <br /> &lt;ul&gt;<br /> &lt;li&gt;Reactome gene sets have been updated to reflect the state of the Reactome pathway architecture as of '''Reactome v83''' (+19 gene sets).&lt;/li&gt;<br /> &lt;li&gt;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.&lt;/li&gt;<br /> &lt;/ul&gt;<br /> <br /> &lt;h2&gt;C2:CP:WikiPathways&lt;/h2&gt;<br /> WikiPathways gene sets have been updated to the February 10, 2023 release (+21 gene sets).<br /> <br /> &lt;h2&gt;C3:TFT:GTRD&lt;/h2&gt;<br /> &lt;p&gt;GTRD data was updated to the 21.12 release. (-12 gene sets)&lt;/p&gt;<br /> <br /> &lt;h2&gt;C5:GO (Gene Ontology)&lt;/h2&gt;<br /> &lt;p&gt; 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 (&lt;span class=&quot;plainlinks&quot;&gt;[http://www.geneontology.org Nature Genet 2000]&lt;/span&gt;). 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.&lt;/p&gt;<br /> <br /> &lt;p&gt;This collection is divided into three sub-collections:&lt;/p&gt;<br /> &lt;ul&gt;<br /> &lt;li&gt;&lt;strong&gt;BP&lt;/strong&gt;: GO Biological process (-12 gene sets). Gene sets derived from the Biological Process Ontology, which are prefixed with &quot;GOBP_&quot;.&lt;/li&gt;<br /> &lt;li&gt;&lt;strong&gt;CC&lt;/strong&gt;: GO Cellular component (-26 gene sets). Gene sets derived from the Cellular Component Ontology, which are prefixed with &quot;GOCC_&quot;.&lt;/li&gt;<br /> &lt;li&gt;&lt;strong&gt;MF&lt;/strong&gt;: GO Molecular function (+9 gene sets). Gene sets derived from the Molecular Function Ontology, which are prefixed with &quot;GOMF_&quot;..&lt;/li&gt;<br /> &lt;/ul&gt;<br /> <br /> &lt;p&gt;These updates were generated in accordance with the procedure described in the [[MSigDB_v7.0_Release_Notes#C5_.28Gene_Ontology_collection.29_-_Major_overhaul | GO release notes for MSigDB 7.0.]]&lt;/p&gt;<br /> <br /> &lt;h2&gt;C5:HPO (Human Phenotype Ontology)&lt;/h2&gt;<br /> <br /> Gene sets in this sub-collection have been updated to reflect the 2023-01-27 release of the Human Phenotype Ontology database (+263 gene sets). This sub-collection has been redundancy filtered through a procedure comparable to that of the GO and Reactome sub-collections.<br /> <br /> &lt;h2&gt;C8 cell type signature gene sets&lt;/h2&gt;<br /> &lt;p&gt;Added gene sets describing lung cell type identity signatures from &lt;span class=&quot;plainlinks&quot;&gt;[https://pubmed.ncbi.nlm.nih.gov/36493756/ He P., Lim K., et al. 2022 A human fetal lung cell atlas uncovers proximal-distal gradients of differentiation and key regulators of epithelial fates.]&lt;/span&gt; &lt;span class=&quot;plainlinks&quot;&gt;(https://lungcellatlas.org)&lt;/span&gt; (+126 gene sets)&lt;/p&gt;<br /> <br /> &lt;h2&gt;CHIP file updates&lt;/h2&gt;<br /> &lt;ul&gt;<br /> &lt;li&gt;MSigDB 2023.1.Hs gene annotations and gene mapping CHIP files have been updated to data from Ensembl 109.&lt;/li&gt;<br /> &lt;li&gt;Gene orthology annotations for mapping mouse and rat genes to their best match human orthologs have been updated to &lt;span class=&quot;plainlinks&quot;&gt;[https://www.alliancegenome.org/ Alliance of Genome Resources]&lt;/span&gt; orthology database release 5.3.0 (2022-10-28)&lt;/li&gt;<br /> &lt;/ul&gt;</div> Acastanza https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=MSigDB_v2023.1.Mm_Release_Notes&diff=4521 MSigDB v2023.1.Mm Release Notes 2023-03-02T20:08:06Z <p>Acastanza: </p> <hr /> <div>&lt;span class=&quot;plainlinks&quot;&gt;<br /> [http://www.broadinstitute.org/gsea/ GSEA Home] |<br /> [http://www.broadinstitute.org/gsea/downloads.jsp Downloads] | <br /> [http://www.broadinstitute.org/gsea/msigdb/ Molecular Signatures Database] | <br /> [http://www.broadinstitute.org/cancer/software/gsea/wiki/index.php/Main_Page Documentation] |<br /> [http://www.broadinstitute.org/gsea/contact.jsp Contact]<br /> &lt;/span&gt;<br /> <br /> &lt;h1&gt;Important Notices&lt;/h1&gt;<br /> <br /> This page describes updates made to the Molecular Signatures Database Mouse Collections for release 2023.1 (MSigDB 2023.1.Mm).<br /> <br /> '''In order to access the MSigBD mouse collections through the GSEA UI, the GSEA 4.3.0 or newer is required.'''<br /> <br /> MSigDB v2023.1 is based on gene annotation data from Ensembl Release 109 (Feb 2023).<br /> <br /> <br /> &lt;h1&gt;Updates to Mouse Collections (MSigDB v2023.1.Mm)&lt;/h1&gt;<br /> <br /> &lt;h2&gt;M1: positional gene sets&lt;/h2&gt;<br /> 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.<br /> <br /> &lt;h2&gt;M2:CGP&lt;/h2&gt;<br /> <br /> XX Gene sets contributed by MSigDB users have been added to M2:CGP<br /> &lt;ul&gt;<br /> &lt;li&gt;&lt;span class=&quot;plainlinks&quot;&gt;[https://gsea-msigdb.org/gsea/msigdb/mouse/geneset/]&lt;/span&gt;&lt;/li&gt;<br /> &lt;/ul&gt;<br /> &lt;br&gt;<br /> <br /> &lt;h2&gt;M2:CP:Reactome&lt;/h2&gt;<br /> <br /> &lt;ul&gt;<br /> &lt;li&gt;Reactome gene sets have been updated to reflect the state of the Reactome pathway architecture as of '''Reactome v83''' (+XX gene sets).&lt;/li&gt;<br /> &lt;li&gt;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.&lt;/li&gt;<br /> &lt;/ul&gt;<br /> <br /> &lt;h2&gt;M2:CP:WikiPathways&lt;/h2&gt;<br /> WikiPathways gene sets have been updated to the February 10, 2023 release (+XX gene sets).<br /> <br /> &lt;h2&gt;M3:GTRD&lt;/h2&gt;<br /> &lt;p&gt;GTRD data was updated to the 21.12 release.&lt;/p&gt;<br /> <br /> &lt;h2&gt;M5:GO (Gene Ontology)&lt;/h2&gt;<br /> &lt;p&gt; 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 (&lt;span class=&quot;plainlinks&quot;&gt;[http://www.geneontology.org Nature Genet 2000]&lt;/span&gt;). 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.&lt;/p&gt;<br /> <br /> &lt;p&gt;This collection is divided into three sub-collections:&lt;/p&gt;<br /> &lt;ul&gt;<br /> &lt;li&gt;&lt;strong&gt;BP&lt;/strong&gt;: GO Biological process (+XX gene sets). Gene sets derived from the Biological Process Ontology, which are prefixed with &quot;GOBP_&quot;.&lt;/li&gt;<br /> &lt;li&gt;&lt;strong&gt;CC&lt;/strong&gt;: GO Cellular component (+XX gene sets). Gene sets derived from the Cellular Component Ontology, which are prefixed with &quot;GOCC_&quot;.&lt;/li&gt;<br /> &lt;li&gt;&lt;strong&gt;MF&lt;/strong&gt;: GO Molecular function (+XX gene sets). Gene sets derived from the Molecular Function Ontology, which are prefixed with &quot;GOMF_&quot;..&lt;/li&gt;<br /> &lt;/ul&gt;<br /> <br /> &lt;p&gt;These updates were generated in accordance with the procedure described in the [[MSigDB_v7.0_Release_Notes#C5_.28Gene_Ontology_collection.29_-_Major_overhaul | GO release notes for MSigDB 7.0.]]&lt;/p&gt;<br /> <br /> <br /> &lt;h2&gt;M8 cell type signature gene sets&lt;/h2&gt;<br /> &lt;p&gt;Added gene sets describing uterine cell type identity signatures from &lt;span class=&quot;plainlinks&quot;&gt;[https://pubmed.ncbi.nlm.nih.gov/35669188/ Zhang, et al. 2022 Digital Cell Atlas of Mouse Uterus: From Regenerative Stage to Maturational Stage.]&lt;/span&gt; (+XX gene sets)&lt;/p&gt;<br /> <br /> &lt;h2&gt;CHIP file updates&lt;/h2&gt;<br /> &lt;ul&gt;<br /> &lt;li&gt;MSigDB 2023.1.Mm gene annotations and gene mapping CHIP files have been updated to data from Ensembl 109.&lt;/li&gt;<br /> &lt;li&gt;Gene orthology annotations for mapping human and rat genes to their best match mouse orthologs have been updated to &lt;span class=&quot;plainlinks&quot;&gt;[https://www.alliancegenome.org/ Alliance of Genome Resources]&lt;/span&gt; orthology database release 5.3.0 (2022-10-28)&lt;/li&gt;<br /> &lt;/ul&gt;</div> Acastanza https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=MSigDB_v2023.1.Hs_Release_Notes&diff=4520 MSigDB v2023.1.Hs Release Notes 2023-03-02T20:07:48Z <p>Acastanza: </p> <hr /> <div>&lt;span class=&quot;plainlinks&quot;&gt;<br /> [http://www.broadinstitute.org/gsea/ GSEA Home] |<br /> [http://www.broadinstitute.org/gsea/downloads.jsp Downloads] | <br /> [http://www.broadinstitute.org/gsea/msigdb/ Molecular Signatures Database] | <br /> [http://www.broadinstitute.org/cancer/software/gsea/wiki/index.php/Main_Page Documentation] |<br /> [http://www.broadinstitute.org/gsea/contact.jsp Contact]<br /> &lt;/span&gt;<br /> <br /> &lt;h1&gt;Important Notices&lt;/h1&gt;<br /> <br /> This page describes updates made to the Molecular Signatures Database Human Collections for release 2023.1 (MSigDB 2023.1.Hs).<br /> <br /> '''In order to access the MSigBD mouse collections through the GSEA UI, the GSEA 4.3.0 or newer is required.'''<br /> <br /> MSigDB v2023.1 is based on gene annotation data from Ensembl Release 109 (Feb 2023).<br /> <br /> <br /> &lt;h1&gt;Updates to Human Collections (MSigDB v2023.1.Hs)&lt;/h1&gt;<br /> <br /> &lt;h2&gt;C1: positional gene sets&lt;/h2&gt;<br /> Updated human gene annotations to Ensembl 109.<br /> &lt;h2&gt;C2:CGP&lt;/h2&gt;<br /> <br /> XX Gene sets contributed by MSigDB users have been added to C2:CGP<br /> &lt;ul&gt;<br /> &lt;li&gt;&lt;span class=&quot;plainlinks&quot;&gt;[https://gsea-msigdb.org/gsea/msigdb/human/geneset/]&lt;/span&gt;&lt;/li&gt;<br /> &lt;/ul&gt;<br /> &lt;br&gt;<br /> <br /> &lt;h2&gt;C2:CP:Reactome&lt;/h2&gt;<br /> <br /> &lt;ul&gt;<br /> &lt;li&gt;Reactome gene sets have been updated to reflect the state of the Reactome pathway architecture as of '''Reactome v83''' (+XX gene sets).&lt;/li&gt;<br /> &lt;li&gt;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.&lt;/li&gt;<br /> &lt;/ul&gt;<br /> <br /> &lt;h2&gt;C2:CP:WikiPathways&lt;/h2&gt;<br /> WikiPathways gene sets have been updated to the February 10, 2023 release (+XX gene sets).<br /> <br /> &lt;h2&gt;C3:TFT:GTRD&lt;/h2&gt;<br /> &lt;p&gt;GTRD data was updated to the 21.12 release.&lt;/p&gt;<br /> <br /> &lt;h2&gt;C5:GO (Gene Ontology)&lt;/h2&gt;<br /> &lt;p&gt; 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 (&lt;span class=&quot;plainlinks&quot;&gt;[http://www.geneontology.org Nature Genet 2000]&lt;/span&gt;). 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.&lt;/p&gt;<br /> <br /> &lt;p&gt;This collection is divided into three sub-collections:&lt;/p&gt;<br /> &lt;ul&gt;<br /> &lt;li&gt;&lt;strong&gt;BP&lt;/strong&gt;: GO Biological process (+XX gene sets). Gene sets derived from the Biological Process Ontology, which are prefixed with &quot;GOBP_&quot;.&lt;/li&gt;<br /> &lt;li&gt;&lt;strong&gt;CC&lt;/strong&gt;: GO Cellular component (+XX gene sets). Gene sets derived from the Cellular Component Ontology, which are prefixed with &quot;GOCC_&quot;.&lt;/li&gt;<br /> &lt;li&gt;&lt;strong&gt;MF&lt;/strong&gt;: GO Molecular function (+XX gene sets). Gene sets derived from the Molecular Function Ontology, which are prefixed with &quot;GOMF_&quot;..&lt;/li&gt;<br /> &lt;/ul&gt;<br /> <br /> &lt;p&gt;These updates were generated in accordance with the procedure described in the [[MSigDB_v7.0_Release_Notes#C5_.28Gene_Ontology_collection.29_-_Major_overhaul | GO release notes for MSigDB 7.0.]]&lt;/p&gt;<br /> <br /> &lt;h2&gt;C5:HPO (Human Phenotype Ontology)&lt;/h2&gt;<br /> <br /> Gene sets in this sub-collection have been updated to reflect the 2023-01-27 release of the Human Phenotype Ontology database (+XX gene sets). This sub-collection has been redundancy filtered through a procedure comparable to that of the GO and Reactome sub-collections.<br /> <br /> &lt;h2&gt;C8 cell type signature gene sets&lt;/h2&gt;<br /> &lt;p&gt;Added gene sets describing lung cell type identity signatures from &lt;span class=&quot;plainlinks&quot;&gt;[https://pubmed.ncbi.nlm.nih.gov/36493756/ He P., Lim K., et al. 2022 A human fetal lung cell atlas uncovers proximal-distal gradients of differentiation and key regulators of epithelial fates.]&lt;/span&gt; &lt;span class=&quot;plainlinks&quot;&gt;(https://lungcellatlas.org)&lt;/span&gt; (+XX gene sets)&lt;/p&gt;<br /> <br /> &lt;h2&gt;CHIP file updates&lt;/h2&gt;<br /> &lt;ul&gt;<br /> &lt;li&gt;MSigDB 2023.1.Hs gene annotations and gene mapping CHIP files have been updated to data from Ensembl 109.&lt;/li&gt;<br /> &lt;li&gt;Gene orthology annotations for mapping mouse and rat genes to their best match human orthologs have been updated to &lt;span class=&quot;plainlinks&quot;&gt;[https://www.alliancegenome.org/ Alliance of Genome Resources]&lt;/span&gt; orthology database release 5.3.0 (2022-10-28)&lt;/li&gt;<br /> &lt;/ul&gt;</div> Acastanza https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=MSigDB_v2023.1.Mm_Release_Notes&diff=4519 MSigDB v2023.1.Mm Release Notes 2023-03-02T20:07:00Z <p>Acastanza: Created page with '&lt;span class=&quot;plainlinks&quot;&gt; [http://www.broadinstitute.org/gsea/ GSEA Home] | [http://www.broadinstitute.org/gsea/downloads.jsp Downloads] | [http://www.broadinstitute.org/gsea/ms…'</p> <hr /> <div>&lt;span class=&quot;plainlinks&quot;&gt;<br /> [http://www.broadinstitute.org/gsea/ GSEA Home] |<br /> [http://www.broadinstitute.org/gsea/downloads.jsp Downloads] | <br /> [http://www.broadinstitute.org/gsea/msigdb/ Molecular Signatures Database] | <br /> [http://www.broadinstitute.org/cancer/software/gsea/wiki/index.php/Main_Page Documentation] |<br /> [http://www.broadinstitute.org/gsea/contact.jsp Contact]<br /> &lt;/span&gt;<br /> <br /> &lt;h1&gt;Important Notices&lt;/h1&gt;<br /> <br /> This page describes updates made to the Molecular Signatures Database Mouse Collections for release 2023.1 (MSigDB 2023.1.Mm).<br /> <br /> '''In order to access the MSigBD mouse collections through the GSEA UI, the GSEA 4.3.0 or newer is required.'''<br /> <br /> MSigDB v2023.1 is based on gene annotation data from Ensembl Release 109 (Feb 2023).<br /> <br /> <br /> &lt;h1&gt;Updates to Mouse Collections (MSigDB v2023.1.Mm)&lt;/h1&gt;<br /> <br /> &lt;h2&gt;M1: positional gene sets&lt;/h2&gt;<br /> 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.<br /> <br /> &lt;h2&gt;M2:CGP&lt;/h2&gt;<br /> <br /> XX Gene sets contributed by MSigDB users have been added to M2:CGP<br /> &lt;ul&gt;<br /> &lt;li&gt;&lt;span class=&quot;plainlinks&quot;&gt;[https://gsea-msigdb.org/gsea/msigdb/mouse/geneset/]&lt;/span&gt;&lt;/li&gt;<br /> &lt;/ul&gt;<br /> &lt;br&gt;<br /> <br /> &lt;h2&gt;M2:CP:Reactome&lt;/h2&gt;<br /> <br /> &lt;ul&gt;<br /> &lt;li&gt;Reactome gene sets have been updated to reflect the state of the Reactome pathway architecture as of '''Reactome v83''' (+XX gene sets).&lt;/li&gt;<br /> &lt;li&gt;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.&lt;/li&gt;<br /> &lt;/ul&gt;<br /> <br /> &lt;h2&gt;M2:CP:WikiPathways&lt;/h2&gt;<br /> WikiPathways gene sets have been updated to the February 10, 2023 release (+XX gene sets).<br /> <br /> &lt;h2&gt;M3:TFT:GTRD&lt;/h2&gt;<br /> &lt;p&gt;GTRD data was updated to the 21.12 release.&lt;/p&gt;<br /> <br /> &lt;h2&gt;M5:GO (Gene Ontology)&lt;/h2&gt;<br /> &lt;p&gt; 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 (&lt;span class=&quot;plainlinks&quot;&gt;[http://www.geneontology.org Nature Genet 2000]&lt;/span&gt;). 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.&lt;/p&gt;<br /> <br /> &lt;p&gt;This collection is divided into three sub-collections:&lt;/p&gt;<br /> &lt;ul&gt;<br /> &lt;li&gt;&lt;strong&gt;BP&lt;/strong&gt;: GO Biological process (+XX gene sets). Gene sets derived from the Biological Process Ontology, which are prefixed with &quot;GOBP_&quot;.&lt;/li&gt;<br /> &lt;li&gt;&lt;strong&gt;CC&lt;/strong&gt;: GO Cellular component (+XX gene sets). Gene sets derived from the Cellular Component Ontology, which are prefixed with &quot;GOCC_&quot;.&lt;/li&gt;<br /> &lt;li&gt;&lt;strong&gt;MF&lt;/strong&gt;: GO Molecular function (+XX gene sets). Gene sets derived from the Molecular Function Ontology, which are prefixed with &quot;GOMF_&quot;..&lt;/li&gt;<br /> &lt;/ul&gt;<br /> <br /> &lt;p&gt;These updates were generated in accordance with the procedure described in the [[MSigDB_v7.0_Release_Notes#C5_.28Gene_Ontology_collection.29_-_Major_overhaul | GO release notes for MSigDB 7.0.]]&lt;/p&gt;<br /> <br /> <br /> &lt;h2&gt;M8 cell type signature gene sets&lt;/h2&gt;<br /> &lt;p&gt;Added gene sets describing uterine cell type identity signatures from &lt;span class=&quot;plainlinks&quot;&gt;[https://pubmed.ncbi.nlm.nih.gov/35669188/ Zhang, et al. 2022 Digital Cell Atlas of Mouse Uterus: From Regenerative Stage to Maturational Stage.]&lt;/span&gt; (+XX gene sets)&lt;/p&gt;<br /> <br /> &lt;h2&gt;CHIP file updates&lt;/h2&gt;<br /> &lt;ul&gt;<br /> &lt;li&gt;MSigDB 2023.1.Mm gene annotations and gene mapping CHIP files have been updated to data from Ensembl 109.&lt;/li&gt;<br /> &lt;li&gt;Gene orthology annotations for mapping human and rat genes to their best match mouse orthologs have been updated to &lt;span class=&quot;plainlinks&quot;&gt;[https://www.alliancegenome.org/ Alliance of Genome Resources]&lt;/span&gt; orthology database release 5.3.0 (2022-10-28)&lt;/li&gt;<br /> &lt;/ul&gt;</div> Acastanza https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=MSigDB_v2023.1.Hs_Release_Notes&diff=4518 MSigDB v2023.1.Hs Release Notes 2023-03-02T19:53:45Z <p>Acastanza: </p> <hr /> <div>&lt;span class=&quot;plainlinks&quot;&gt;<br /> [http://www.broadinstitute.org/gsea/ GSEA Home] |<br /> [http://www.broadinstitute.org/gsea/downloads.jsp Downloads] | <br /> [http://www.broadinstitute.org/gsea/msigdb/ Molecular Signatures Database] | <br /> [http://www.broadinstitute.org/cancer/software/gsea/wiki/index.php/Main_Page Documentation] |<br /> [http://www.broadinstitute.org/gsea/contact.jsp Contact]<br /> &lt;/span&gt;<br /> <br /> &lt;h1&gt;Important Notices&lt;/h1&gt;<br /> <br /> This page describes updates made to the Molecular Signatures Database Human Collections for release 2023.1 (MSigDB 2023.1.Hs).<br /> <br /> '''In order to access the MSigBD mouse collections through the GSEA UI, the GSEA 4.3.0 or newer is required.'''<br /> <br /> MSigDB v2023.1 is based on gene annotation data from Ensembl Release 109 (Feb 2023).<br /> <br /> <br /> &lt;h1&gt;Updates to Human Collections (MSigDB v2023.1.Hs)&lt;/h1&gt;<br /> <br /> &lt;h2&gt;C1: positional gene sets&lt;/h2&gt;<br /> Updated human gene annotations to Ensembl 109.<br /> &lt;h2&gt;C2:CGP&lt;/h2&gt;<br /> <br /> 15 Gene sets contributed by MSigDB users have been added to C2:CGP<br /> &lt;ul&gt;<br /> &lt;li&gt;&lt;span class=&quot;plainlinks&quot;&gt;[https://gsea-msigdb.org/gsea/msigdb/human/geneset/]&lt;/span&gt;&lt;/li&gt;<br /> &lt;/ul&gt;<br /> &lt;br&gt;<br /> <br /> &lt;h2&gt;C2:CP:Reactome&lt;/h2&gt;<br /> <br /> &lt;ul&gt;<br /> &lt;li&gt;Reactome gene sets have been updated to reflect the state of the Reactome pathway architecture as of '''Reactome v83''' (+XX gene sets).&lt;/li&gt;<br /> &lt;li&gt;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.&lt;/li&gt;<br /> &lt;/ul&gt;<br /> <br /> &lt;h2&gt;C2:CP:WikiPathways&lt;/h2&gt;<br /> WikiPathways gene sets have been updated to the February 10, 2023 release (+XX gene sets).<br /> <br /> &lt;h2&gt;C3:TFT:GTRD&lt;/h2&gt;<br /> &lt;p&gt;GTRD data was updated to the 21.12 release.&lt;/p&gt;<br /> <br /> &lt;h2&gt;C5:GO (Gene Ontology)&lt;/h2&gt;<br /> &lt;p&gt; 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 (&lt;span class=&quot;plainlinks&quot;&gt;[http://www.geneontology.org Nature Genet 2000]&lt;/span&gt;). 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.&lt;/p&gt;<br /> <br /> &lt;p&gt;This collection is divided into three sub-collections:&lt;/p&gt;<br /> &lt;ul&gt;<br /> &lt;li&gt;&lt;strong&gt;BP&lt;/strong&gt;: GO Biological process (+XX gene sets). Gene sets derived from the Biological Process Ontology, and are prefixed with &quot;GOBP_&quot;.&lt;/li&gt;<br /> &lt;li&gt;&lt;strong&gt;CC&lt;/strong&gt;: GO Cellular component (+XX gene sets). Gene sets derived from the Cellular Component Ontology, and are prefixed with &quot;GOCC_&quot;.&lt;/li&gt;<br /> &lt;li&gt;&lt;strong&gt;MF&lt;/strong&gt;: GO Molecular function (+XX gene sets). Gene sets derived from the Molecular Function Ontology, and are prefixed with &quot;GOMF_&quot;..&lt;/li&gt;<br /> &lt;/ul&gt;<br /> <br /> &lt;p&gt;These updates were generated in accordance with the procedure described in the [[MSigDB_v7.0_Release_Notes#C5_.28Gene_Ontology_collection.29_-_Major_overhaul | GO release notes for MSigDB 7.0.]]&lt;/p&gt;<br /> <br /> &lt;h2&gt;C5:HPO (Human Phenotype Ontology)&lt;/h2&gt;<br /> <br /> Gene sets in this sub-collection have been updated to reflect the 2023-01-27 release of the Human Phenotype Ontology database (+XX gene sets). This sub-collection has been redundancy filtered through a procedure comparable to that of the GO and Reactome sub-collections.<br /> <br /> &lt;h2&gt;C8 cell type signature gene sets&lt;/h2&gt;<br /> &lt;p&gt;Added gene sets describing lung cell type identity signatures from &lt;span class=&quot;plainlinks&quot;&gt;[https://pubmed.ncbi.nlm.nih.gov/36493756/ He P., Lim K., et al. 2022 A human fetal lung cell atlas uncovers proximal-distal gradients of differentiation and key regulators of epithelial fates.]&lt;/span&gt; &lt;span class=&quot;plainlinks&quot;&gt;(https://lungcellatlas.org)&lt;/span&gt; (+XX gene sets)&lt;/p&gt;<br /> <br /> &lt;h2&gt;CHIP file updates&lt;/h2&gt;<br /> &lt;ul&gt;<br /> &lt;li&gt;MSigDB 2023.1.Hs gene annotations and gene mapping CHIP files have been updated to data from Ensembl 109.&lt;/li&gt;<br /> &lt;li&gt;Gene orthology annotations for mapping mouse and rat genes to their best match human orthologs have been updated to &lt;span class=&quot;plainlinks&quot;&gt;[https://www.alliancegenome.org/ Alliance of Genome Resources]&lt;/span&gt; orthology database release 5.3.0 (2022-10-28)&lt;/li&gt;<br /> &lt;/ul&gt;</div> Acastanza https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=MSigDB_v2023.1.Hs_Release_Notes&diff=4517 MSigDB v2023.1.Hs Release Notes 2023-03-02T19:51:05Z <p>Acastanza: </p> <hr /> <div>&lt;span class=&quot;plainlinks&quot;&gt;<br /> [http://www.broadinstitute.org/gsea/ GSEA Home] |<br /> [http://www.broadinstitute.org/gsea/downloads.jsp Downloads] | <br /> [http://www.broadinstitute.org/gsea/msigdb/ Molecular Signatures Database] | <br /> [http://www.broadinstitute.org/cancer/software/gsea/wiki/index.php/Main_Page Documentation] |<br /> [http://www.broadinstitute.org/gsea/contact.jsp Contact]<br /> &lt;/span&gt;<br /> <br /> &lt;h1&gt;Important Notices&lt;/h1&gt;<br /> <br /> This page describes updates made to the Molecular Signatures Database Human Collections for release 2023.1 (MSigDB 2023.1.Hs).<br /> <br /> '''In order to access the MSigBD mouse collections through the GSEA UI, the latest version of GSEA (4.3+) is required.'''<br /> <br /> MSigDB v2023.1 is based on gene annotation data from Ensembl Release 109 (Feb 2023).<br /> <br /> <br /> &lt;h1&gt;Updates to Human Collections (MSigDB v2023.1.Hs)&lt;/h1&gt;<br /> <br /> &lt;h2&gt;C1: positional gene sets&lt;/h2&gt;<br /> Updated human gene annotations to Ensembl 109.<br /> &lt;h2&gt;C2:CGP&lt;/h2&gt;<br /> <br /> 15 Gene sets contributed by MSigDB users have been added to C2:CGP<br /> &lt;ul&gt;<br /> &lt;li&gt;&lt;span class=&quot;plainlinks&quot;&gt;[https://gsea-msigdb.org/gsea/msigdb/human/geneset/]&lt;/span&gt;&lt;/li&gt;<br /> &lt;/ul&gt;<br /> &lt;br&gt;<br /> <br /> &lt;h2&gt;C2:CP:Reactome&lt;/h2&gt;<br /> <br /> &lt;ul&gt;<br /> &lt;li&gt;Reactome gene sets have been updated to reflect the state of the Reactome pathway architecture as of '''Reactome v83''' (+XX gene sets).&lt;/li&gt;<br /> &lt;li&gt;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.&lt;/li&gt;<br /> &lt;/ul&gt;<br /> <br /> &lt;h2&gt;C2:CP:WikiPathways&lt;/h2&gt;<br /> WikiPathways gene sets have been updated to the February 10, 2023 release (+XX gene sets).<br /> <br /> &lt;h2&gt;C3:TFT:GTRD&lt;/h2&gt;<br /> &lt;p&gt;GTRD data was updated to the 21.12 release.&lt;/p&gt;<br /> <br /> &lt;h2&gt;C5:GO (Gene Ontology)&lt;/h2&gt;<br /> &lt;p&gt; 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 (&lt;span class=&quot;plainlinks&quot;&gt;[http://www.geneontology.org Nature Genet 2000]&lt;/span&gt;). 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.&lt;/p&gt;<br /> <br /> &lt;p&gt;This collection is divided into three sub-collections:&lt;/p&gt;<br /> &lt;ul&gt;<br /> &lt;li&gt;&lt;strong&gt;BP&lt;/strong&gt;: GO Biological process (+XX gene sets). Gene sets derived from the Biological Process Ontology, and are prefixed with &quot;GOBP_&quot;.&lt;/li&gt;<br /> &lt;li&gt;&lt;strong&gt;CC&lt;/strong&gt;: GO Cellular component (+XX gene sets). Gene sets derived from the Cellular Component Ontology, and are prefixed with &quot;GOCC_&quot;.&lt;/li&gt;<br /> &lt;li&gt;&lt;strong&gt;MF&lt;/strong&gt;: GO Molecular function (+XX gene sets). Gene sets derived from the Molecular Function Ontology, and are prefixed with &quot;GOMF_&quot;..&lt;/li&gt;<br /> &lt;/ul&gt;<br /> <br /> &lt;p&gt;These updates were generated in accordance with the procedure described in the [[MSigDB_v7.0_Release_Notes#C5_.28Gene_Ontology_collection.29_-_Major_overhaul | GO release notes for MSigDB 7.0.]]&lt;/p&gt;<br /> <br /> &lt;h2&gt;C5:HPO (Human Phenotype Ontology)&lt;/h2&gt;<br /> <br /> Gene sets in this sub-collection have been updated to reflect the 2023-01-27 release of the Human Phenotype Ontology database (+XX gene sets). This sub-collection has been redundancy filtered through a procedure comparable to that of the GO and Reactome sub-collections.<br /> <br /> &lt;h2&gt;C8 cell type signature gene sets&lt;/h2&gt;<br /> &lt;p&gt;Added gene sets describing lung cell type identity signatures from &lt;span class=&quot;plainlinks&quot;&gt;[https://pubmed.ncbi.nlm.nih.gov/36493756/ He P., Lim K., et al. 2022 A human fetal lung cell atlas uncovers proximal-distal gradients of differentiation and key regulators of epithelial fates.]&lt;/span&gt; &lt;span class=&quot;plainlinks&quot;&gt;(https://lungcellatlas.org)&lt;/span&gt; (+XX gene sets)&lt;/p&gt;<br /> <br /> &lt;h2&gt;CHIP file updates&lt;/h2&gt;<br /> &lt;ul&gt;<br /> &lt;li&gt;MSigDB 2023.1.Hs gene annotations and gene mapping CHIP files have been updated to data from Ensembl 109.&lt;/li&gt;<br /> &lt;li&gt;Gene orthology annotations for mapping mouse and rat genes to their best match human orthologs have been updated to &lt;span class=&quot;plainlinks&quot;&gt;[https://www.alliancegenome.org/ Alliance of Genome Resources]&lt;/span&gt; orthology database release 5.3.0 (2022-10-28)&lt;/li&gt;<br /> &lt;/ul&gt;</div> Acastanza https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=MSigDB_v2023.1.Hs_Release_Notes&diff=4516 MSigDB v2023.1.Hs Release Notes 2023-03-02T19:49:09Z <p>Acastanza: Created page with '&lt;span class=&quot;plainlinks&quot;&gt; [http://www.broadinstitute.org/gsea/ GSEA Home] | [http://www.broadinstitute.org/gsea/downloads.jsp Downloads] | [http://www.broadinstitute.org/gsea/ms…'</p> <hr /> <div>&lt;span class=&quot;plainlinks&quot;&gt;<br /> [http://www.broadinstitute.org/gsea/ GSEA Home] |<br /> [http://www.broadinstitute.org/gsea/downloads.jsp Downloads] | <br /> [http://www.broadinstitute.org/gsea/msigdb/ Molecular Signatures Database] | <br /> [http://www.broadinstitute.org/cancer/software/gsea/wiki/index.php/Main_Page Documentation] |<br /> [http://www.broadinstitute.org/gsea/contact.jsp Contact]<br /> &lt;/span&gt;<br /> <br /> &lt;h1&gt;Important Notices&lt;/h1&gt;<br /> <br /> This page describes updates made to the Molecular Signatures Database Human Collections for release 2023.1 (MSigDB 2023.1.Hs).<br /> <br /> '''In order to access the MSigBD mouse collections through the GSEA UI, the latest version of GSEA (4.3+) is required.'''<br /> <br /> MSigDB v2023.1 is based on gene annotation data from Ensembl Release 109 (Feb 2023).<br /> <br /> <br /> &lt;h1&gt;Updates to Human Collections (MSigDB v2022.1.Hs)&lt;/h1&gt;<br /> <br /> &lt;h2&gt;C1: positional gene sets&lt;/h2&gt;<br /> Updated human gene annotations to Ensembl 107.<br /> &lt;h2&gt;C2:CGP&lt;/h2&gt;<br /> <br /> 15 Gene sets contributed by MSigDB users have been added to C2:CGP<br /> &lt;ul&gt;<br /> &lt;li&gt;&lt;span class=&quot;plainlinks&quot;&gt;[https://gsea-msigdb.org/gsea/msigdb/human/geneset/]&lt;/span&gt;&lt;/li&gt;<br /> &lt;/ul&gt;<br /> &lt;br&gt;<br /> <br /> &lt;h2&gt;C2:CP:Reactome&lt;/h2&gt;<br /> <br /> &lt;ul&gt;<br /> &lt;li&gt;Reactome gene sets have been updated to reflect the state of the Reactome pathway architecture as of '''Reactome v83''' (+XX gene sets).&lt;/li&gt;<br /> &lt;li&gt;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.&lt;/li&gt;<br /> &lt;/ul&gt;<br /> <br /> &lt;h2&gt;C2:CP:WikiPathways&lt;/h2&gt;<br /> WikiPathways gene sets have been updated to the February 10, 2023 release (+XX gene sets).<br /> <br /> &lt;h2&gt;C3:TFT:GTRD&lt;/h2&gt;<br /> &lt;p&gt;GTRD data was updated to the 21.12 release.&lt;/p&gt;<br /> <br /> &lt;h2&gt;C5:GO (Gene Ontology)&lt;/h2&gt;<br /> &lt;p&gt; 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 (&lt;span class=&quot;plainlinks&quot;&gt;[http://www.geneontology.org Nature Genet 2000]&lt;/span&gt;). 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.&lt;/p&gt;<br /> <br /> &lt;p&gt;This collection is divided into three sub-collections:&lt;/p&gt;<br /> &lt;ul&gt;<br /> &lt;li&gt;&lt;strong&gt;BP&lt;/strong&gt;: GO Biological process (+XX gene sets). Gene sets derived from the Biological Process Ontology, and are prefixed with &quot;GOBP_&quot;.&lt;/li&gt;<br /> &lt;li&gt;&lt;strong&gt;CC&lt;/strong&gt;: GO Cellular component (+XX gene sets). Gene sets derived from the Cellular Component Ontology, and are prefixed with &quot;GOCC_&quot;.&lt;/li&gt;<br /> &lt;li&gt;&lt;strong&gt;MF&lt;/strong&gt;: GO Molecular function (+XX gene sets). Gene sets derived from the Molecular Function Ontology, and are prefixed with &quot;GOMF_&quot;..&lt;/li&gt;<br /> &lt;/ul&gt;<br /> <br /> &lt;p&gt;These updates were generated in accordance with the procedure described in the [[MSigDB_v7.0_Release_Notes#C5_.28Gene_Ontology_collection.29_-_Major_overhaul | GO release notes for MSigDB 7.0.]]&lt;/p&gt;<br /> <br /> &lt;h2&gt;C5:HPO (Human Phenotype Ontology)&lt;/h2&gt;<br /> <br /> Gene sets in this sub-collection have been updated to reflect the 2023-01-27 release of the Human Phenotype Ontology database (+XX gene sets). This sub-collection has been redundancy filtered through a procedure comparable to that of the GO and Reactome sub-collections.<br /> <br /> &lt;h2&gt;C8 cell type signature gene sets&lt;/h2&gt;<br /> &lt;p&gt;Added gene sets describing lung cell type identity signatures from &lt;span class=&quot;plainlinks&quot;&gt;[https://pubmed.ncbi.nlm.nih.gov/36493756/ He P., Lim K., et al. 2022 A human fetal lung cell atlas uncovers proximal-distal gradients of differentiation and key regulators of epithelial fates.] &lt;span class=&quot;plainlinks&quot;&gt;[(https://lungcellatlas.org)]&lt;/span&gt; (+XX gene sets) &lt;/p&gt;<br /> <br /> &lt;h2&gt;CHIP file updates&lt;/h2&gt;<br /> &lt;ul&gt;<br /> &lt;li&gt;MSigDB 2023.1.Hs gene annotations and gene mapping CHIP files have been updated to data from Ensembl 109.&lt;/li&gt;<br /> &lt;li&gt;Gene orthology annotations for mapping mouse and rat genes to their best match human orthologs have been updated to &lt;span class=&quot;plainlinks&quot;&gt;[https://www.alliancegenome.org/ Alliance of Genome Resources]&lt;/span&gt; orthology database release 5.3.0 (2022-10-28)&lt;/li&gt;<br /> &lt;/ul&gt;</div> Acastanza https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=Version_check&diff=4512 Version check 2022-09-15T21:06:27Z <p>Acastanza: Created page with 'TCGA_SampleSelection: 2022.1.Hs'</p> <hr /> <div>TCGA_SampleSelection: 2022.1.Hs</div> Acastanza https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=CHIP_File_Selection_Help&diff=4511 CHIP File Selection Help 2022-09-15T17:12:44Z <p>Acastanza: </p> <hr /> <div>&lt;span class=&quot;plainlinks&quot;&gt;<br /> [http://www.broadinstitute.org/gsea/ GSEA Home] |<br /> [http://www.broadinstitute.org/gsea/downloads.jsp Downloads] | <br /> [http://www.broadinstitute.org/gsea/msigdb/ Molecular Signatures Database] | <br /> [http://www.broadinstitute.org/cancer/software/gsea/wiki/index.php/Main_Page Documentation] |<br /> [http://www.broadinstitute.org/gsea/contact.jsp Contact]<br /> &lt;/span&gt;<br /> <br /> <br /> The 4.3.0 version of GSEA introduced support for the new gene set database files and chip files to support native analysis of mouse data first made available with MSigDB v2022.1.<br /> <br /> These files are now split into two different tabs in both the GSEA gene sets and chip files UI windows.<br /> <br /> Gene set files from the Human Collections have the suffix &quot;.'''Hs'''.symbols.gmt&quot; following the MSigDB version (v2022.1 in this initial release), gene set files from the Mouse Collections have the suffix &quot;.'''Mm'''.symbols.gmt&quot;. Gene set files from the Human Collections have their contents provided in HGNC Gene Symbols, gene set files from the Mouse Collections have their contents provided in MGI Gene Symbols. These symbols follow different canonical formats (i.e. MTOR for human vs. Mtor for mouse). <br /> <br /> As such, it is critical to pick CHIP files that map your data into the appropriate namespace (either human or mouse symbols).<br /> <br /> Therefore, if a gene set file from the ''Human Collection (MSigDB)'' window is selected, you must also select a CHIP file from the ''Human Collection Chips (MSigDB)'' tab of the Chip platform selector window, and if a gene set file from the ''Mouse Collection (MSigDB)'' window is selected, you must also select a CHIP file from the ''Mouse Collection Chips (MSigDB)'' tab of the Chip platform selector window.<br /> <br /> Chip files, like gene set database files are versioned and have a species specific suffix, i.e. &quot;.'''Hs'''.chip&quot; following the MSigDB version (v2022.1 in this initial release) for files targeting the Human Collections, and &quot;.'''Mm'''.chip&quot; for files targeting the Mouse Collections.<br /> <br /> Both Human Collection Chips, and Mouse Collection Chips contain a full complement of Chips for native as well as orthology based analysis. Chips from the Human Collection Chips tab (files ending in .Hs.chip) that begin with '''Human_''' convert human gene IDs to human symbols, files from this tab (still with the .Hs.chip suffix) that begin with ''Mouse_'' or ''Rat_'' will also have the text &quot;_Human_Orthologs_&quot; in the file name, and when used will apply orthology mapping data to convert the dataset to match the human gene symbols namespace of the MSigDB Human Collections database.<br /> <br /> Likewise, chips from the Mouse Collection Chips tab (files ending in .Mm.chip) that begin with '''Mouse''' convert mouse gene IDs to mouse symbols, files from this tab (still with the .Mm.chip suffix) that begin with ''Human'' or ''Rat_'' will also have the text &quot;_Mouse_Orthologs_&quot; in the file name, and when used will apply orthology mapping data to convert the dataset to match the mouse gene symbols namespace of the MSigDB mouse Collections database.<br /> <br /> So, if the gene set database file ''c5.go.bp.v2022.1.Hs.symbols.gmt'' was selected from the Human Collection's tab, the appropriate CHIP file regardless of dataset species would be one of the ''_MSigDB.v.2022.1.Hs.chip'' files available from the Human Collection CHIPs (MSigDB) tab, and if the gene set database file ''m5.go.bp.v2022.1.Mm.symbols.gmt'' was selected from the Mouse Collection's tab the appropriate CHIP file regardless of dataset species would be one of the ''_MSigDB.v.2022.1.Mm.chip'' files available from the Mouse Collection CHIPs (MSigDB) tab.</div> Acastanza https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=MSigDB_v2022.1.Hs_Release_Notes&diff=4510 MSigDB v2022.1.Hs Release Notes 2022-09-13T06:30:34Z <p>Acastanza: </p> <hr /> <div>&lt;span class=&quot;plainlinks&quot;&gt;<br /> [http://www.broadinstitute.org/gsea/ GSEA Home] |<br /> [http://www.broadinstitute.org/gsea/downloads.jsp Downloads] | <br /> [http://www.broadinstitute.org/gsea/msigdb/ Molecular Signatures Database] | <br /> [http://www.broadinstitute.org/cancer/software/gsea/wiki/index.php/Main_Page Documentation] |<br /> [http://www.broadinstitute.org/gsea/contact.jsp Contact]<br /> &lt;/span&gt;<br /> <br /> &lt;h1&gt;Important Notices&lt;/h1&gt;<br /> <br /> This page describes updates made to the Molecular Signatures Database for release 2022.1. This release introduces several major changes to previous conventions. MSigDB is now split into two major divisions; a series of gene set collections that are provided in the namespace of human gene symbols, and a series of gene set collections that are provided in the namespace of mouse gene symbols. As such the versioning convention of MSigDB has changed to adopt the format Year.Release.Species. This initial release in the new format is versioned 2022.1.Hs for the human collections and 2022.1.Mm for the mouse collections. Likewise, CHIP files have been updated to reflect this convention, as well as the specific series of collections (i.e. human or mouse) that they are targeted towards.<br /> <br /> '''In order to access the MSigBD mouse collections through the GSEA UI, the latest version of GSEA (4.3.0) is required.'''<br /> <br /> MSigDB v2022.1 is based on gene annotation data from Ensembl Release 107 (Jul 2022).<br /> <br /> &lt;b&gt;Note: &lt;/b&gt;Please be aware that on September 12th we hot-fixed an issue where two gene sets in the Reactome sub-collection were identified by identical standard names due to an issue upstream in the Reactome database. As this issue resulted in GSEA failing to process the GMT file this should not have affected any GSEA results. If you previously encountered an error regarding &quot;GeneSets should have unique names&quot; when running MSigDB v2022.1.Hs Reactome gene sets please re-run the analysis as this has been resolved.<br /> <br /> &lt;h1&gt;Updates to Human Collections (MSigDB v2022.1.Hs)&lt;/h1&gt;<br /> <br /> &lt;h2&gt;C1: positional gene sets&lt;/h2&gt;<br /> Updated human gene annotations to Ensembl 107.<br /> &lt;h2&gt;C2:CGP&lt;/h2&gt;<br /> <br /> 15 Gene sets contributed by MSigDB users have been added to C2:CGP<br /> &lt;ul&gt;<br /> &lt;span class=&quot;plainlinks&quot;&gt;[https://gsea-msigdb.org/gsea/msigdb/human/geneset/LIU_OVARIAN_CANCER_TUMORS_AND_XENOGRAFTS_XDGS_UP LIU_OVARIAN_CANCER_TUMORS_AND_XENOGRAFTS_XDGS_UP]&lt;/span&gt;&lt;/li&gt;<br /> &lt;li&gt;&lt;span class=&quot;plainlinks&quot;&gt;[https://gsea-msigdb.org/gsea/msigdb/human/geneset/LIU_OVARIAN_CANCER_TUMORS_AND_XENOGRAFTS_XDGS_DN LIU_OVARIAN_CANCER_TUMORS_AND_XENOGRAFTS_XDGS_DN]&lt;/span&gt;&lt;/li&gt;<br /> &lt;li&gt;&lt;span class=&quot;plainlinks&quot;&gt;[https://gsea-msigdb.org/gsea/msigdb/human/geneset/LIU_OVARIAN_CANCER_TUMORS_AND_XENOGRAFTS_KINASES_DN LIU_OVARIAN_CANCER_TUMORS_AND_XENOGRAFTS_KINASES_DN]&lt;/span&gt;&lt;/li&gt;<br /> &lt;li&gt;&lt;span class=&quot;plainlinks&quot;&gt;[https://gsea-msigdb.org/gsea/msigdb/human/geneset/BANG_VERTEPORFIN_ENDOMETRIAL_CANCER_CELLS_UP BANG_VERTEPORFIN_ENDOMETRIAL_CANCER_CELLS_UP]&lt;/span&gt;&lt;/li&gt;<br /> &lt;li&gt;&lt;span class=&quot;plainlinks&quot;&gt;[https://gsea-msigdb.org/gsea/msigdb/human/geneset/BANG_VERTEPORFIN_ENDOMETRIAL_CANCER_CELLS_DN BANG_VERTEPORFIN_ENDOMETRIAL_CANCER_CELLS_DN]&lt;/span&gt;&lt;/li&gt;<br /> &lt;li&gt;&lt;span class=&quot;plainlinks&quot;&gt;[https://gsea-msigdb.org/gsea/msigdb/human/geneset/CARRILLOREIXACH_HEPATOBLASTOMA_VS_NORMAL_UP CARRILLOREIXACH_HEPATOBLASTOMA_VS_NORMAL_UP]&lt;/span&gt;&lt;/li&gt;<br /> &lt;li&gt;&lt;span class=&quot;plainlinks&quot;&gt;[https://gsea-msigdb.org/gsea/msigdb/human/geneset/CARRILLOREIXACH_HEPATOBLASTOMA_VS_NORMAL_DN CARRILLOREIXACH_HEPATOBLASTOMA_VS_NORMAL_DN]&lt;/span&gt;&lt;/li&gt;<br /> &lt;li&gt;&lt;span class=&quot;plainlinks&quot;&gt;[https://gsea-msigdb.org/gsea/msigdb/human/geneset/CARRILLOREIXACH_14Q32OVEREXPRESSION_IN_HEPATOBLASTOMA CARRILLOREIXACH_14Q32OVEREXPRESSION_IN_HEPATOBLASTOMA]&lt;/span&gt;&lt;/li&gt;<br /> &lt;li&gt;&lt;span class=&quot;plainlinks&quot;&gt;[https://gsea-msigdb.org/gsea/msigdb/human/geneset/CARRILLOREIXACH_HEPATOBLASTOMA_VS_NORMAL_HYPERMETHYLATED_AND_DN CARRILLOREIXACH_HEPATOBLASTOMA_VS_NORMAL_HYPERMETHYLATED_AND_DN]&lt;/span&gt;&lt;/li&gt;<br /> &lt;li&gt;&lt;span class=&quot;plainlinks&quot;&gt;[https://gsea-msigdb.org/gsea/msigdb/human/geneset/CARRILLOREIXACH_HEPATOBLASTOMA_VS_NORMAL_HYPOMETHYLATED_AND_UP CARRILLOREIXACH_HEPATOBLASTOMA_VS_NORMAL_HYPOMETHYLATED_AND_UP]&lt;/span&gt;&lt;/li&gt;<br /> &lt;li&gt;&lt;span class=&quot;plainlinks&quot;&gt;[https://gsea-msigdb.org/gsea/msigdb/human/geneset/CARRILLOREIXACH_MRS3_VS_LOWER_RISK_HEPATOBLASTOMA_UP CARRILLOREIXACH_MRS3_VS_LOWER_RISK_HEPATOBLASTOMA_UP]&lt;/span&gt;&lt;/li&gt;<br /> &lt;li&gt;&lt;span class=&quot;plainlinks&quot;&gt;[https://gsea-msigdb.org/gsea/msigdb/human/geneset/CARRILLOREIXACH_MRS3_VS_LOWER_RISK_HEPATOBLASTOMA_DN CARRILLOREIXACH_MRS3_VS_LOWER_RISK_HEPATOBLASTOMA_DN]&lt;/span&gt;&lt;/li&gt;<br /> &lt;li&gt;&lt;span class=&quot;plainlinks&quot;&gt;[https://gsea-msigdb.org/gsea/msigdb/human/geneset/CURSONS_NATURAL_KILLER_CELLS CURSONS_NATURAL_KILLER_CELLS]&lt;/span&gt;&lt;/li&gt;<br /> &lt;li&gt;&lt;span class=&quot;plainlinks&quot;&gt;[https://gsea-msigdb.org/gsea/msigdb/human/geneset/MISIAK_ANAPLASTIC_THYROID_CARCINOMA_UP MISIAK_ANAPLASTIC_THYROID_CARCINOMA_UP]&lt;/span&gt;&lt;/li&gt;<br /> &lt;li&gt;&lt;span class=&quot;plainlinks&quot;&gt;[https://gsea-msigdb.org/gsea/msigdb/human/geneset/MISIAK_ANAPLASTIC_THYROID_CARCINOMA_DN MISIAK_ANAPLASTIC_THYROID_CARCINOMA_DN]&lt;/span&gt;&lt;/li&gt;<br /> &lt;/ul&gt;<br /> &lt;br&gt;<br /> &lt;p&gt;STANHILL_HRAS_TRANSFROMATION_UP and SHARMA_ASTROCYTOMA_WITH_NF1_SYNDROM were archived in previous MSigDB releases due to no longer passing thresholds for inclusion (&lt;5 genes), these set once again pass thresholds and has been included in MSigDB.&lt;/p&gt;<br /> &lt;p&gt;Two gene sets, BIERIE_INFLAMMATORY_RESPONSE_TGFB1, and FUJIWARA_PARK2_IN_LIVER_CANCER_DN, are no longer included in this release of MSigDB as they no longer pass MSigDB inclusion thresholds (&gt;5 genes).&lt;/p&gt;<br /> &lt;p&gt;SATOH_COLORECTAL_CANCER_MYC_UP and SATOH_COLORECTAL_CANCER_MYC_DN have been renamed SOGA_COLORECTAL_CANCER_MYC_UP and SOGA_COLORECTAL_CANCER_MYC_DN respectively to reflect the wishes of the set contributors&lt;/p&gt;<br /> <br /> &lt;h2&gt;C2:CP:Reactome&lt;/h2&gt;<br /> <br /> &lt;ul&gt;<br /> &lt;li&gt;Reactome gene sets have been updated to reflect the state of the Reactome pathway architecture as of '''Reactome v81''' (+19 gene sets).&lt;/li&gt;<br /> &lt;li&gt;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.&lt;/li&gt;<br /> &lt;/ul&gt;<br /> <br /> &lt;h2&gt;C2:CP:WikiPathways&lt;/h2&gt;<br /> WikiPathways gene sets have been updated to the August 10, 2022 release (+48 gene sets).<br /> <br /> &lt;h2&gt;C3:TFT:GTRD&lt;/h2&gt;<br /> &lt;p&gt;GCM2_TARGET_GENES was removed as it no longer passes MSigDB inclusion thresholds. (set members &gt;2000 genes).&lt;/p&gt;<br /> <br /> &lt;h2&gt;C5:GO (Gene Ontology)&lt;/h2&gt;<br /> &lt;p&gt; 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 (&lt;span class=&quot;plainlinks&quot;&gt;[http://www.geneontology.org Nature Genet 2000]&lt;/span&gt;). 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 2022-07-01 and NCBI gene2go annotations downloaded on 2022-07-15.&lt;/p&gt;<br /> <br /> &lt;p&gt;This collection is divided into three sub-collections:&lt;/p&gt;<br /> &lt;ul&gt;<br /> &lt;li&gt;&lt;strong&gt;BP&lt;/strong&gt;: GO Biological process (+105 gene sets). Gene sets derived from the Biological Process Ontology, and are prefixed with &quot;GOBP_&quot;.&lt;/li&gt;<br /> &lt;li&gt;&lt;strong&gt;CC&lt;/strong&gt;: GO Cellular component (+29 gene sets). Gene sets derived from the Cellular Component Ontology, and are prefixed with &quot;GOCC_&quot;.&lt;/li&gt;<br /> &lt;li&gt;&lt;strong&gt;MF&lt;/strong&gt;: GO Molecular function (+25 gene sets). Gene sets derived from the Molecular Function Ontology, and are prefixed with &quot;GOMF_&quot;..&lt;/li&gt;<br /> &lt;/ul&gt;<br /> <br /> &lt;p&gt;These updates were generated in accordance with the procedure described in the [[MSigDB_v7.0_Release_Notes#C5_.28Gene_Ontology_collection.29_-_Major_overhaul | GO release notes for MSigDB 7.0.]]&lt;/p&gt;<br /> <br /> &lt;h2&gt;C5:HPO (Human Phenotype Ontology)&lt;/h2&gt;<br /> <br /> Gene sets in this sub-collection have been updated to reflect the 2022-06-11 release of the Human Phenotype Ontology database (+71 gene sets). This sub-collection has been redundancy filtered through a procedure comparable to that of the GO and Reactome sub-collections.<br /> <br /> &lt;h2&gt;C8 cell type signature gene sets&lt;/h2&gt;<br /> &lt;p&gt;Added gene sets describing pancreatic cell type identity signatures from &lt;span class=&quot;plainlinks&quot;&gt;[https://www.ncbi.nlm.nih.gov/labs/pmc/articles/PMC9019032/ van Gurp et al. 2022 Generation of human islet cell type-specific identity genesets]&lt;/span&gt; (+4 gene sets) &lt;/p&gt;<br /> <br /> &lt;h2&gt;CHIP file updates&lt;/h2&gt;<br /> &lt;ul&gt;<br /> &lt;li&gt;MSigDB 2022.1.Hs gene annotations and gene mapping CHIP files have been updated to data from Ensembl 107.&lt;/li&gt;<br /> &lt;li&gt;Gene orthology annotations for mapping mouse and rat genes to their best match human orthologs have been updated to &lt;span class=&quot;plainlinks&quot;&gt;[https://www.alliancegenome.org/ Alliance of Genome Resources]&lt;/span&gt; orthology database release 5.2.1 (2022-07-15)&lt;/li&gt;<br /> &lt;li&gt;Rat Microarray annotations derived from mappings to the mRatBN7.2 assembly are now available, the previous warning associated with remapped data from the deprecated Rnor_6.0 assembly has been removed.&lt;/li&gt;<br /> &lt;/ul&gt;</div> Acastanza https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=MSigDB_v2022.1.Mm_Release_Notes&diff=4509 MSigDB v2022.1.Mm Release Notes 2022-09-07T22:20:31Z <p>Acastanza: </p> <hr /> <div>&lt;span class=&quot;plainlinks&quot;&gt;<br /> [http://www.broadinstitute.org/gsea/ GSEA Home] |<br /> [http://www.broadinstitute.org/gsea/downloads.jsp Downloads] | <br /> [http://www.broadinstitute.org/gsea/msigdb/ Molecular Signatures Database] | <br /> [http://www.broadinstitute.org/cancer/software/gsea/wiki/index.php/Main_Page Documentation] |<br /> [http://www.broadinstitute.org/gsea/contact.jsp Contact]<br /> &lt;/span&gt;<br /> <br /> &lt;h1&gt;Important Notices&lt;/h1&gt;<br /> <br /> This page describes updates made to the Molecular Signatures Database for release 2022.1. This release introduces several major changes to previous conventions. MSigDB is now split into two major divisions; a series of gene set collections that are provided in the namespace of human gene symbols, and a series of gene set collections that are provided in the namespace of mouse gene symbols. As such the versioning convention of MSigDB has changed to adopt the format Year.Release.Species. This initial release in the new format is versioned 2022.1.Hs for the human collections and 2022.1.Mm for the mouse collections. Likewise, CHIP files have been updated to reflect this convention, as well as the specific series of collections (i.e. human or mouse) that they are targeted towards.<br /> <br /> '''Note that in order to access the MSigBD mouse collections through the GSEA UI, the latest version of GSEA (4.3.0) is required.'''<br /> <br /> MSigDB v2022.1 is based on gene annotation data from Ensembl Release 107 (Jul 2022).<br /> <br /> &lt;h1&gt;Initial Release of Mouse Collections (MSigDB v2022.1.Mm)&lt;/h1&gt;<br /> <br /> The initial release of the MSigDB Mouse Collections contains the following 6 collections, with some collection numbers reserved for future development. Please see the &lt;span class=&quot;plainlinks&quot;&gt;[https://gsea-msigdb.org/gsea/msigdb/mouse/collection_details.jsp Collection Details Page]&lt;/span&gt; for collection-specific general information.<br /> <br /> &lt;h2&gt;MH: mouse-ortholog hallmark gene sets&lt;/h2&gt;<br /> The MSigDB Hallmarks collection is being made available in an orthology converted form to aid in initial exploratory analysis of mouse datasets utilizing orthology mappings to MGI IDs provided by the Mouse Genome Informatics (MGI) institute at The Jackson Laboratory.<br /> <br /> &lt;h2&gt;M1: positional gene sets&lt;/h2&gt;<br /> Ensembl IDs for genes were retrieved from the cytogenetic band annotations provided in Ensembl 102 release, corresponding to the GRCm38 assembly as cytogentic band annotatations for GRCm39 are not presently available.<br /> <br /> &lt;h2&gt;M2: curated gene sets&lt;/h2&gt;<br /> &lt;h3&gt;M2:CGP&lt;/h3&gt;<br /> 932 gene sets consisting of:<br /> &lt;ul&gt;<br /> &lt;li&gt;869 miscellaneous gene sets derived from studies originally conducted in mouse models were copied from the Human C2:CGP subcollection and are included in M2:CGP in their native mouse namespace&lt;/li&gt;<br /> &lt;li&gt;21 gene sets describing the mouse turmor models and xenografts curated by Jill Recla of the Mouse Genome Informatics (MGI) institute at The Jackson Laboratory&lt;/li&gt;<br /> &lt;li&gt;42 gene sets describing neurogenic fates and cortical patterning from mouse experiments provided by Robert Hevner&lt;/li&gt;<br /> &lt;/ul&gt;<br /> <br /> &lt;h3&gt;M2:CP&lt;/h3&gt;<br /> The initial release of the mouse C2:CP collection contains:<br /> &lt;ul&gt;<br /> &lt;li&gt;252 gene sets from the BioCarta mouse database&lt;/li&gt;<br /> &lt;li&gt;1249 gene sets from the Reactome mouse database&lt;/li&gt;<br /> &lt;li&gt;186 gene sets from the WikiPathways mouse dabase&lt;/li&gt;<br /> &lt;/ul&gt;<br /> <br /> &lt;h2&gt;M3: regulatory target gene sets&lt;/h2&gt;<br /> &lt;ul&gt;<br /> &lt;li&gt;Transcription factor target gene sets from the Gene Transcription Regulation Database (GTRD) corresponding to experiments performed using mouse ChIP-seq experiments&lt;/li&gt;<br /> &lt;li&gt;miRNA target gene sets from computationally predicted mouse gene targets of miRNAs using the MirTarget algorithm. Data was curated from [http://mirdb.org miRDB v6.0] target predictions with MirTarget scores &gt;80 (high confidence predictions). miRNAs catalogued in miRDB v6.0 are derived from miRBase v22 (March 2018).<br /> &lt;/li&gt;<br /> &lt;/ul&gt;<br /> <br /> &lt;h2&gt;M5: ontology gene sets&lt;/h2&gt;<br /> <br /> &lt;p&gt;M5:GO which is divided into three sub-collections:&lt;/p&gt;<br /> &lt;ul&gt;<br /> &lt;li&gt;&lt;strong&gt;BP&lt;/strong&gt;: GO Biological process (7775 gene sets). Gene sets derived from the Biological Process Ontology.&lt;/li&gt;<br /> &lt;li&gt;&lt;strong&gt;CC&lt;/strong&gt;: GO Cellular component (1039 gene sets). Gene sets derived from the Cellular Component Ontology.&lt;/li&gt;<br /> &lt;li&gt;&lt;strong&gt;MF&lt;/strong&gt;: GO Molecular function (1746 gene sets). Gene sets derived from the Molecular Function Ontology.&lt;/li&gt;<br /> &lt;/ul&gt;<br /> <br /> &lt;p&gt;M5:MPT&lt;/p&gt;<br /> 92 gene sets mined from the &lt;span class=&quot;plainlinks&quot;&gt;[http://www.informatics.jax.org/vocab/mp_ontology Mammalian Phenotype Ontology database] corresponding to tumor specific ontology terms.&lt;/span&gt;<br /> <br /> &lt;h2&gt;M8: cell type signature gene sets&lt;/h2&gt;<br /> Two initial groups of gene sets are being provided in this initial release<br /> &lt;ul&gt;<br /> &lt;li&gt;38 gene sets derived from cell identity signatures from the &lt;span class=&quot;plainlinks&quot;&gt;[https://oncoscape.v3.sttrcancer.org/atlas.gs.washington.edu.mouse.rna/mouse Mouse Organogenesis Cell Atlas (MOCA)]&lt;/span&gt;&lt;/li&gt;<br /> &lt;li&gt;176 gene sets derived from cell aging signatures from the &lt;span class=&quot;plainlinks&quot;&gt;[http://tabula-muris-senis.ds.czbiohub.org/ Tabula Muris Senis, or 'Mouse Ageing Cell Atlas']&lt;/span&gt;&lt;/li&gt;<br /> &lt;/ul&gt;<br /> <br /> &lt;h1&gt;CHIP file release&lt;/h1&gt;<br /> &lt;ul&gt;<br /> &lt;li&gt;MSigDB 2022.1.Mm gene annotations and gene mapping CHIP files are being provided utilizing data from Ensembl 107.&lt;/li&gt;<br /> &lt;li&gt;Gene orthology annotations for mapping human and rat genes to their best match mouse orthologs are being provided utilizing information from &lt;span class=&quot;plainlinks&quot;&gt;[https://www.alliancegenome.org/ Alliance of Genome Resources]&lt;/span&gt; orthology database release 5.2.1 (2022-07-15).&lt;/li&gt;<br /> &lt;/ul&gt;<br /> <br /> &lt;h1&gt;Compendia expression profiles&lt;/h1&gt;<br /> The investigate gene sets tool provides a mouse transcriptomic expression atlas derived from the &lt;span class=&quot;plainlinks&quot;&gt;[https://pubmed.ncbi.nlm.nih.gov/28646208/ Mouse Transcriptomic BodyMap compendium] allowing for visualization of the expression of gene set genes across 17 mouse tissues.&lt;/span&gt;</div> Acastanza https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=MSigDB_v2022.1.Mm_Release_Notes&diff=4508 MSigDB v2022.1.Mm Release Notes 2022-09-07T22:15:43Z <p>Acastanza: </p> <hr /> <div>&lt;span class=&quot;plainlinks&quot;&gt;<br /> [http://www.broadinstitute.org/gsea/ GSEA Home] |<br /> [http://www.broadinstitute.org/gsea/downloads.jsp Downloads] | <br /> [http://www.broadinstitute.org/gsea/msigdb/ Molecular Signatures Database] | <br /> [http://www.broadinstitute.org/cancer/software/gsea/wiki/index.php/Main_Page Documentation] |<br /> [http://www.broadinstitute.org/gsea/contact.jsp Contact]<br /> &lt;/span&gt;<br /> <br /> &lt;h1&gt;Important Notices&lt;/h1&gt;<br /> <br /> This page describes updates made to the Molecular Signatures Database for release 2022.1. This release introduces several major changes to previous conventions. MSigDB is now split into two major divisions; a series of gene set collections that are provided in the namespace of human gene symbols, and a series of gene set collections that are provided in the namespace of mouse gene symbols. As such the versioning convention of MSigDB has changed to adopt the format Year.Release.Species. This initial release in the new format is versioned 2022.1.Hs for the human collections and 2022.1.Mm for the mouse collections. Likewise, CHIP files have been updated to reflect this convention, as well as the specific series of collections (i.e. human or mouse) that they are targeted towards.<br /> <br /> '''Note that in order to access the MSigBD mouse collections through the GSEA UI, the latest version of GSEA (4.3.0) is required.'''<br /> <br /> MSigDB v2022.1 is based on gene annotation data from Ensembl Release 107 (Jul 2022).<br /> <br /> &lt;h1&gt;Initial Release of Mouse Collections (MSigDB v2022.1.Mm)&lt;/h1&gt;<br /> <br /> The initial release of the MSigDB Mouse Collections contains the following 6 collections, with some collection numbers reserved for future development. Please see the &lt;span class=&quot;plainlinks&quot;&gt;[https://gsea-msigdb.org/gsea/msigdb/mouse/collection_details.jsp Collection Details Page]&lt;/span&gt; for collection-specific general information.<br /> <br /> &lt;h2&gt;MH: mouse-ortholog hallmark gene sets&lt;/h2&gt;<br /> The MSigDB Hallmarks collection is being made available in an orthology converted form to aid in initial exploratory analysis of mouse datasets utilizing orthology mappings to MGI IDs provided by the Mouse Genome Informatics (MGI) institute at The Jackson Laboratory.<br /> <br /> &lt;h2&gt;M1: positional gene sets&lt;/h2&gt;<br /> Ensembl IDs for genes were retrieved from the cytogenetic band annotations provided in Ensembl 102 release, corresponding to the GRCm38 assembly as cytogentic band annotatations for GRCm39 are not presently available.<br /> <br /> &lt;h2&gt;M2: curated gene sets&lt;/h2&gt;<br /> &lt;h3&gt;M2:CGP&lt;/h3&gt;<br /> 932 gene sets consisting of:<br /> &lt;ul&gt;<br /> &lt;li&gt;869 miscellaneous gene sets derived from studies originally conducted in mouse models were copied from the Human C2:CGP subcollection and are included in M2:CGP in their native mouse namespace&lt;/li&gt;<br /> &lt;li&gt;21 gene sets describing the mouse turmor models and xenografts curated by Jill Recla of the Mouse Genome Informatics (MGI) institute at The Jackson Laboratory&lt;/li&gt;<br /> &lt;li&gt;42 gene sets describing neurogenic fates and cortical patterning from mouse experiments provided by Robert Hevner&lt;/li&gt;<br /> &lt;/ul&gt;<br /> <br /> &lt;h3&gt;M2:CP&lt;/h3&gt;<br /> The initial release of the mouse C2:CP collection contains:<br /> &lt;ul&gt;<br /> &lt;li&gt;252 gene sets from the BioCarta mouse database&lt;/li&gt;<br /> &lt;li&gt;1249 gene sets from the Reactome mouse database&lt;/li&gt;<br /> &lt;li&gt;186 gene sets from the WikiPathways mouse dabase&lt;/li&gt;<br /> &lt;/ul&gt;<br /> <br /> &lt;h2&gt;M3: regulatory target gene sets&lt;/h2&gt;<br /> &lt;ul&gt;<br /> &lt;li&gt;Transcription factor target gene sets from the Gene Transcription Regulation Database (GTRD) corresponding to experiments performed using mouse ChIP-seq experiments&lt;/li&gt;<br /> &lt;li&gt;miRNA target gene sets from computationally predicted mouse gene targets of miRNAs using the MirTarget algorithm. Data was curated from [http://mirdb.org miRDB v6.0] target predictions with MirTarget scores &gt;80 (high confidence predictions). miRNAs catalogued in miRDB v6.0 are derived from miRBase v22 (March 2018).<br /> &lt;/li&gt;<br /> &lt;/ul&gt;<br /> <br /> &lt;h2&gt;M5: ontology gene sets&lt;/h2&gt;<br /> <br /> &lt;p&gt;M5:GO which is divided into three sub-collections:&lt;/p&gt;<br /> &lt;ul&gt;<br /> &lt;li&gt;&lt;strong&gt;BP&lt;/strong&gt;: GO Biological process (7775 gene sets). Gene sets derived from the Biological Process Ontology.&lt;/li&gt;<br /> &lt;li&gt;&lt;strong&gt;CC&lt;/strong&gt;: GO Cellular component (1039 gene sets). Gene sets derived from the Cellular Component Ontology.&lt;/li&gt;<br /> &lt;li&gt;&lt;strong&gt;MF&lt;/strong&gt;: GO Molecular function (1746 gene sets). Gene sets derived from the Molecular Function Ontology.&lt;/li&gt;<br /> &lt;/ul&gt;<br /> <br /> <br /> &lt;h2&gt;M8: cell type signature gene sets&lt;/h2&gt;<br /> Two initial groups of gene sets are being provided in this initial release<br /> &lt;ul&gt;<br /> &lt;li&gt;38 gene sets derived from cell identity signatures from the &lt;span class=&quot;plainlinks&quot;&gt;[https://oncoscape.v3.sttrcancer.org/atlas.gs.washington.edu.mouse.rna/mouse Mouse Organogenesis Cell Atlas (MOCA)]&lt;/span&gt;&lt;/li&gt;<br /> &lt;li&gt;176 gene sets derived from cell aging signatures from the &lt;span class=&quot;plainlinks&quot;&gt;[http://tabula-muris-senis.ds.czbiohub.org/ Tabula Muris Senis, or 'Mouse Ageing Cell Atlas']&lt;/span&gt;&lt;/li&gt;<br /> &lt;/ul&gt;<br /> <br /> &lt;h1&gt;CHIP file release&lt;/h1&gt;<br /> &lt;ul&gt;<br /> &lt;li&gt;MSigDB 2022.1.Mm gene annotations and gene mapping CHIP files are being provided utilizing data from Ensembl 107.&lt;/li&gt;<br /> &lt;li&gt;Gene orthology annotations for mapping human and rat genes to their best match mouse orthologs are being provided utilizing information from &lt;span class=&quot;plainlinks&quot;&gt;[https://www.alliancegenome.org/ Alliance of Genome Resources]&lt;/span&gt; orthology database release 5.2.1 (2022-07-15)&lt;/li&gt;<br /> &lt;/ul&gt;<br /> <br /> &lt;h1&gt;Compendia expression profiles&lt;/h1&gt;<br /> The investigate gene sets tool provides a mouse transcriptomic expression atlas derived from the &lt;span class=&quot;plainlinks&quot;&gt;[https://pubmed.ncbi.nlm.nih.gov/28646208/ Mouse Transcriptomic BodyMap compendium] allowing for visualization of the expression of gene set genes across 17 mouse tissues&lt;/span&gt;</div> Acastanza https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=MSigDB_v2022.1.Mm_Release_Notes&diff=4507 MSigDB v2022.1.Mm Release Notes 2022-09-07T22:08:47Z <p>Acastanza: </p> <hr /> <div>&lt;span class=&quot;plainlinks&quot;&gt;<br /> [http://www.broadinstitute.org/gsea/ GSEA Home] |<br /> [http://www.broadinstitute.org/gsea/downloads.jsp Downloads] | <br /> [http://www.broadinstitute.org/gsea/msigdb/ Molecular Signatures Database] | <br /> [http://www.broadinstitute.org/cancer/software/gsea/wiki/index.php/Main_Page Documentation] |<br /> [http://www.broadinstitute.org/gsea/contact.jsp Contact]<br /> &lt;/span&gt;<br /> <br /> &lt;h1&gt;Important Notices&lt;/h1&gt;<br /> <br /> This page describes updates made to the Molecular Signatures Database for release 2022.1. This release introduces several major changes to previous conventions. MSigDB is now split into two major divisions; a series of gene set collections that are provided in the namespace of human gene symbols, and a series of gene set collections that are provided in the namespace of mouse gene symbols. As such the versioning convention of MSigDB has changed to adopt the format Year.Release.Species. This initial release in the new format is versioned 2022.1.Hs for the human collections and 2022.1.Mm for the mouse collections. Likewise, CHIP files have been updated to reflect this convention, as well as the specific series of collections (i.e. human or mouse) that they are targeted towards.<br /> <br /> '''Note that in order to access the MSigBD mouse collections through the GSEA UI, the latest version of GSEA (4.3.0) is required.'''<br /> <br /> MSigDB v2022.1 is based on gene annotation data from Ensembl Release 107 (Jul 2022).<br /> <br /> &lt;h1&gt;Initial Release of Mouse Collections (MSigDB v2022.1.Mm)&lt;/h1&gt;<br /> <br /> The initial release of the MSigDB Mouse Collections contains the following 6 collections, with some collection numbers reserved for future development. Please see the &lt;span class=&quot;plainlinks&quot;&gt;[https://gsea-msigdb.org/gsea/msigdb/mouse/collection_details.jsp Collection Details Page]&lt;/span&gt; for collection-specific general information.<br /> <br /> &lt;h2&gt;MH: mouse-ortholog hallmark gene sets&lt;/h2&gt;<br /> The MSigDB Hallmarks collection is being made available in an orthology converted form to aid in initial exploratory analysis of mouse datasets utilizing orthology mappings to MGI IDs provided by the Mouse Genome Informatics (MGI) institute at The Jackson Laboratory.<br /> <br /> &lt;h2&gt;M1: positional gene sets&lt;/h2&gt;<br /> Ensembl IDs for genes were retrieved from the cytogenetic band annotations provided in Ensembl 102 release, corresponding to the GRCm38 assembly as cytogentic band annotatations for GRCm39 are not presently available.<br /> <br /> &lt;h2&gt;M2: curated gene sets&lt;/h2&gt;<br /> &lt;h3&gt;M2:CGP&lt;/h3&gt;<br /> 932 gene sets consisting of:<br /> &lt;ul&gt;<br /> &lt;li&gt;869 miscellaneous gene sets derived from studies originally conducted in mouse models were copied from the Human C2:CGP subcollection and are included in M2:CGP in their native mouse namespace&lt;/li&gt;<br /> &lt;li&gt;21 gene sets describing the mouse turmor models and xenografts curated by Jill Recla of the Mouse Genome Informatics (MGI) institute at The Jackson Laboratory&lt;/li&gt;<br /> &lt;li&gt;42 gene sets describing neurogenic fates and cortical patterning from mouse experiments provided by Robert Hevner&lt;/li&gt;<br /> &lt;/ul&gt;<br /> <br /> &lt;h3&gt;M2:CP&lt;/h3&gt;<br /> The initial release of the mouse C2:CP collection contains:<br /> &lt;ul&gt;<br /> &lt;li&gt;252 gene sets from the BioCarta mouse database&lt;/li&gt;<br /> &lt;li&gt;1249 gene sets from the Reactome mouse database&lt;/li&gt;<br /> &lt;li&gt;186 gene sets from the WikiPathways mouse dabase&lt;/li&gt;<br /> &lt;/ul&gt;<br /> <br /> &lt;h2&gt;M3: regulatory target gene sets&lt;/h2&gt;<br /> &lt;ul&gt;<br /> &lt;li&gt;Transcription factor target gene sets from the Gene Transcription Regulation Database (GTRD) corresponding to experiments performed using mouse ChIP-seq experiments&lt;/li&gt;<br /> &lt;li&gt;miRNA target gene sets from computationally predicted mouse gene targets of miRNAs using the MirTarget algorithm. Data was curated from [http://mirdb.org miRDB v6.0] target predictions with MirTarget scores &gt;80 (high confidence predictions). miRNAs catalogued in miRDB v6.0 are derived from miRBase v22 (March 2018).<br /> &lt;/li&gt;<br /> &lt;/ul&gt;<br /> <br /> &lt;h2&gt;M5: ontology gene sets&lt;/h2&gt;<br /> <br /> &lt;p&gt;M5:GO which is divided into three sub-collections:&lt;/p&gt;<br /> &lt;ul&gt;<br /> &lt;li&gt;&lt;strong&gt;BP&lt;/strong&gt;: GO Biological process (2 gene sets). Gene sets derived from the Biological Process Ontology.&lt;/li&gt;<br /> &lt;li&gt;&lt;strong&gt;CC&lt;/strong&gt;: GO Cellular component (0 gene sets). Gene sets derived from the Cellular Component Ontology.&lt;/li&gt;<br /> &lt;li&gt;&lt;strong&gt;MF&lt;/strong&gt;: GO Molecular function (0 gene sets). Gene sets derived from the Molecular Function Ontology.&lt;/li&gt;<br /> &lt;/ul&gt;<br /> <br /> <br /> &lt;h2&gt;M8: cell type signature gene sets&lt;/h2&gt;<br /> Two initial groups of gene sets are being provided in this initial release<br /> &lt;ul&gt;<br /> &lt;li&gt;38 gene sets derived from cell identity signatures from the &lt;span class=&quot;plainlinks&quot;&gt;[https://oncoscape.v3.sttrcancer.org/atlas.gs.washington.edu.mouse.rna/mouse Mouse Organogenesis Cell Atlas (MOCA)]&lt;/span&gt;&lt;/li&gt;<br /> &lt;li&gt;176 gene sets derived from cell aging signatures fromo the &lt;span class=&quot;plainlinks&quot;&gt;[http://tabula-muris-senis.ds.czbiohub.org/ Tabula Muris Senis, or 'Mouse Ageing Cell Atlas']&lt;/span&gt;&lt;/li&gt;<br /> &lt;/ul&gt;<br /> <br /> &lt;h1&gt;CHIP file release&lt;/h1&gt;<br /> &lt;ul&gt;<br /> &lt;li&gt;MSigDB 2022.1.Mm gene annotations and gene mapping CHIP files are being provided utilizing data from Ensembl 107.&lt;/li&gt;<br /> &lt;li&gt;Gene orthology annotations for mapping human and rat genes to their best match mouse orthologs are being provided utilizing information from &lt;span class=&quot;plainlinks&quot;&gt;[https://www.alliancegenome.org/ Alliance of Genome Resources]&lt;/span&gt; orthology database release 5.2.1 (2022-07-15)&lt;/li&gt;<br /> &lt;/ul&gt;<br /> <br /> &lt;h1&gt;Compendia expression profiles&lt;/h1&gt;<br /> The investigate gene sets tool provides a mouse transcriptomic expression atlas derived from the &lt;span class=&quot;plainlinks&quot;&gt;[https://pubmed.ncbi.nlm.nih.gov/28646208/ Mouse Transcriptomic BodyMap compendium] allowing for visualization of the expression of gene set genes across 17 mouse tissues&lt;/span&gt;</div> Acastanza https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=MSigDB_v2022.1.Mm_Release_Notes&diff=4506 MSigDB v2022.1.Mm Release Notes 2022-09-07T22:08:27Z <p>Acastanza: </p> <hr /> <div>&lt;span class=&quot;plainlinks&quot;&gt;<br /> [http://www.broadinstitute.org/gsea/ GSEA Home] |<br /> [http://www.broadinstitute.org/gsea/downloads.jsp Downloads] | <br /> [http://www.broadinstitute.org/gsea/msigdb/ Molecular Signatures Database] | <br /> [http://www.broadinstitute.org/cancer/software/gsea/wiki/index.php/Main_Page Documentation] |<br /> [http://www.broadinstitute.org/gsea/contact.jsp Contact]<br /> &lt;/span&gt;<br /> <br /> &lt;h1&gt;Important Notices&lt;/h1&gt;<br /> <br /> This page describes updates made to the Molecular Signatures Database for release 2022.1. This release introduces several major changes to previous conventions. MSigDB is now split into two major divisions; a series of gene set collections that are provided in the namespace of human gene symbols, and a series of gene set collections that are provided in the namespace of mouse gene symbols. As such the versioning convention of MSigDB has changed to adopt the format Year.Release.Species. This initial release in the new format is versioned 2022.1.Hs for the human collections and 2022.1.Mm for the mouse collections. Likewise, CHIP files have been updated to reflect this convention, as well as the specific series of collections (i.e. human or mouse) that they are targeted towards.<br /> <br /> '''Note that in order to access the MSigBD mouse collections through the GSEA UI, the latest version of GSEA (4.3.0) is required.'''<br /> <br /> MSigDB v2022.1 is based on gene annotation data from Ensembl Release 107 (Jul 2022).<br /> <br /> &lt;h1&gt;Initial Release of Mouse Collections (MSigDB v2022.1.Mm)&lt;/h1&gt;<br /> <br /> The initial release of the MSigDB Mouse Collections contains the following 6 collections, with some collection numbers reserved for future development. Please see the &lt;span class=&quot;plainlinks&quot;&gt;[https://gsea-msigdb.org/gsea/msigdb/mouse/collection_details.jsp Collection Details Page]&lt;/span&gt; for collection-specific general information.<br /> <br /> &lt;h2&gt;MH: mouse-ortholog hallmark gene sets&lt;/h2&gt;<br /> The MSigDB Hallmarks collection is being made available in an orthology converted form to aid in initial exploratory analysis of mouse datasets utilizing orthology mappings to MGI IDs provided by the Mouse Genome Informatics (MGI) institute at The Jackson Laboratory.<br /> <br /> &lt;h2&gt;M1: positional gene sets&lt;/h2&gt;<br /> Ensembl IDs for genes were retrieved from the cytogenetic band annotations provided in Ensembl 102 release, corresponding to the GRCm38 assembly as cytogentic band annotatations for GRCm39 are not presently available.<br /> <br /> &lt;h2&gt;M2: curated gene sets&lt;/h2&gt;<br /> &lt;h3&gt;M2:CGP&lt;/h3&gt;<br /> 932 gene sets consisting of:<br /> &lt;ul&gt;<br /> &lt;li&gt;869 miscellaneous gene sets derived from studies originally conducted in mouse models were copied from the Human C2:CGP subcollection and are included in M2:CGP in their native mouse namespace&lt;/li&gt;<br /> &lt;li&gt;21 gene sets describing the mouse turmor models and xenografts curated by Jill Recla of the Mouse Genome Informatics (MGI) institute at The Jackson Laboratory&lt;/li&gt;<br /> &lt;li&gt;42 gene sets describing neurogenic fates and cortical patterning from mouse experiments provided by Robert Hevner&lt;/li&gt;<br /> &lt;/ul&gt;<br /> <br /> &lt;h3&gt;M2:CP&lt;/h3&gt;<br /> The initial release of the mouse C2:CP collection contains:<br /> &lt;ul&gt;<br /> &lt;li&gt;252 gene sets from the BioCarta mouse database&lt;/li&gt;<br /> &lt;li&gt;1249 gene sets from the Reactome mouse database&lt;/li&gt;<br /> &lt;li&gt;186 gene sets from the WikiPathways mouse dabase&lt;/li&gt;<br /> &lt;/ul&gt;<br /> <br /> &lt;h2&gt;M3: regulatory target gene sets&lt;/h2&gt;<br /> &lt;ul&gt;<br /> &lt;li&gt;Transcription factor target gene sets from the Gene Transcription Regulation Database (GTRD) corresponding to experiments performed using mouse ChIP-seq experiments&lt;/li&gt;<br /> &lt;li&gt;miRNA target gene sets from computationally predicted mouse gene targets of miRNAs using the MirTarget algorithm. Data was curated from [http://mirdb.org miRDB v6.0] target predictions with MirTarget scores &gt;80 (high confidence predictions). miRNAs catalogued in miRDB v6.0 are derived from miRBase v22 (March 2018).<br /> &lt;/li&gt;<br /> &lt;/ul&gt;<br /> <br /> &lt;h2&gt;M5: ontology gene sets&lt;/h2&gt;<br /> <br /> &lt;p&gt;M5:GO which is divided into three sub-collections:&lt;/p&gt;<br /> &lt;ul&gt;<br /> &lt;li&gt;&lt;strong&gt;BP&lt;/strong&gt;: GO Biological process (2 gene sets). Gene sets derived from the Biological Process Ontology.&lt;/li&gt;<br /> &lt;li&gt;&lt;strong&gt;CC&lt;/strong&gt;: GO Cellular component (0 gene sets). Gene sets derived from the Cellular Component Ontology.&lt;/li&gt;<br /> &lt;li&gt;&lt;strong&gt;MF&lt;/strong&gt;: GO Molecular function (0 gene sets). Gene sets derived from the Molecular Function Ontology.&lt;/li&gt;<br /> &lt;/ul&gt;<br /> <br /> <br /> &lt;h2&gt;M8: cell type signature gene sets&lt;/h2&gt;<br /> Two initial groups of gene sets are being provided in this initial release<br /> &lt;ul&gt;<br /> &lt;li&gt;38 gene sets derived from cell identity signatures from the &lt;span class=&quot;plainlinks&quot;&gt;[https://oncoscape.v3.sttrcancer.org/atlas.gs.washington.edu.mouse.rna/mouse Mouse Organogenesis Cell Atlas (MOCA)]&lt;/span&gt;&lt;/li&gt;<br /> &lt;li&gt;176 gene sets derived from cell aging signatures fromo the &lt;span class=&quot;plainlinks&quot;&gt;[http://tabula-muris-senis.ds.czbiohub.org/ Tabula Muris Senis, or 'Mouse Ageing Cell Atlas']&lt;/span&gt;&lt;/li&gt;<br /> &lt;/ul&gt;<br /> <br /> &lt;h1&gt;CHIP file release&lt;/h1&gt;<br /> &lt;ul&gt;<br /> &lt;li&gt;MSigDB 2022.1.Mm gene annotations and gene mapping CHIP files are being provided utilizing data from Ensembl 107.&lt;/li&gt;<br /> &lt;li&gt;Gene orthology annotations for mapping human and rat genes to their best match mouse orthologs are being provided utilizing information from &lt;span class=&quot;plainlinks&quot;&gt;[https://www.alliancegenome.org/ Alliance of Genome Resources]&lt;/span&gt; orthology database release 5.2.1 (2022-07-15)&lt;/li&gt;<br /> <br /> &lt;h1&gt;Compendia expression profiles&lt;/h1&gt;<br /> The investigate gene sets tool provides a mouse transcriptomic expression atlas derived from the &lt;span class=&quot;plainlinks&quot;&gt;[https://pubmed.ncbi.nlm.nih.gov/28646208/ Mouse Transcriptomic BodyMap compendium] allowing for visualization of the expression of gene set genes across 17 mouse tissues&lt;/span&gt;</div> Acastanza https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=MSigDB_v2022.1.Mm_Release_Notes&diff=4505 MSigDB v2022.1.Mm Release Notes 2022-09-07T22:08:10Z <p>Acastanza: </p> <hr /> <div>&lt;span class=&quot;plainlinks&quot;&gt;<br /> [http://www.broadinstitute.org/gsea/ GSEA Home] |<br /> [http://www.broadinstitute.org/gsea/downloads.jsp Downloads] | <br /> [http://www.broadinstitute.org/gsea/msigdb/ Molecular Signatures Database] | <br /> [http://www.broadinstitute.org/cancer/software/gsea/wiki/index.php/Main_Page Documentation] |<br /> [http://www.broadinstitute.org/gsea/contact.jsp Contact]<br /> &lt;/span&gt;<br /> <br /> &lt;h1&gt;Important Notices&lt;/h1&gt;<br /> <br /> This page describes updates made to the Molecular Signatures Database for release 2022.1. This release introduces several major changes to previous conventions. MSigDB is now split into two major divisions; a series of gene set collections that are provided in the namespace of human gene symbols, and a series of gene set collections that are provided in the namespace of mouse gene symbols. As such the versioning convention of MSigDB has changed to adopt the format Year.Release.Species. This initial release in the new format is versioned 2022.1.Hs for the human collections and 2022.1.Mm for the mouse collections. Likewise, CHIP files have been updated to reflect this convention, as well as the specific series of collections (i.e. human or mouse) that they are targeted towards.<br /> <br /> '''Note that in order to access the MSigBD mouse collections through the GSEA UI, the latest version of GSEA (4.3.0) is required.'''<br /> <br /> MSigDB v2022.1 is based on gene annotation data from Ensembl Release 107 (Jul 2022).<br /> <br /> &lt;h1&gt;Initial Release of Mouse Collections (MSigDB v2022.1.Mm)&lt;/h1&gt;<br /> <br /> The initial release of the MSigDB Mouse Collections contains the following 6 collections, with some collection numbers reserved for future development. Please see the &lt;span class=&quot;plainlinks&quot;&gt;[https://gsea-msigdb.org/gsea/msigdb/mouse/collection_details.jsp Collection Details Page]&lt;/span&gt; for collection-specific general information.<br /> <br /> &lt;h2&gt;MH: mouse-ortholog hallmark gene sets&lt;/h2&gt;<br /> The MSigDB Hallmarks collection is being made available in an orthology converted form to aid in initial exploratory analysis of mouse datasets utilizing orthology mappings to MGI IDs provided by the Mouse Genome Informatics (MGI) institute at The Jackson Laboratory.<br /> <br /> &lt;h2&gt;M1: positional gene sets&lt;/h2&gt;<br /> Ensembl IDs for genes were retrieved from the cytogenetic band annotations provided in Ensembl 102 release, corresponding to the GRCm38 assembly as cytogentic band annotatations for GRCm39 are not presently available.<br /> <br /> &lt;h2&gt;M2: curated gene sets&lt;/h2&gt;<br /> &lt;h3&gt;M2:CGP&lt;/h3&gt;<br /> 932 gene sets consisting of:<br /> &lt;ul&gt;<br /> &lt;li&gt;869 miscellaneous gene sets derived from studies originally conducted in mouse models were copied from the Human C2:CGP subcollection and are included in M2:CGP in their native mouse namespace&lt;/li&gt;<br /> &lt;li&gt;21 gene sets describing the mouse turmor models and xenografts curated by Jill Recla of the Mouse Genome Informatics (MGI) institute at The Jackson Laboratory&lt;/li&gt;<br /> &lt;li&gt;42 gene sets describing neurogenic fates and cortical patterning from mouse experiments provided by Robert Hevner&lt;/li&gt;<br /> &lt;/ul&gt;<br /> <br /> &lt;h3&gt;M2:CP&lt;/h3&gt;<br /> The initial release of the mouse C2:CP collection contains:<br /> &lt;ul&gt;<br /> &lt;li&gt;252 gene sets from the BioCarta mouse database&lt;/li&gt;<br /> &lt;li&gt;1249 gene sets from the Reactome mouse database&lt;/li&gt;<br /> &lt;li&gt;186 gene sets from the WikiPathways mouse dabase&lt;/li&gt;<br /> &lt;/ul&gt;<br /> <br /> &lt;h2&gt;M3: regulatory target gene sets&lt;/h2&gt;<br /> &lt;ul&gt;<br /> &lt;li&gt;Transcription factor target gene sets from the Gene Transcription Regulation Database (GTRD) corresponding to experiments performed using mouse ChIP-seq experiments&lt;/li&gt;<br /> &lt;li&gt;miRNA target gene sets from computationally predicted mouse gene targets of miRNAs using the MirTarget algorithm. Data was curated from [http://mirdb.org miRDB v6.0] target predictions with MirTarget scores &gt;80 (high confidence predictions). miRNAs catalogued in miRDB v6.0 are derived from miRBase v22 (March 2018).<br /> &lt;/li&gt;<br /> &lt;/ul&gt;<br /> <br /> &lt;h2&gt;M5: ontology gene sets&lt;/h2&gt;<br /> <br /> &lt;p&gt;M5:GO which is divided into three sub-collections:&lt;/p&gt;<br /> &lt;ul&gt;<br /> &lt;li&gt;&lt;strong&gt;BP&lt;/strong&gt;: GO Biological process (2 gene sets). Gene sets derived from the Biological Process Ontology.&lt;/li&gt;<br /> &lt;li&gt;&lt;strong&gt;CC&lt;/strong&gt;: GO Cellular component (0 gene sets). Gene sets derived from the Cellular Component Ontology.&lt;/li&gt;<br /> &lt;li&gt;&lt;strong&gt;MF&lt;/strong&gt;: GO Molecular function (0 gene sets). Gene sets derived from the Molecular Function Ontology.&lt;/li&gt;<br /> &lt;/ul&gt;<br /> <br /> <br /> &lt;h2&gt;M8: cell type signature gene sets&lt;/h2&gt;<br /> Two initial groups of gene sets are being provided in this initial release<br /> &lt;ul&gt;<br /> &lt;li&gt;38 gene sets derived from cell identity signatures from the &lt;span class=&quot;plainlinks&quot;&gt;[https://oncoscape.v3.sttrcancer.org/atlas.gs.washington.edu.mouse.rna/mouse Mouse Organogenesis Cell Atlas (MOCA)]&lt;/span&gt;&lt;/li&gt;<br /> &lt;li&gt;176 gene sets derived from cell aging signatures fromo the &lt;span class=&quot;plainlinks&quot;&gt;[http://tabula-muris-senis.ds.czbiohub.org/ Tabula Muris Senis, or 'Mouse Ageing Cell Atlas']&lt;/span&gt;&lt;/li&gt;<br /> &lt;/ul&gt;<br /> <br /> &lt;h1&gt;CHIP file release&lt;/h2&gt;<br /> &lt;ul&gt;<br /> &lt;li&gt;MSigDB 2022.1.Mm gene annotations and gene mapping CHIP files are being provided utilizing data from Ensembl 107.&lt;/li&gt;<br /> &lt;li&gt;Gene orthology annotations for mapping human and rat genes to their best match mouse orthologs are being provided utilizing information from &lt;span class=&quot;plainlinks&quot;&gt;[https://www.alliancegenome.org/ Alliance of Genome Resources]&lt;/span&gt; orthology database release 5.2.1 (2022-07-15)&lt;/li&gt;<br /> <br /> &lt;h1&gt;Compendia expression profiles&lt;/h2&gt;<br /> The investigate gene sets tool provides a mouse transcriptomic expression atlas derived from the &lt;span class=&quot;plainlinks&quot;&gt;[https://pubmed.ncbi.nlm.nih.gov/28646208/ Mouse Transcriptomic BodyMap compendium] allowing for visualization of the expression of gene set genes across 17 mouse tissues&lt;/span&gt;</div> Acastanza https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=MSigDB_v2022.1.Mm_Release_Notes&diff=4504 MSigDB v2022.1.Mm Release Notes 2022-09-07T22:02:20Z <p>Acastanza: </p> <hr /> <div>&lt;span class=&quot;plainlinks&quot;&gt;<br /> [http://www.broadinstitute.org/gsea/ GSEA Home] |<br /> [http://www.broadinstitute.org/gsea/downloads.jsp Downloads] | <br /> [http://www.broadinstitute.org/gsea/msigdb/ Molecular Signatures Database] | <br /> [http://www.broadinstitute.org/cancer/software/gsea/wiki/index.php/Main_Page Documentation] |<br /> [http://www.broadinstitute.org/gsea/contact.jsp Contact]<br /> &lt;/span&gt;<br /> <br /> &lt;h1&gt;Important Notices&lt;/h1&gt;<br /> <br /> This page describes updates made to the Molecular Signatures Database for release 2022.1. This release introduces several major changes to previous conventions. MSigDB is now split into two major divisions; a series of gene set collections that are provided in the namespace of human gene symbols, and a series of gene set collections that are provided in the namespace of mouse gene symbols. As such the versioning convention of MSigDB has changed to adopt the format Year.Release.Species. This initial release in the new format is versioned 2022.1.Hs for the human collections and 2022.1.Mm for the mouse collections. Likewise, CHIP files have been updated to reflect this convention, as well as the specific series of collections (i.e. human or mouse) that they are targeted towards.<br /> <br /> '''Note that in order to access the MSigBD mouse collections through the GSEA UI, the latest version of GSEA (4.3.0) is required.'''<br /> <br /> MSigDB v2022.1 is based on gene annotation data from Ensembl Release 107 (Jul 2022).<br /> <br /> &lt;h1&gt;Initial Release of Mouse Collections (MSigDB v2022.1.Mm)&lt;/h1&gt;<br /> <br /> The initial release of the MSigDB Mouse Collections contains the following 6 collections, with some collection numbers reserved for future development. Please see the &lt;span class=&quot;plainlinks&quot;&gt;[https://gsea-msigdb.org/gsea/msigdb/mouse/collection_details.jsp Collection Details Page]&lt;/span&gt; for collection-specific general information.<br /> <br /> &lt;h2&gt;MH: mouse-ortholog hallmark gene sets&lt;/h2&gt;<br /> The MSigDB Hallmarks collection is being made available in an orthology converted form to aid in initial exploratory analysis of mouse datasets utilizing orthology mappings to MGI IDs provided by the Mouse Genome Informatics (MGI) institute at The Jackson Laboratory.<br /> <br /> &lt;h2&gt;M1: positional gene sets&lt;/h2&gt;<br /> Ensembl IDs for genes were retrieved from the cytogenetic band annotations provided in Ensembl 102 release, corresponding to the GRCm38 assembly as cytogentic band annotatations for GRCm39 are not presently available.<br /> <br /> &lt;h2&gt;M2: curated gene sets&lt;/h2&gt;<br /> &lt;h3&gt;M2:CGP&lt;/h3&gt;<br /> 932 gene sets consisting of:<br /> &lt;ul&gt;<br /> &lt;li&gt;869 miscellaneous gene sets derived from studies originally conducted in mouse models were copied from the Human C2:CGP subcollection and are included in M2:CGP in their native mouse namespace&lt;/li&gt;<br /> &lt;li&gt;21 gene sets describing the mouse turmor models and xenografts curated by Jill Recla of the Mouse Genome Informatics (MGI) institute at The Jackson Laboratory&lt;/li&gt;<br /> &lt;li&gt;42 gene sets describing neurogenic fates and cortical patterning from mouse experiments provided by Robert Hevner&lt;/li&gt;<br /> &lt;/ul&gt;<br /> <br /> &lt;h3&gt;M2:CP&lt;/h3&gt;<br /> The initial release of the mouse C2:CP collection contains:<br /> &lt;ul&gt;<br /> &lt;li&gt;252 gene sets from the BioCarta mouse database&lt;/li&gt;<br /> &lt;li&gt;1249 gene sets from the Reactome mouse database&lt;/li&gt;<br /> &lt;li&gt;186 gene sets from the WikiPathways mouse dabase&lt;/li&gt;<br /> &lt;/ul&gt;<br /> <br /> &lt;h2&gt;M3: regulatory target gene sets&lt;/h2&gt;<br /> &lt;ul&gt;<br /> &lt;li&gt;Transcription factor target gene sets from the Gene Transcription Regulation Database (GTRD) corresponding to experiments performed using mouse ChIP-seq experiments&lt;/li&gt;<br /> &lt;li&gt;miRNA target gene sets from computationally predicted mouse gene targets of miRNAs using the MirTarget algorithm. Data was curated from [http://mirdb.org miRDB v6.0] target predictions with MirTarget scores &gt;80 (high confidence predictions). miRNAs catalogued in miRDB v6.0 are derived from miRBase v22 (March 2018).<br /> &lt;/li&gt;<br /> &lt;/ul&gt;<br /> <br /> &lt;h2&gt;M5: ontology gene sets&lt;/h2&gt;<br /> <br /> &lt;h2&gt;M8: cell type signature gene sets&lt;/h2&gt;<br /> Two initial groups of gene sets are being provided in this initial release<br /> &lt;ul&gt;<br /> &lt;li&gt;38 gene sets derived from cell identity signatures from the &lt;span class=&quot;plainlinks&quot;&gt;[https://oncoscape.v3.sttrcancer.org/atlas.gs.washington.edu.mouse.rna/mouse Mouse Organogenesis Cell Atlas (MOCA)]&lt;/span&gt;&lt;/li&gt;<br /> &lt;li&gt;176 gene sets derived from cell aging signatures fromo the &lt;span class=&quot;plainlinks&quot;&gt;[http://tabula-muris-senis.ds.czbiohub.org/ Tabula Muris Senis, or 'Mouse Ageing Cell Atlas']&lt;/span&gt;&lt;/li&gt;<br /> &lt;/ul&gt;<br /> <br /> &lt;h2&gt;CHIP file release&lt;/h2&gt;<br /> &lt;ul&gt;<br /> &lt;li&gt;MSigDB 2022.1.Mm gene annotations and gene mapping CHIP files are being provided utilizing data from Ensembl 107.&lt;/li&gt;<br /> &lt;li&gt;Gene orthology annotations for mapping human and rat genes to their best match mouse orthologs are being provided utilizing information from &lt;span class=&quot;plainlinks&quot;&gt;[https://www.alliancegenome.org/ Alliance of Genome Resources]&lt;/span&gt; orthology database release 5.2.1 (2022-07-15)&lt;/li&gt;</div> Acastanza https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=MSigDB_v2022.1.Mm_Release_Notes&diff=4503 MSigDB v2022.1.Mm Release Notes 2022-09-07T21:25:14Z <p>Acastanza: </p> <hr /> <div>&lt;span class=&quot;plainlinks&quot;&gt;<br /> [http://www.broadinstitute.org/gsea/ GSEA Home] |<br /> [http://www.broadinstitute.org/gsea/downloads.jsp Downloads] | <br /> [http://www.broadinstitute.org/gsea/msigdb/ Molecular Signatures Database] | <br /> [http://www.broadinstitute.org/cancer/software/gsea/wiki/index.php/Main_Page Documentation] |<br /> [http://www.broadinstitute.org/gsea/contact.jsp Contact]<br /> &lt;/span&gt;<br /> <br /> &lt;h1&gt;Important Notices&lt;/h1&gt;<br /> <br /> This page describes updates made to the Molecular Signatures Database for release 2022.1. This release introduces several major changes to previous conventions. MSigDB is now split into two major divisions; a series of gene set collections that are provided in the namespace of human gene symbols, and a series of gene set collections that are provided in the namespace of mouse gene symbols. As such the versioning convention of MSigDB has changed to adopt the format Year.Release.Species. This initial release in the new format is versioned 2022.1.Hs for the human collections and 2022.1.Mm for the mouse collections. Likewise, CHIP files have been updated to reflect this convention, as well as the specific series of collections (i.e. human or mouse) that they are targeted towards.<br /> <br /> '''Note that in order to access the MSigBD mouse collections through the GSEA UI, the latest version of GSEA (4.3.0) is required.'''<br /> <br /> MSigDB v2022.1 is based on gene annotation data from Ensembl Release 107 (Jul 2022).<br /> <br /> &lt;h1&gt;Initial Release of Mouse Collections (MSigDB v2022.1.Mm)&lt;/h1&gt;<br /> <br /> The initial release of the MSigDB Mouse Collections contains the following 6 collections, with some collection numbers reserved for future development. Please see the &lt;span class=&quot;plainlinks&quot;&gt;[https://gsea-msigdb.org/gsea/msigdb/mouse/collection_details.jsp Collection Details Page]&lt;/span&gt; for collection-specific general information.<br /> <br /> &lt;h2&gt;MH: mouse-ortholog hallmark gene sets&lt;/h2&gt;<br /> <br /> &lt;h2&gt;M1: positional gene sets&lt;/h2&gt;<br /> <br /> &lt;h2&gt;M2: curated gene sets&lt;/h2&gt;<br /> <br /> &lt;h2&gt;M3: regulatory target gene sets&lt;/h2&gt;<br /> <br /> &lt;h2&gt;M5: ontology gene sets&lt;/h2&gt;<br /> <br /> &lt;h2&gt;M8: cell type signature gene sets&lt;/h2&gt;<br /> <br /> &lt;h2&gt;CHIP file release&lt;/h2&gt;<br /> &lt;ul&gt;<br /> &lt;li&gt;MSigDB 2022.1.Mm gene annotations and gene mapping CHIP files are being provided utilizing data from Ensembl 107.&lt;/li&gt;<br /> &lt;li&gt;Gene orthology annotations for mapping human and rat genes to their best match mouse orthologs are being provided utilizing information from &lt;span class=&quot;plainlinks&quot;&gt;[https://www.alliancegenome.org/ Alliance of Genome Resources]&lt;/span&gt; orthology database release 5.2.1 (2022-07-15)&lt;/li&gt;</div> Acastanza https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=MSigDB_v2022.1.Mm_Release_Notes&diff=4502 MSigDB v2022.1.Mm Release Notes 2022-09-07T21:22:58Z <p>Acastanza: </p> <hr /> <div>&lt;span class=&quot;plainlinks&quot;&gt;<br /> [http://www.broadinstitute.org/gsea/ GSEA Home] |<br /> [http://www.broadinstitute.org/gsea/downloads.jsp Downloads] | <br /> [http://www.broadinstitute.org/gsea/msigdb/ Molecular Signatures Database] | <br /> [http://www.broadinstitute.org/cancer/software/gsea/wiki/index.php/Main_Page Documentation] |<br /> [http://www.broadinstitute.org/gsea/contact.jsp Contact]<br /> &lt;/span&gt;<br /> <br /> &lt;h1&gt;Important Notices&lt;/h1&gt;<br /> <br /> This page describes updates made to the Molecular Signatures Database for release 2022.1. This release introduces several major changes to previous conventions. MSigDB is now split into two major divisions; a series of gene set collections that are provided in the namespace of human gene symbols, and a series of gene set collections that are provided in the namespace of mouse gene symbols. As such the versioning convention of MSigDB has changed to adopt the format Year.Release.Species. This initial release in the new format is versioned 2022.1.Hs for the human collections and 2022.1.Mm for the mouse collections. Likewise, CHIP files have been updated to reflect this convention, as well as the specific series of collections (i.e. human or mouse) that they are targeted towards.<br /> <br /> '''Note that in order to access the MSigBD mouse collections through the GSEA UI, the latest version of GSEA (4.3.0) is required.'''<br /> <br /> MSigDB v2022.1 is based on gene annotation data from Ensembl Release 107 (Jul 2022).<br /> <br /> &lt;h1&gt;Initial Release of Mouse Collections (MSigDB v2022.1.Mm)&lt;/h1&gt;<br /> <br /> The initial release of the MSigDB Mouse Collections contains the following 6 collections, with some collection numbers reserved for future development. Please see the &lt;span class=&quot;plainlinks&quot;&gt;[https://gsea-msigdb.org/gsea/msigdb/mouse/collection_details.jsp Collection Details Page]&lt;/span&gt; for collection-specific general information.<br /> <br /> &lt;h2&gt;MH: mouse-ortholog hallmark gene sets&lt;/h2&gt;<br /> <br /> &lt;h2&gt;M1: positional gene sets&lt;/h2&gt;<br /> <br /> &lt;h2&gt;M2: curated gene sets&lt;/h2&gt;<br /> <br /> &lt;h2&gt;M3: regulatory target gene sets&lt;/h2&gt;<br /> <br /> &lt;h2&gt;M5: ontology gene sets&lt;/h2&gt;<br /> <br /> &lt;h2&gt;M8: cell type signature gene sets&lt;/h2&gt;</div> Acastanza https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=MSigDB_v2022.1.Mm_Release_Notes&diff=4501 MSigDB v2022.1.Mm Release Notes 2022-09-07T21:21:22Z <p>Acastanza: </p> <hr /> <div>&lt;span class=&quot;plainlinks&quot;&gt;<br /> [http://www.broadinstitute.org/gsea/ GSEA Home] |<br /> [http://www.broadinstitute.org/gsea/downloads.jsp Downloads] | <br /> [http://www.broadinstitute.org/gsea/msigdb/ Molecular Signatures Database] | <br /> [http://www.broadinstitute.org/cancer/software/gsea/wiki/index.php/Main_Page Documentation] |<br /> [http://www.broadinstitute.org/gsea/contact.jsp Contact]<br /> &lt;/span&gt;<br /> <br /> &lt;h1&gt;Important Notices&lt;/h1&gt;<br /> <br /> This page describes updates made to the Molecular Signatures Database for release 2022.1. This release introduces several major changes to previous conventions. MSigDB is now split into two major divisions; a series of gene set collections that are provided in the namespace of human gene symbols, and a series of gene set collections that are provided in the namespace of mouse gene symbols. As such the versioning convention of MSigDB has changed to adopt the format Year.Release.Species. This initial release in the new format is versioned 2022.1.Hs for the human collections and 2022.1.Mm for the mouse collections. Likewise, CHIP files have been updated to reflect this convention, as well as the specific series of collections (i.e. human or mouse) that they are targeted towards.<br /> <br /> '''Note that in order to access the MSigBD mouse collections through the GSEA UI, the latest version of GSEA (4.3.0) is required.'''<br /> <br /> MSigDB v2022.1 is based on gene annotation data from Ensembl Release 107 (Jul 2022).<br /> <br /> &lt;h1&gt;Initial Release of Mouse Collections (MSigDB v2022.1.Mm)&lt;/h1&gt;<br /> <br /> The initial release of the MSigDB Mouse Collections contains the following 6 collections, with some collection numbers reserved for future development.<br /> <br /> &lt;h2&gt;MH: mouse-ortholog hallmark gene sets&lt;/h2&gt;<br /> <br /> &lt;h2&gt;M1: positional gene sets&lt;/h2&gt;<br /> <br /> &lt;h2&gt;M2: curated gene sets&lt;/h2&gt;<br /> <br /> &lt;h2&gt;M3: regulatory target gene sets&lt;/h2&gt;<br /> <br /> &lt;h2&gt;M5: ontology gene sets&lt;/h2&gt;<br /> <br /> &lt;h2&gt;M8: cell type signature gene sets&lt;/h2&gt;</div> Acastanza https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=MSigDB_v2022.1.Hs_Release_Notes&diff=4500 MSigDB v2022.1.Hs Release Notes 2022-09-07T21:17:41Z <p>Acastanza: </p> <hr /> <div>&lt;span class=&quot;plainlinks&quot;&gt;<br /> [http://www.broadinstitute.org/gsea/ GSEA Home] |<br /> [http://www.broadinstitute.org/gsea/downloads.jsp Downloads] | <br /> [http://www.broadinstitute.org/gsea/msigdb/ Molecular Signatures Database] | <br /> [http://www.broadinstitute.org/cancer/software/gsea/wiki/index.php/Main_Page Documentation] |<br /> [http://www.broadinstitute.org/gsea/contact.jsp Contact]<br /> &lt;/span&gt;<br /> <br /> &lt;h1&gt;Important Notices&lt;/h1&gt;<br /> <br /> This page describes updates made to the Molecular Signatures Database for release 2022.1. This release introduces several major changes to previous conventions. MSigDB is now split into two major divisions; a series of gene set collections that are provided in the namespace of human gene symbols, and a series of gene set collections that are provided in the namespace of mouse gene symbols. As such the versioning convention of MSigDB has changed to adopt the format Year.Release.Species. This initial release in the new format is versioned 2022.1.Hs for the human collections and 2022.1.Mm for the mouse collections. Likewise, CHIP files have been updated to reflect this convention, as well as the specific series of collections (i.e. human or mouse) that they are targeted towards.<br /> <br /> '''Note that in order to access the MSigBD mouse collections through the GSEA UI, the latest version of GSEA (4.3.0) is required.'''<br /> <br /> MSigDB v2022.1 is based on gene annotation data from Ensembl Release 107 (Jul 2022).<br /> <br /> &lt;h1&gt;Updates to Human Collections (MSigDB v2022.1.Hs)&lt;/h1&gt;<br /> <br /> &lt;h2&gt;C1: positional gene sets&lt;/h2&gt;<br /> Updated human gene annotations to Ensembl 107.<br /> &lt;h2&gt;C2:CGP&lt;/h2&gt;<br /> <br /> 15 Gene sets contributed by MSigDB users have been added to C2:CGP<br /> &lt;ul&gt;<br /> &lt;span class=&quot;plainlinks&quot;&gt;[https://gsea-msigdb.org/gsea/msigdb/human/geneset/LIU_OVARIAN_CANCER_TUMORS_AND_XENOGRAFTS_XDGS_UP LIU_OVARIAN_CANCER_TUMORS_AND_XENOGRAFTS_XDGS_UP]&lt;/span&gt;&lt;/li&gt;<br /> &lt;li&gt;&lt;span class=&quot;plainlinks&quot;&gt;[https://gsea-msigdb.org/gsea/msigdb/human/geneset/LIU_OVARIAN_CANCER_TUMORS_AND_XENOGRAFTS_XDGS_DN LIU_OVARIAN_CANCER_TUMORS_AND_XENOGRAFTS_XDGS_DN]&lt;/span&gt;&lt;/li&gt;<br /> &lt;li&gt;&lt;span class=&quot;plainlinks&quot;&gt;[https://gsea-msigdb.org/gsea/msigdb/human/geneset/LIU_OVARIAN_CANCER_TUMORS_AND_XENOGRAFTS_KINASES_DN LIU_OVARIAN_CANCER_TUMORS_AND_XENOGRAFTS_KINASES_DN]&lt;/span&gt;&lt;/li&gt;<br /> &lt;li&gt;&lt;span class=&quot;plainlinks&quot;&gt;[https://gsea-msigdb.org/gsea/msigdb/human/geneset/BANG_VERTEPORFIN_ENDOMETRIAL_CANCER_CELLS_UP BANG_VERTEPORFIN_ENDOMETRIAL_CANCER_CELLS_UP]&lt;/span&gt;&lt;/li&gt;<br /> &lt;li&gt;&lt;span class=&quot;plainlinks&quot;&gt;[https://gsea-msigdb.org/gsea/msigdb/human/geneset/BANG_VERTEPORFIN_ENDOMETRIAL_CANCER_CELLS_DN BANG_VERTEPORFIN_ENDOMETRIAL_CANCER_CELLS_DN]&lt;/span&gt;&lt;/li&gt;<br /> &lt;li&gt;&lt;span class=&quot;plainlinks&quot;&gt;[https://gsea-msigdb.org/gsea/msigdb/human/geneset/CARRILLOREIXACH_HEPATOBLASTOMA_VS_NORMAL_UP CARRILLOREIXACH_HEPATOBLASTOMA_VS_NORMAL_UP]&lt;/span&gt;&lt;/li&gt;<br /> &lt;li&gt;&lt;span class=&quot;plainlinks&quot;&gt;[https://gsea-msigdb.org/gsea/msigdb/human/geneset/CARRILLOREIXACH_HEPATOBLASTOMA_VS_NORMAL_DN CARRILLOREIXACH_HEPATOBLASTOMA_VS_NORMAL_DN]&lt;/span&gt;&lt;/li&gt;<br /> &lt;li&gt;&lt;span class=&quot;plainlinks&quot;&gt;[https://gsea-msigdb.org/gsea/msigdb/human/geneset/CARRILLOREIXACH_14Q32OVEREXPRESSION_IN_HEPATOBLASTOMA CARRILLOREIXACH_14Q32OVEREXPRESSION_IN_HEPATOBLASTOMA]&lt;/span&gt;&lt;/li&gt;<br /> &lt;li&gt;&lt;span class=&quot;plainlinks&quot;&gt;[https://gsea-msigdb.org/gsea/msigdb/human/geneset/CARRILLOREIXACH_HEPATOBLASTOMA_VS_NORMAL_HYPERMETHYLATED_AND_DN CARRILLOREIXACH_HEPATOBLASTOMA_VS_NORMAL_HYPERMETHYLATED_AND_DN]&lt;/span&gt;&lt;/li&gt;<br /> &lt;li&gt;&lt;span class=&quot;plainlinks&quot;&gt;[https://gsea-msigdb.org/gsea/msigdb/human/geneset/CARRILLOREIXACH_HEPATOBLASTOMA_VS_NORMAL_HYPOMETHYLATED_AND_UP CARRILLOREIXACH_HEPATOBLASTOMA_VS_NORMAL_HYPOMETHYLATED_AND_UP]&lt;/span&gt;&lt;/li&gt;<br /> &lt;li&gt;&lt;span class=&quot;plainlinks&quot;&gt;[https://gsea-msigdb.org/gsea/msigdb/human/geneset/CARRILLOREIXACH_MRS3_VS_LOWER_RISK_HEPATOBLASTOMA_UP CARRILLOREIXACH_MRS3_VS_LOWER_RISK_HEPATOBLASTOMA_UP]&lt;/span&gt;&lt;/li&gt;<br /> &lt;li&gt;&lt;span class=&quot;plainlinks&quot;&gt;[https://gsea-msigdb.org/gsea/msigdb/human/geneset/CARRILLOREIXACH_MRS3_VS_LOWER_RISK_HEPATOBLASTOMA_DN CARRILLOREIXACH_MRS3_VS_LOWER_RISK_HEPATOBLASTOMA_DN]&lt;/span&gt;&lt;/li&gt;<br /> &lt;li&gt;&lt;span class=&quot;plainlinks&quot;&gt;[https://gsea-msigdb.org/gsea/msigdb/human/geneset/CURSONS_NATURAL_KILLER_CELLS CURSONS_NATURAL_KILLER_CELLS]&lt;/span&gt;&lt;/li&gt;<br /> &lt;li&gt;&lt;span class=&quot;plainlinks&quot;&gt;[https://gsea-msigdb.org/gsea/msigdb/human/geneset/MISIAK_ANAPLASTIC_THYROID_CARCINOMA_UP MISIAK_ANAPLASTIC_THYROID_CARCINOMA_UP]&lt;/span&gt;&lt;/li&gt;<br /> &lt;li&gt;&lt;span class=&quot;plainlinks&quot;&gt;[https://gsea-msigdb.org/gsea/msigdb/human/geneset/MISIAK_ANAPLASTIC_THYROID_CARCINOMA_DN MISIAK_ANAPLASTIC_THYROID_CARCINOMA_DN]&lt;/span&gt;&lt;/li&gt;<br /> &lt;/ul&gt;<br /> &lt;br&gt;<br /> &lt;p&gt;STANHILL_HRAS_TRANSFROMATION_UP and SHARMA_ASTROCYTOMA_WITH_NF1_SYNDROM were archived in previous MSigDB releases due to no longer passing thresholds for inclusion (&lt;5 genes), these set once again pass thresholds and has been included in MSigDB.&lt;/p&gt;<br /> &lt;p&gt;Two gene sets, BIERIE_INFLAMMATORY_RESPONSE_TGFB1, and FUJIWARA_PARK2_IN_LIVER_CANCER_DN, are no longer included in this release of MSigDB as they no longer pass MSigDB inclusion thresholds (&gt;5 genes).&lt;/p&gt;<br /> &lt;p&gt;SATOH_COLORECTAL_CANCER_MYC_UP and SATOH_COLORECTAL_CANCER_MYC_DN have been renamed SOGA_COLORECTAL_CANCER_MYC_UP and SOGA_COLORECTAL_CANCER_MYC_DN respectively to reflect the wishes of the set contributors&lt;/p&gt;<br /> <br /> &lt;h2&gt;C2:CP:Reactome&lt;/h2&gt;<br /> <br /> &lt;ul&gt;<br /> &lt;li&gt;Reactome gene sets have been updated to reflect the state of the Reactome pathway architecture as of '''Reactome v81''' (+19 gene sets).&lt;/li&gt;<br /> &lt;li&gt;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.&lt;/li&gt;<br /> &lt;/ul&gt;<br /> <br /> &lt;h2&gt;C2:CP:WikiPathways&lt;/h2&gt;<br /> WikiPathways gene sets have been updated to the August 10, 2022 release (+48 gene sets).<br /> <br /> &lt;h2&gt;C3:TFT:GTRD&lt;/h2&gt;<br /> &lt;p&gt;GCM2_TARGET_GENES was removed as it no longer passes MSigDB inclusion thresholds. (set members &gt;2000 genes).&lt;/p&gt;<br /> <br /> &lt;h2&gt;C5:GO (Gene Ontology)&lt;/h2&gt;<br /> &lt;p&gt; 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 (&lt;span class=&quot;plainlinks&quot;&gt;[http://www.geneontology.org Nature Genet 2000]&lt;/span&gt;). 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 2022-07-01 and NCBI gene2go annotations downloaded on 2022-07-15.&lt;/p&gt;<br /> <br /> &lt;p&gt;This collection is divided into three sub-collections:&lt;/p&gt;<br /> &lt;ul&gt;<br /> &lt;li&gt;&lt;strong&gt;BP&lt;/strong&gt;: GO Biological process (+105 gene sets). Gene sets derived from the Biological Process Ontology, and are prefixed with &quot;GOBP_&quot;.&lt;/li&gt;<br /> &lt;li&gt;&lt;strong&gt;CC&lt;/strong&gt;: GO Cellular component (+29 gene sets). Gene sets derived from the Cellular Component Ontology, and are prefixed with &quot;GOCC_&quot;.&lt;/li&gt;<br /> &lt;li&gt;&lt;strong&gt;MF&lt;/strong&gt;: GO Molecular function (+25 gene sets). Gene sets derived from the Molecular Function Ontology, and are prefixed with &quot;GOMF_&quot;..&lt;/li&gt;<br /> &lt;/ul&gt;<br /> <br /> &lt;p&gt;These updates were generated in accordance with the procedure described in the [[MSigDB_v7.0_Release_Notes#C5_.28Gene_Ontology_collection.29_-_Major_overhaul | GO release notes for MSigDB 7.0.]]&lt;/p&gt;<br /> <br /> &lt;h2&gt;C5:HPO (Human Phenotype Ontology)&lt;/h2&gt;<br /> <br /> Gene sets in this sub-collection have been updated to reflect the 2022-06-11 release of the Human Phenotype Ontology database (+71 gene sets). This sub-collection has been redundancy filtered through a procedure comparable to that of the GO and Reactome sub-collections.<br /> <br /> &lt;h2&gt;C8 cell type signature gene sets&lt;/h2&gt;<br /> &lt;p&gt;Added gene sets describing pancreatic cell type identity signatures from &lt;span class=&quot;plainlinks&quot;&gt;[https://www.ncbi.nlm.nih.gov/labs/pmc/articles/PMC9019032/ van Gurp et al. 2022 Generation of human islet cell type-specific identity genesets]&lt;/span&gt; (+4 gene sets) &lt;/p&gt;<br /> <br /> &lt;h2&gt;CHIP file updates&lt;/h2&gt;<br /> &lt;ul&gt;<br /> &lt;li&gt;MSigDB 2022.1.Hs gene annotations and gene mapping CHIP files have been updated to data from Ensembl 107.&lt;/li&gt;<br /> &lt;li&gt;Gene orthology annotations for mapping mouse and rat genes to their best match human orthologs have been updated to &lt;span class=&quot;plainlinks&quot;&gt;[https://www.alliancegenome.org/ Alliance of Genome Resources]&lt;/span&gt; orthology database release 5.2.1 (2022-07-15)&lt;/li&gt;<br /> &lt;li&gt;Rat Microarray annotations derived from mappings to the mRatBN7.2 assembly are now available, the previous warning associated with remapped data from the deprecated Rnor_6.0 assembly has been removed.&lt;/li&gt;<br /> &lt;/ul&gt;</div> Acastanza https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=MSigDB_v2022.1.Hs_Release_Notes&diff=4499 MSigDB v2022.1.Hs Release Notes 2022-09-07T21:00:44Z <p>Acastanza: </p> <hr /> <div>&lt;span class=&quot;plainlinks&quot;&gt;<br /> [http://www.broadinstitute.org/gsea/ GSEA Home] |<br /> [http://www.broadinstitute.org/gsea/downloads.jsp Downloads] | <br /> [http://www.broadinstitute.org/gsea/msigdb/ Molecular Signatures Database] | <br /> [http://www.broadinstitute.org/cancer/software/gsea/wiki/index.php/Main_Page Documentation] |<br /> [http://www.broadinstitute.org/gsea/contact.jsp Contact]<br /> &lt;/span&gt;<br /> <br /> &lt;h1&gt;Important Notices&lt;/h1&gt;<br /> <br /> This page describes updates made to the Molecular Signatures Database for release 2022.1. This release introduces several major changes to previous conventions. MSigDB is now split into two major divisions; a series of gene set collections that are provided in the namespace of human gene symbols, and a series of gene set collections that are provided in the namespace of mouse gene symbols. As such the versioning convention of MSigDB has changed to adopt the format Year.Release.Species. This initial release in the new format is versioned 2022.1.Hs for the human collections and 2022.1.Mm for the mouse collections. Likewise, CHIP files have been updated to reflect this convention, as well as the specific series of collections (i.e. human or mouse) that they are targeted towards.<br /> <br /> '''Note that in order to access the MSigBD mouse collections through the GSEA UI, the latest version of GSEA (4.3.0) is required.'''<br /> <br /> MSigDB v2022.1 is based on gene annotation data from Ensembl Release 107 (Jul 2022).<br /> <br /> &lt;h1&gt;Updates to Human Collections (MSigDB v2022.1.Hs)&lt;/h1&gt;<br /> <br /> &lt;h2&gt;C1: positional gene sets&lt;/h2&gt;<br /> Updated human gene annotations to Ensembl 107.<br /> &lt;h2&gt;C2:CGP&lt;/h2&gt;<br /> 14 Gene sets contributed by MSigDB users have been added to C2:CGP<br /> &lt;ul&gt;<br /> &lt;li&gt;[https://pubmed.ncbi.nlm.nih.gov/ (PMID:)]&lt;/li&gt;<br /> &lt;/ul&gt;<br /> <br /> &lt;h2&gt;C2:CP:Reactome&lt;/h2&gt;<br /> <br /> &lt;ul&gt;<br /> &lt;li&gt;Reactome gene sets have been updated to reflect the state of the Reactome pathway architecture as of '''Reactome v81''' (+19 gene sets).&lt;/li&gt;<br /> &lt;li&gt;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.&lt;/li&gt;<br /> &lt;/ul&gt;<br /> <br /> &lt;h2&gt;C2:CP:WikiPathways&lt;/h2&gt;<br /> WikiPathways gene sets have been updated to the August 10, 2022 release (+48 gene sets).<br /> <br /> &lt;h2&gt;C3:TFT:GTRD&lt;/h2&gt;<br /> &lt;p&gt;GCM2_TARGET_GENES was removed as it no longer passes MSigDB inclusion thresholds. (set members &gt;2000 genes).&lt;/p&gt;<br /> <br /> &lt;h2&gt;C5:GO (Gene Ontology)&lt;/h2&gt;<br /> &lt;p&gt; 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 (&lt;span class=&quot;plainlinks&quot;&gt;[http://www.geneontology.org Nature Genet 2000]&lt;/span&gt;). 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 2022-07-01 and NCBI gene2go annotations downloaded on 2022-07-15.&lt;/p&gt;<br /> <br /> &lt;p&gt;This collection is divided into three sub-collections:&lt;/p&gt;<br /> &lt;ul&gt;<br /> &lt;li&gt;&lt;strong&gt;BP&lt;/strong&gt;: GO Biological process (+105 gene sets). Gene sets derived from the Biological Process Ontology, and are prefixed with &quot;GOBP_&quot;.&lt;/li&gt;<br /> &lt;li&gt;&lt;strong&gt;CC&lt;/strong&gt;: GO Cellular component (+29 gene sets). Gene sets derived from the Cellular Component Ontology, and are prefixed with &quot;GOCC_&quot;.&lt;/li&gt;<br /> &lt;li&gt;&lt;strong&gt;MF&lt;/strong&gt;: GO Molecular function (+25 gene sets). Gene sets derived from the Molecular Function Ontology, and are prefixed with &quot;GOMF_&quot;..&lt;/li&gt;<br /> &lt;/ul&gt;<br /> <br /> &lt;p&gt;These updates were generated in accordance with the procedure described in the [[MSigDB_v7.0_Release_Notes#C5_.28Gene_Ontology_collection.29_-_Major_overhaul | GO release notes for MSigDB 7.0.]]&lt;/p&gt;<br /> <br /> &lt;h2&gt;C5:HPO (Human Phenotype Ontology)&lt;/h2&gt;<br /> <br /> Gene sets in this sub-collection have been updated to reflect the 2022-06-11 release of the Human Phenotype Ontology database (+71 gene sets). This sub-collection has been redundancy filtered through a procedure comparable to that of the GO and Reactome sub-collections.<br /> <br /> &lt;h2&gt;C8 cell type signature gene sets&lt;/h2&gt;<br /> &lt;p&gt;Added gene sets describing pancreatic cell type identity signatures from &lt;span class=&quot;plainlinks&quot;&gt;[https://www.ncbi.nlm.nih.gov/labs/pmc/articles/PMC9019032/ van Gurp et al. 2022 Generation of human islet cell type-specific identity genesets]&lt;/span&gt; (+4 gene sets) &lt;/p&gt;<br /> <br /> &lt;h2&gt;CHIP file updates&lt;/h2&gt;<br /> &lt;ul&gt;<br /> &lt;li&gt;MSigDB 2022.1.Hs gene annotations and gene mapping CHIP files have been updated to data from Ensembl 107.&lt;/li&gt;<br /> &lt;li&gt;Gene orthology annotations for mapping mouse and rat genes to their best match human orthologs have been updated to &lt;span class=&quot;plainlinks&quot;&gt;[https://www.alliancegenome.org/ Alliance of Genome Resources]&lt;/span&gt; orthology database release 5.2.1 (2022-07-15)&lt;/li&gt;<br /> &lt;li&gt;Rat Microarray annotations derived from mappings to the mRatBN7.2 assembly are now available, the previous warning associated with remapped data from the deprecated Rnor_6.0 assembly has been removed.&lt;/li&gt;<br /> &lt;/ul&gt;</div> Acastanza https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=MSigDB_v2022.1.Hs_Release_Notes&diff=4495 MSigDB v2022.1.Hs Release Notes 2022-08-31T18:37:19Z <p>Acastanza: </p> <hr /> <div>&lt;span class=&quot;plainlinks&quot;&gt;<br /> [http://www.broadinstitute.org/gsea/ GSEA Home] |<br /> [http://www.broadinstitute.org/gsea/downloads.jsp Downloads] | <br /> [http://www.broadinstitute.org/gsea/msigdb/ Molecular Signatures Database] | <br /> [http://www.broadinstitute.org/cancer/software/gsea/wiki/index.php/Main_Page Documentation] |<br /> [http://www.broadinstitute.org/gsea/contact.jsp Contact]<br /> &lt;/span&gt;<br /> <br /> &lt;h1&gt;Important Notices&lt;/h1&gt;<br /> <br /> This page describes updates made to the Molecular Signatures Database for release 2022.1. This release introduces several major changes to previous conventions. MSigDB is now split into two major divisions; a series of gene set collections that are provided in the namespace of human gene symbols, and a series of gene set collections that are provided in the namespace of mouse gene symbols. As such the versioning convention of MSigDB has changed to adopt the format Year.Release.Species. This initial release in the new format is versioned 2022.1.Hs for the human collections and 2022.1.Mm for the mouse collections. Likewise, CHIP files have been updated to reflect this convention, as well as the specific series of collections (i.e. human or mouse) that they are targeted towards.<br /> <br /> '''Note that in order to access the MSigBD mouse collections through the GSEA UI, the latest version of GSEA (4.3.0) is required.'''<br /> <br /> MSigDB v2022.1 is based on gene annotation data from Ensembl Release 107 (Jul 2022).<br /> <br /> &lt;h1&gt;Updates to Human Collections (MSigDB v2022.1.Hs)&lt;/h1&gt;<br /> <br /> &lt;h2&gt;C1&lt;/h2&gt;<br /> Updated human gene annotations to Ensembl 107 (+XX gene sets).<br /> &lt;h2&gt;C2:CGP&lt;/h2&gt;<br /> Gene sets contributed by the following individuals have been added to C2:CGP<br /> &lt;ul&gt;<br /> &lt;li&gt;[https://pubmed.ncbi.nlm.nih.gov/ (PMID:)]&lt;/li&gt;<br /> &lt;/ul&gt;<br /> <br /> &lt;h2&gt;C2:CP:Reactome&lt;/h2&gt;<br /> <br /> &lt;ul&gt;<br /> &lt;li&gt;Reactome gene sets have been updated to reflect the state of the Reactome pathway architecture as of '''Reactome v81''' (+XX gene sets).&lt;/li&gt;<br /> &lt;li&gt;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.&lt;/li&gt;<br /> &lt;/ul&gt;<br /> <br /> &lt;h2&gt;C2:CP:WikiPathways&lt;/h2&gt;<br /> WikiPathways gene sets have been updated to the August 10, 2022 release (+XX gene sets).<br /> <br /> &lt;h2&gt;C5:GO (Gene Ontology)&lt;/h2&gt;<br /> &lt;p&gt; 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 (&lt;span class=&quot;plainlinks&quot;&gt;[http://www.geneontology.org Nature Genet 2000]&lt;/span&gt;). 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 2022-07-01 and NCBI gene2go annotations downloaded on 2022-07-15.&lt;/p&gt;<br /> <br /> &lt;p&gt;This collection is divided into three sub-collections:&lt;/p&gt;<br /> &lt;ul&gt;<br /> &lt;li&gt;&lt;strong&gt;BP&lt;/strong&gt;: GO Biological process (+XX gene sets). Gene sets derived from the Biological Process Ontology, and are prefixed with &quot;GOBP_&quot;.&lt;/li&gt;<br /> &lt;li&gt;&lt;strong&gt;CC&lt;/strong&gt;: GO Cellular component (+XX gene sets). Gene sets derived from the Cellular Component Ontology, and are prefixed with &quot;GOCC_&quot;.&lt;/li&gt;<br /> &lt;li&gt;&lt;strong&gt;MF&lt;/strong&gt;: GO Molecular function (+XX gene sets). Gene sets derived from the Molecular Function Ontology, and are prefixed with &quot;GOMF_&quot;..&lt;/li&gt;<br /> &lt;/ul&gt;<br /> <br /> &lt;p&gt;These updates were generated in accordance with the procedure described in the [[MSigDB_v7.0_Release_Notes#C5_.28Gene_Ontology_collection.29_-_Major_overhaul | GO release notes for MSigDB 7.0.]]<br /> <br /> &lt;h2&gt;C5:HPO (Human Phenotype Ontology)&lt;/h2&gt;<br /> <br /> Gene sets in this sub-collection have been updated to reflect the 2022-06-11 release of the Human Phenotype Ontology database (+XX gene sets). This sub-collection has been redundancy filtered through a procedure comparable to that of the GO and Reactome sub-collections.<br /> <br /> &lt;h2&gt;CHIP file updates&lt;/h2&gt;<br /> &lt;ul&gt;<br /> &lt;li&gt;MSigDB 2022.1.Hs gene annotations and gene mapping CHIP files have been updated to data from Ensembl 107.&lt;/li&gt;<br /> &lt;li&gt;Gene orthology annotations for mapping mouse and rat genes to their best match human orthologs have been updated to &lt;span class=&quot;plainlinks&quot;&gt;[https://www.alliancegenome.org/ Alliance of Genome Resources]&lt;/span&gt; orthology database release 5.2.1 (2022-07-15)&lt;/li&gt;<br /> &lt;li&gt;Rat Microarray annotations derived from mappings to the mRatBN7.2 assembly are now available, the previous warning associated with remapped data from the deprecated Rnor_6.0 assembly has been removed.&lt;/li&gt;<br /> &lt;/ul&gt;</div> Acastanza https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=MSigDB_v2022.1.Hs_Release_Notes&diff=4494 MSigDB v2022.1.Hs Release Notes 2022-08-31T18:36:27Z <p>Acastanza: </p> <hr /> <div>&lt;span class=&quot;plainlinks&quot;&gt;<br /> [http://www.broadinstitute.org/gsea/ GSEA Home] |<br /> [http://www.broadinstitute.org/gsea/downloads.jsp Downloads] | <br /> [http://www.broadinstitute.org/gsea/msigdb/ Molecular Signatures Database] | <br /> [http://www.broadinstitute.org/cancer/software/gsea/wiki/index.php/Main_Page Documentation] |<br /> [http://www.broadinstitute.org/gsea/contact.jsp Contact]<br /> &lt;/span&gt;<br /> <br /> &lt;h1&gt;Important Notices&lt;/h1&gt;<br /> <br /> This page describes updates made to the Molecular Signatures Database for release 2022.1. This release introduces several major changes to previous conventions. MSigDB is now split into two major divisions; a series of gene set collections that are provided in the namespace of human gene symbols, and a series of gene set collections that are provided in the namespace of mouse gene symbols. As such the versioning convention of MSigDB has changed to adopt the format Year.Release.Species. This initial release in the new format is versioned 2022.1.Hs for the human collections and 2022.1.Mm for the mouse collections. Likewise, CHIP files have been updated to reflect this convention, as well as the specific series of collections (i.e. human or mouse) that they are targeted towards.<br /> <br /> '''Note that in order to access the MSigBD mouse collections through the GSEA UI, the latest version of GSEA (4.3.0) is required.'''<br /> <br /> MSigDB v2022.1 is based on gene annotation data from Ensembl Release 107 (Jul 2022).<br /> <br /> &lt;h1&gt;Updates to Human Collections (MSigDB v2022.1.Hs)&lt;/h1&gt;<br /> <br /> &lt;h3&gt;C1&lt;/h3&gt;<br /> Updated human gene annotations to Ensembl 107 (+XX gene sets).<br /> &lt;h3&gt;C2:CGP&lt;/h3&gt;<br /> Gene sets contributed by the following individuals have been added to C2:CGP<br /> &lt;ul&gt;<br /> &lt;li&gt;[https://pubmed.ncbi.nlm.nih.gov/ (PMID:)]&lt;/li&gt;<br /> &lt;/ul&gt;<br /> <br /> &lt;h3&gt;C2:CP:Reactome&lt;/h3&gt;<br /> <br /> &lt;ul&gt;<br /> &lt;li&gt;Reactome gene sets have been updated to reflect the state of the Reactome pathway architecture as of '''Reactome v81''' (+XX gene sets).&lt;/li&gt;<br /> &lt;li&gt;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.&lt;/li&gt;<br /> &lt;/ul&gt;<br /> <br /> &lt;h3&gt;C2:CP:WikiPathways&lt;/h3&gt;<br /> WikiPathways gene sets have been updated to the August 10, 2022 release (+XX gene sets).<br /> <br /> &lt;h3&gt;C5:GO (Gene Ontology)&lt;/h3&gt;<br /> &lt;p&gt; 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 (&lt;span class=&quot;plainlinks&quot;&gt;[http://www.geneontology.org Nature Genet 2000]&lt;/span&gt;). 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 2022-07-01 and NCBI gene2go annotations downloaded on 2022-07-15.&lt;/p&gt;<br /> <br /> &lt;p&gt;This collection is divided into three sub-collections:&lt;/p&gt;<br /> &lt;ul&gt;<br /> &lt;li&gt;&lt;strong&gt;BP&lt;/strong&gt;: GO Biological process (+XX gene sets). Gene sets derived from the Biological Process Ontology, and are prefixed with &quot;GOBP_&quot;.&lt;/li&gt;<br /> &lt;li&gt;&lt;strong&gt;CC&lt;/strong&gt;: GO Cellular component (+XX gene sets). Gene sets derived from the Cellular Component Ontology, and are prefixed with &quot;GOCC_&quot;.&lt;/li&gt;<br /> &lt;li&gt;&lt;strong&gt;MF&lt;/strong&gt;: GO Molecular function (+XX gene sets). Gene sets derived from the Molecular Function Ontology, and are prefixed with &quot;GOMF_&quot;..&lt;/li&gt;<br /> &lt;/ul&gt;<br /> <br /> &lt;p&gt;These updates were generated in accordance with the procedure described in the [[MSigDB_v7.0_Release_Notes#C5_.28Gene_Ontology_collection.29_-_Major_overhaul | GO release notes for MSigDB 7.0.]]<br /> <br /> &lt;h3&gt;C5:HPO (Human Phenotype Ontology)&lt;/h3&gt;<br /> <br /> Gene sets in this sub-collection have been updated to reflect the 2022-06-11 release of the Human Phenotype Ontology database (+XX gene sets). This sub-collection has been redundancy filtered through a procedure comparable to that of the GO and Reactome sub-collections.<br /> <br /> &lt;h3&gt;CHIP file updates&lt;/h3&gt;<br /> &lt;ul&gt;<br /> &lt;li&gt;MSigDB 2022.1.Hs gene annotations and gene mapping CHIP files have been updated to data from Ensembl 107.&lt;/li&gt;<br /> &lt;li&gt;Gene orthology annotations for mapping mouse and rat genes to their best match human orthologs have been updated to &lt;span class=&quot;plainlinks&quot;&gt;[https://www.alliancegenome.org/ Alliance of Genome Resources]&lt;/span&gt; orthology database release 5.2.1 (2022-07-15)&lt;/li&gt;<br /> &lt;li&gt;Rat Microarray annotations derived from mappings to the mRatBN7.2 assembly are now available, the previous warning associated with remapped data from the deprecated Rnor_6.0 assembly has been removed.&lt;/li&gt;<br /> &lt;/ul&gt;</div> Acastanza https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=MSigDB_v2022.1.Hs_Release_Notes&diff=4493 MSigDB v2022.1.Hs Release Notes 2022-08-31T18:35:56Z <p>Acastanza: </p> <hr /> <div>&lt;span class=&quot;plainlinks&quot;&gt;<br /> [http://www.broadinstitute.org/gsea/ GSEA Home] |<br /> [http://www.broadinstitute.org/gsea/downloads.jsp Downloads] | <br /> [http://www.broadinstitute.org/gsea/msigdb/ Molecular Signatures Database] | <br /> [http://www.broadinstitute.org/cancer/software/gsea/wiki/index.php/Main_Page Documentation] |<br /> [http://www.broadinstitute.org/gsea/contact.jsp Contact]<br /> &lt;/span&gt;<br /> <br /> &lt;h1&gt;Important Notices&lt;/h1&gt;<br /> <br /> This page describes updates made to the Molecular Signatures Database for release 2022.1. This release introduces several major changes to previous conventions. MSigDB is now split into two major divisions; a series of gene set collections that are provided in the namespace of human gene symbols, and a series of gene set collections that are provided in the namespace of mouse gene symbols. As such the versioning convention of MSigDB has changed to adopt the format Year.Release.Species. This initial release in the new format is versioned 2022.1.Hs for the human collections and 2022.1.Mm for the mouse collections. Likewise, CHIP files have been updated to reflect this convention, as well as the specific series of collections (i.e. human or mouse) that they are targeted towards.<br /> <br /> '''Note that in order to access the MSigBD mouse collections through the GSEA UI, the latest version of GSEA (4.3.0) is required.'''<br /> <br /> MSigDB v2022.1 is based on gene annotation data from Ensembl Release 107 (Jul 2022).<br /> <br /> &lt;h1&gt;Updates to Human Collections (MSigDB v2022.1.Hs)&lt;/h1&gt;<br /> <br /> &lt;h2&gt;Updates to Collections&lt;/h2&gt;<br /> <br /> &lt;h3&gt;C1&lt;/h3&gt;<br /> Updated human gene annotations to Ensembl 107 (+XX gene sets).<br /> &lt;h3&gt;C2:CGP&lt;/h3&gt;<br /> Gene sets contributed by the following individuals have been added to C2:CGP<br /> &lt;ul&gt;<br /> &lt;li&gt;[https://pubmed.ncbi.nlm.nih.gov/ (PMID:)]&lt;/li&gt;<br /> &lt;/ul&gt;<br /> <br /> &lt;h3&gt;C2:CP:Reactome&lt;/h3&gt;<br /> <br /> &lt;ul&gt;<br /> &lt;li&gt;Reactome gene sets have been updated to reflect the state of the Reactome pathway architecture as of '''Reactome v81''' (+XX gene sets).&lt;/li&gt;<br /> &lt;li&gt;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.&lt;/li&gt;<br /> &lt;/ul&gt;<br /> <br /> &lt;h3&gt;C2:CP:WikiPathways&lt;/h3&gt;<br /> WikiPathways gene sets have been updated to the August 10, 2022 release (+XX gene sets).<br /> <br /> &lt;h3&gt;C5:GO (Gene Ontology)&lt;/h3&gt;<br /> &lt;p&gt; 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 (&lt;span class=&quot;plainlinks&quot;&gt;[http://www.geneontology.org Nature Genet 2000]&lt;/span&gt;). 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 2022-07-01 and NCBI gene2go annotations downloaded on 2022-07-15.&lt;/p&gt;<br /> <br /> &lt;p&gt;This collection is divided into three sub-collections:&lt;/p&gt;<br /> &lt;ul&gt;<br /> &lt;li&gt;&lt;strong&gt;BP&lt;/strong&gt;: GO Biological process (+XX gene sets). Gene sets derived from the Biological Process Ontology, and are prefixed with &quot;GOBP_&quot;.&lt;/li&gt;<br /> &lt;li&gt;&lt;strong&gt;CC&lt;/strong&gt;: GO Cellular component (+XX gene sets). Gene sets derived from the Cellular Component Ontology, and are prefixed with &quot;GOCC_&quot;.&lt;/li&gt;<br /> &lt;li&gt;&lt;strong&gt;MF&lt;/strong&gt;: GO Molecular function (+XX gene sets). Gene sets derived from the Molecular Function Ontology, and are prefixed with &quot;GOMF_&quot;..&lt;/li&gt;<br /> &lt;/ul&gt;<br /> <br /> &lt;p&gt;These updates were generated in accordance with the procedure described in the [[MSigDB_v7.0_Release_Notes#C5_.28Gene_Ontology_collection.29_-_Major_overhaul | GO release notes for MSigDB 7.0.]]<br /> <br /> &lt;h3&gt;C5:HPO (Human Phenotype Ontology)&lt;/h3&gt;<br /> <br /> Gene sets in this sub-collection have been updated to reflect the 2022-06-11 release of the Human Phenotype Ontology database (+XX gene sets). This sub-collection has been redundancy filtered through a procedure comparable to that of the GO and Reactome sub-collections.<br /> <br /> &lt;h3&gt;CHIP file updates&lt;/h3&gt;<br /> &lt;ul&gt;<br /> &lt;li&gt;MSigDB 2022.1.Hs gene annotations and gene mapping CHIP files have been updated to data from Ensembl 107.&lt;/li&gt;<br /> &lt;li&gt;Gene orthology annotations for mapping mouse and rat genes to their best match human orthologs have been updated to &lt;span class=&quot;plainlinks&quot;&gt;[https://www.alliancegenome.org/ Alliance of Genome Resources]&lt;/span&gt; orthology database release 5.2.1 (2022-07-15)&lt;/li&gt;<br /> &lt;li&gt;Rat Microarray annotations derived from mappings to the mRatBN7.2 assembly are now available, the previous warning associated with remapped data from the deprecated Rnor_6.0 assembly has been removed.&lt;/li&gt;<br /> &lt;/ul&gt;</div> Acastanza https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=MSigDB_v2022.1.Hs_Release_Notes&diff=4492 MSigDB v2022.1.Hs Release Notes 2022-08-31T18:34:43Z <p>Acastanza: </p> <hr /> <div>&lt;span class=&quot;plainlinks&quot;&gt;<br /> [http://www.broadinstitute.org/gsea/ GSEA Home] |<br /> [http://www.broadinstitute.org/gsea/downloads.jsp Downloads] | <br /> [http://www.broadinstitute.org/gsea/msigdb/ Molecular Signatures Database] | <br /> [http://www.broadinstitute.org/cancer/software/gsea/wiki/index.php/Main_Page Documentation] |<br /> [http://www.broadinstitute.org/gsea/contact.jsp Contact]<br /> &lt;/span&gt;<br /> <br /> &lt;h1&gt;Important Notices&lt;/h1&gt;<br /> <br /> This page describes updates made to the Molecular Signatures Database for release 2022.1. This release introduces several major changes to previous conventions. MSigDB is now split into two major divisions; a series of gene set collections that are provided in the namespace of human gene symbols, and a series of gene set collections that are provided in the namespace of mouse gene symbols. As such the versioning convention of MSigDB has changed to adopt the format Year.Release.Species. This initial release in the new format is versioned 2022.1.Hs for the human collections and 2022.1.Mm for the mouse collections. Likewise, CHIP files have been updated to reflect this convention, as well as the specific series of collections (i.e. human or mouse) that they are targeted towards.<br /> <br /> '''Note that in order to access the MSigBD mouse collections through the GSEA UI, the latest version of GSEA (4.3.0) is required.'''<br /> <br /> MSigDB v2022.1 is based on gene annotation data from Ensembl Release 107 (Jul 2022).<br /> <br /> &lt;h1&gt;Updates to Human Collections (MSigDB v2022.1.Hs)&lt;/h1&gt;<br /> <br /> &lt;span class=&quot;plainlinks&quot;&gt;<br /> [http://www.broadinstitute.org/gsea/ GSEA Home] |<br /> [http://www.broadinstitute.org/gsea/downloads.jsp Downloads] | <br /> [http://www.broadinstitute.org/gsea/msigdb/ Molecular Signatures Database] | <br /> [http://www.broadinstitute.org/cancer/software/gsea/wiki/index.php/Main_Page Documentation] |<br /> [http://www.broadinstitute.org/gsea/contact.jsp Contact]<br /> &lt;/span&gt;<br /> <br /> &lt;h2&gt;Updates to Collections&lt;/h2&gt;<br /> <br /> &lt;h3&gt;C1&lt;/h3&gt;<br /> Updated human gene annotations to Ensembl 107 (+XX gene sets).<br /> &lt;h3&gt;C2:CGP&lt;/h3&gt;<br /> Gene sets contributed by the following individuals have been added to C2:CGP<br /> &lt;ul&gt;<br /> &lt;li&gt;[https://pubmed.ncbi.nlm.nih.gov/ (PMID:)]&lt;/li&gt;<br /> &lt;/ul&gt;<br /> <br /> &lt;h3&gt;C2:CP:Reactome&lt;/h3&gt;<br /> <br /> &lt;ul&gt;<br /> &lt;li&gt;Reactome gene sets have been updated to reflect the state of the Reactome pathway architecture as of '''Reactome v81''' (+XX gene sets).&lt;/li&gt;<br /> &lt;li&gt;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.&lt;/li&gt;<br /> &lt;/ul&gt;<br /> <br /> &lt;h3&gt;C2:CP:WikiPathways&lt;/h3&gt;<br /> WikiPathways gene sets have been updated to the August 10, 2022 release (+XX gene sets).<br /> <br /> &lt;h3&gt;C5:GO (Gene Ontology)&lt;/h3&gt;<br /> &lt;p&gt; 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 (&lt;span class=&quot;plainlinks&quot;&gt;[http://www.geneontology.org Nature Genet 2000]&lt;/span&gt;). 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 2022-07-01 and NCBI gene2go annotations downloaded on 2022-07-15.&lt;/p&gt;<br /> <br /> &lt;p&gt;This collection is divided into three sub-collections:&lt;/p&gt;<br /> &lt;ul&gt;<br /> &lt;li&gt;&lt;strong&gt;BP&lt;/strong&gt;: GO Biological process (+XX gene sets). Gene sets derived from the Biological Process Ontology, and are prefixed with &quot;GOBP_&quot;.&lt;/li&gt;<br /> &lt;li&gt;&lt;strong&gt;CC&lt;/strong&gt;: GO Cellular component (+XX gene sets). Gene sets derived from the Cellular Component Ontology, and are prefixed with &quot;GOCC_&quot;.&lt;/li&gt;<br /> &lt;li&gt;&lt;strong&gt;MF&lt;/strong&gt;: GO Molecular function (+XX gene sets). Gene sets derived from the Molecular Function Ontology, and are prefixed with &quot;GOMF_&quot;..&lt;/li&gt;<br /> &lt;/ul&gt;<br /> <br /> &lt;p&gt;These updates were generated in accordance with the procedure described in the [[MSigDB_v7.0_Release_Notes#C5_.28Gene_Ontology_collection.29_-_Major_overhaul | GO release notes for MSigDB 7.0.]]<br /> <br /> &lt;h3&gt;C5:HPO (Human Phenotype Ontology)&lt;/h3&gt;<br /> <br /> Gene sets in this sub-collection have been updated to reflect the 2022-06-11 release of the Human Phenotype Ontology database (+XX gene sets). This sub-collection has been redundancy filtered through a procedure comparable to that of the GO and Reactome sub-collections.<br /> <br /> &lt;h3&gt;CHIP file updates&lt;/h3&gt;<br /> &lt;ul&gt;<br /> &lt;li&gt;MSigDB 2022.1.Hs gene annotations and gene mapping CHIP files have been updated to data from Ensembl 107.&lt;/li&gt;<br /> &lt;li&gt;Gene orthology annotations for mapping mouse and rat genes to their best match human orthologs have been updated to &lt;span class=&quot;plainlinks&quot;&gt;[https://www.alliancegenome.org/ Alliance of Genome Resources]&lt;/span&gt; orthology database release 5.2.1 (2022-07-15)&lt;/li&gt;<br /> &lt;li&gt;Rat Microarray annotations derived from mappings to the mRatBN7.2 assembly are now available, the previous warning associated with remapped data from the deprecated Rnor_6.0 assembly has been removed.&lt;/li&gt;<br /> &lt;/ul&gt;</div> Acastanza https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=MSigDB_v2022.1.Mm_Release_Notes&diff=4491 MSigDB v2022.1.Mm Release Notes 2022-08-30T20:58:38Z <p>Acastanza: Created page with '&lt;span class=&quot;plainlinks&quot;&gt; [http://www.broadinstitute.org/gsea/ GSEA Home] | [http://www.broadinstitute.org/gsea/downloads.jsp Downloads] | [http://www.broadinstitute.org/gsea/ms…'</p> <hr /> <div>&lt;span class=&quot;plainlinks&quot;&gt;<br /> [http://www.broadinstitute.org/gsea/ GSEA Home] |<br /> [http://www.broadinstitute.org/gsea/downloads.jsp Downloads] | <br /> [http://www.broadinstitute.org/gsea/msigdb/ Molecular Signatures Database] | <br /> [http://www.broadinstitute.org/cancer/software/gsea/wiki/index.php/Main_Page Documentation] |<br /> [http://www.broadinstitute.org/gsea/contact.jsp Contact]<br /> &lt;/span&gt;<br /> <br /> &lt;h1&gt;Important Notices&lt;/h1&gt;<br /> <br /> This page describes updates made to the Molecular Signatures Database for release 2022.1. This release introduces several major changes to previous conventions. MSigDB is now split into two major divisions; a series of gene set collections that are provided in the namespace of human gene symbols, and a series of gene set collections that are provided in the namespace of mouse gene symbols. As such the versioning convention of MSigDB has changed to adopt the format Year.Release.Species. This initial release in the new format is versioned 2022.1.Hs for the human collections and 2022.1.Mm for the mouse collections. Likewise, CHIP files have been updated to reflect this convention, as well as the specific series of collections (i.e. human or mouse) that they are targeted towards.<br /> <br /> '''Note that in order to access the MSigBD mouse collections through the GSEA UI, the latest version of GSEA (4.3.0) is required.'''<br /> <br /> MSigDB v2022.1 is based on gene annotation data from Ensembl Release 107 (Jul 2022).<br /> <br /> &lt;h1&gt;Initial Release of Mouse Collections (MSigDB v2022.1.Mm)&lt;/h1&gt;</div> Acastanza https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=MSigDB_v2022.1.Hs_Release_Notes&diff=4490 MSigDB v2022.1.Hs Release Notes 2022-08-30T20:57:35Z <p>Acastanza: Created page with '&lt;span class=&quot;plainlinks&quot;&gt; [http://www.broadinstitute.org/gsea/ GSEA Home] | [http://www.broadinstitute.org/gsea/downloads.jsp Downloads] | [http://www.broadinstitute.org/gsea/ms…'</p> <hr /> <div>&lt;span class=&quot;plainlinks&quot;&gt;<br /> [http://www.broadinstitute.org/gsea/ GSEA Home] |<br /> [http://www.broadinstitute.org/gsea/downloads.jsp Downloads] | <br /> [http://www.broadinstitute.org/gsea/msigdb/ Molecular Signatures Database] | <br /> [http://www.broadinstitute.org/cancer/software/gsea/wiki/index.php/Main_Page Documentation] |<br /> [http://www.broadinstitute.org/gsea/contact.jsp Contact]<br /> &lt;/span&gt;<br /> <br /> &lt;h1&gt;Important Notices&lt;/h1&gt;<br /> <br /> This page describes updates made to the Molecular Signatures Database for release 2022.1. This release introduces several major changes to previous conventions. MSigDB is now split into two major divisions; a series of gene set collections that are provided in the namespace of human gene symbols, and a series of gene set collections that are provided in the namespace of mouse gene symbols. As such the versioning convention of MSigDB has changed to adopt the format Year.Release.Species. This initial release in the new format is versioned 2022.1.Hs for the human collections and 2022.1.Mm for the mouse collections. Likewise, CHIP files have been updated to reflect this convention, as well as the specific series of collections (i.e. human or mouse) that they are targeted towards.<br /> <br /> '''Note that in order to access the MSigBD mouse collections through the GSEA UI, the latest version of GSEA (4.3.0) is required.'''<br /> <br /> MSigDB v2022.1 is based on gene annotation data from Ensembl Release 107 (Jul 2022).<br /> <br /> &lt;h1&gt;Updates to Human Collections (MSigDB v2022.1.Hs)&lt;/h1&gt;</div> Acastanza https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=MSigDB_v2022.1_Release_Notes&diff=4489 MSigDB v2022.1 Release Notes 2022-08-22T19:04:02Z <p>Acastanza: </p> <hr /> <div>&lt;span class=&quot;plainlinks&quot;&gt;<br /> [http://www.broadinstitute.org/gsea/ GSEA Home] |<br /> [http://www.broadinstitute.org/gsea/downloads.jsp Downloads] | <br /> [http://www.broadinstitute.org/gsea/msigdb/ Molecular Signatures Database] | <br /> [http://www.broadinstitute.org/cancer/software/gsea/wiki/index.php/Main_Page Documentation] |<br /> [http://www.broadinstitute.org/gsea/contact.jsp Contact]<br /> &lt;/span&gt;<br /> <br /> &lt;h1&gt;Important Notices&lt;/h1&gt;<br /> <br /> This page describes updates made to the Molecular Signatures Database for release 2022.1. This release introduces several major changes to previous conventions. MSigDB is now split into two major divisions; a series of gene set collections that are provided in the namespace of human gene symbols, and a series of gene set collections that are provided in the namespace of mouse gene symbols. As such the versioning convention of MSigDB has changed to adopt the format Year.Release.Species. This initial release in the new format is versioned 2022.1.Hs for the human collections and 2022.1.Mm for the mouse collections. Likewise, CHIP files have been updated to reflect this convention, as well as the specific series of collections (i.e. human or mouse) that they are targeted towards.<br /> <br /> '''Note that in order to access the MSigBD mouse collections through the GSEA UI, the latest version of GSEA (4.3.0) is required.'''<br /> <br /> MSigDB v2022.1 is based on gene annotation data from Ensembl Release 107 (Jul 2022).<br /> <br /> &lt;h1&gt;Updates to Human Collections (MSigDB v2022.1.Hs)&lt;/h1&gt;<br /> <br /> &lt;br&gt;<br /> &lt;h1&gt;Release of Mouse Collections (MSigDB v2022.1.Mm)&lt;/h1&gt;</div> Acastanza https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=CHIP_File_Selection_Help&diff=4488 CHIP File Selection Help 2022-08-18T21:07:56Z <p>Acastanza: Creating Page</p> <hr /> <div>&lt;span class=&quot;plainlinks&quot;&gt;<br /> [http://www.broadinstitute.org/gsea/ GSEA Home] |<br /> [http://www.broadinstitute.org/gsea/downloads.jsp Downloads] | <br /> [http://www.broadinstitute.org/gsea/msigdb/ Molecular Signatures Database] | <br /> [http://www.broadinstitute.org/cancer/software/gsea/wiki/index.php/Main_Page Documentation] |<br /> [http://www.broadinstitute.org/gsea/contact.jsp Contact]<br /> &lt;/span&gt;</div> Acastanza https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=MSigDB_v2022.1_Release_Notes&diff=4487 MSigDB v2022.1 Release Notes 2022-08-18T21:06:47Z <p>Acastanza: Creating Page</p> <hr /> <div>&lt;span class=&quot;plainlinks&quot;&gt;<br /> [http://www.broadinstitute.org/gsea/ GSEA Home] |<br /> [http://www.broadinstitute.org/gsea/downloads.jsp Downloads] | <br /> [http://www.broadinstitute.org/gsea/msigdb/ Molecular Signatures Database] | <br /> [http://www.broadinstitute.org/cancer/software/gsea/wiki/index.php/Main_Page Documentation] |<br /> [http://www.broadinstitute.org/gsea/contact.jsp Contact]<br /> &lt;/span&gt;</div> Acastanza https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=MSigDB_v7.5.1_Release_Notes&diff=4486 MSigDB v7.5.1 Release Notes 2022-03-17T23:10:10Z <p>Acastanza: </p> <hr /> <div>&lt;span class=&quot;plainlinks&quot;&gt;<br /> [http://www.broadinstitute.org/gsea/ GSEA Home] |<br /> [http://www.broadinstitute.org/gsea/downloads.jsp Downloads] | <br /> [http://www.broadinstitute.org/gsea/msigdb/ Molecular Signatures Database] | <br /> [http://www.broadinstitute.org/cancer/software/gsea/wiki/index.php/Main_Page Documentation] |<br /> [http://www.broadinstitute.org/gsea/contact.jsp Contact]<br /> &lt;/span&gt;<br /> <br /> This page describes the changes made to the gene set collections for Release 7.5.x of the Molecular Signatures Database (MSigDB). This release contains updates to: C1, GO, HPO, and Reactome, as well as the addition of curated sets to C8 and user submitted sets to C2:CGP. This update incorporates the removal of clone based gene IDs introduced in Ensembl 104. <br /> <br /> <br /> &lt;b&gt;Note:&lt;/b&gt; Due to substantial changes introduced in MSigDB 7.0, using GSEA 4.0.0+ is recommended when utilizing MSigDB 7.0+ resources.&lt;br&gt;<br /> &lt;b&gt;Advisory&lt;/b&gt;: It is strongly recommended that users of MSigDB 7.5 '''always''' use the GSEA &quot;Collapse/Remap to gene symbols&quot; feature with the provided Symbol Remapping chip file if your dataset was generated with a transcriptome other than '''Ensembl v105/GENCODE v39'''.<br /> <br /> &lt;h1&gt;Specific Updates in the MSigDB 7.5.1 Patch Release&lt;/h1&gt;<br /> &lt;h3&gt;C2:CGP and C2:CP:WikiPathways&lt;/h3&gt;<br /> &lt;ul&gt;<br /> &lt;li&gt;SATOH_COLORECTAL_CANCER_MYC_DN contributed by Rintaro Saito, Institute for Advanced Biosciences, Keio University (+1 gene set) from [https://pubmed.ncbi.nlm.nih.gov/28847964 (PMID:28847964)] was inadvertently omitted from MSigDB 7.5, this has been corrected&lt;/li&gt;<br /> &lt;li&gt;In C2:CP:WikiPathways duplicate WP_ARYL_HYDROCARBON_RECEPTOR_PATHWAY gene sets have been disambiguated by using the specific WikiPathways ID number as a suffix; the two sets are now indicated as &lt;span class=&quot;plainlinks&quot;&gt;[https://www.gsea-msigdb.org/gsea/msigdb/cards/WP_ARYL_HYDROCARBON_RECEPTOR_PATHWAY_WP2586.html WP_ARYL_HYDROCARBON_RECEPTOR_PATHWAY_WP2586]&lt;/span&gt; and &lt;span class=&quot;plainlinks&quot;&gt;[https://www.gsea-msigdb.org/gsea/msigdb/cards/WP_ARYL_HYDROCARBON_RECEPTOR_PATHWAY_WP2873 WP_ARYL_HYDROCARBON_RECEPTOR_PATHWAY_WP2873]&lt;/span&gt;&lt;/li&gt;<br /> &lt;li&gt;In C2:CP:WikiPathways duplicate WP_HEDGEHOG_SIGNALING_PATHWAYgene sets have been disambiguated by using the specific WikiPathways ID number as a suffix; the two sets are now indicated as &lt;span class=&quot;plainlinks&quot;&gt;[https://www.gsea-msigdb.org/gsea/msigdb/cards/WP_HEDGEHOG_SIGNALING_PATHWAY_WP4249.html WP_HEDGEHOG_SIGNALING_PATHWAY_WP4249]&lt;/span&gt; and &lt;span class=&quot;plainlinks&quot;&gt;[https://www.gsea-msigdb.org/gsea/msigdb/cards/WP_HEDGEHOG_SIGNALING_PATHWAY_WP47 WP_HEDGEHOG_SIGNALING_PATHWAY_WP47]&lt;/span&gt;&lt;/li&gt;<br /> &lt;li&gt;MSigDB version numbers in CHIP files and other collection GMTs have also been incremented to MSigDB 7.5.1.<br /> &lt;/ul&gt;<br /> <br /> &lt;h3&gt;Known Issues&lt;/h3&gt;<br /> &lt;ul&gt;&lt;li&gt;The gene set descriptions in C1 incorrectly state that the gene positional information was taken from Ensembl 103. This is stated correctly in the &quot;Version history&quot; field to be from Ensembl 105&lt;/li&gt;&lt;/ul&gt;<br /> &lt;br&gt;<br /> &lt;h1&gt;MSigDB 7.5 Initial Release&lt;/h1&gt;<br /> <br /> &lt;h2&gt;Updates to Collections&lt;/h2&gt;<br /> <br /> &lt;h3&gt;C1&lt;/h3&gt;<br /> Updated human gene annotations to Ensembl 105 (+21 gene sets).<br /> &lt;h3&gt;C2:CGP&lt;/h3&gt;<br /> Gene sets contributed by the following individuals have been added to C2:CGP<br /> &lt;ul&gt;<br /> &lt;li&gt;NRF response gene sets contributed by Lara Ibrahim, The Scripps Research Institute (+6 gene sets) from [https://pubmed.ncbi.nlm.nih.gov/33096892/ (PMID:33096892)]&lt;/li&gt;<br /> &lt;li&gt;Gene sets describing the epithelial-mesenchymal transition (EMT) upon transforming growth factor beta (TGFb) stimulation contributed by Dharmesh D. Bhuva, Walter and Eliza Hall Institute of Medical Research (+6 gene sets) from [https://pubmed.ncbi.nlm.nih.gov/28119430 (PMID:28119430)]&lt;/li&gt;<br /> &lt;li&gt;SEAVEY_EPITHELIOID_HEMANGIOENDOTHELIOMA contributed by Caleb Seavey, Cleveland Clinic Foundation (+1 gene set) from [https://pubmed.ncbi.nlm.nih.gov/33766982 (PMID:33766982)]&lt;/li&gt;<br /> &lt;li&gt;SATOH_COLORECTAL_CANCER_MYC_UP contributed by Rintaro Saito, Institute for Advanced Biosciences, Keio University (+1 gene set) from [https://pubmed.ncbi.nlm.nih.gov/28847964 (PMID:28847964)]&lt;/li&gt;<br /> &lt;li&gt;GLASS_IGF2BP1_CLIP_TARGETS_KNOCKDOWN_DN contributed by Markus Gla&amp;szlig;, Martin Luther University Halle-Wittenberg (+1 gene set) from [https://pubmed.ncbi.nlm.nih.gov/33829040 (PMID:33829040)]&lt;/li&gt;<br /> <br /> &lt;/ul&gt;<br /> <br /> &lt;h3&gt;C2:CP:Reactome&lt;/h3&gt;<br /> <br /> &lt;ul&gt;<br /> &lt;li&gt;Reactome gene sets have been updated to reflect the state of the Reactome pathway architecture as of '''Reactome v78''' (+11 gene sets).&lt;/li&gt;<br /> &lt;li&gt;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.&lt;/li&gt;<br /> &lt;/ul&gt;<br /> <br /> &lt;h3&gt;C2:CP:WikiPathways&lt;/h3&gt;<br /> WikiPathways gene sets have been updated to the January 10, 2022 release (+47 gene sets).<br /> <br /> &lt;h3&gt;C3:TFT:GTRD&lt;/h3&gt;<br /> As a result of Ensembl gene annotations, 5 gene sets were removed from GTRD as they no fall below the the maximum number genes threshold (&lt;2000 genes). (-5)<br /> <br /> &lt;h3&gt;C5:GO (Gene Ontology)&lt;/h3&gt;<br /> &lt;p&gt; 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 (&lt;span class=&quot;plainlinks&quot;&gt;[http://www.geneontology.org Nature Genet 2000]&lt;/span&gt;). 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 2021-12-15 and NCBI gene2go annotations downloaded on 2022-01-03.&lt;/p&gt;<br /> &lt;p&gt;This collection is divided into three sub-collections:&lt;/p&gt;<br /> &lt;ul&gt;<br /> &lt;li&gt;&lt;strong&gt;BP&lt;/strong&gt;: GO Biological process (+177 gene sets). Gene sets derived from the Biological Process Ontology.&lt;/li&gt;<br /> &lt;li&gt;&lt;strong&gt;CC&lt;/strong&gt;: GO Cellular component (+10 gene sets). Gene sets derived from the Cellular Component Ontology.&lt;/li&gt;<br /> &lt;li&gt;&lt;strong&gt;MF&lt;/strong&gt;: GO Molecular function (+30 gene sets). Gene sets derived from the Molecular Function Ontology.&lt;/li&gt;<br /> &lt;/ul&gt;<br /> <br /> &lt;p&gt;These updates were generated in accordance with the procedure described in the [[MSigDB_v7.0_Release_Notes#C5_.28Gene_Ontology_collection.29_-_Major_overhaul | GO release notes for MSigDB 7.0.]]<br /> <br /> &lt;h3&gt;C5:HPO (Human Phenotype Ontology)&lt;/h3&gt;<br /> <br /> Gene sets in this sub-collection have been updated to reflect the 2021-10-10 release of the Human Phenotype Ontology database (+258 gene sets). This sub-collection has been redundancy filtered through a procedure comparable to that of the GO and Reactome sub-collections.<br /> <br /> &lt;h3&gt;C8: cell type signature gene sets&lt;/h3&gt;<br /> Added eye gene sets from &lt;span class=&quot;plainlinks&quot;&gt;[https://www.ncbi.nlm.nih.gov/labs/pmc/articles/PMC8478974/ Gautam and Hamashima et al. 2021. Multi-species single-cell transcriptomic analysis of ocular compartment regulons.]&lt;/span&gt; (+29 gene sets)<br /> <br /> &lt;h3&gt;CHIP file updates&lt;/h3&gt;<br /> &lt;ul&gt;<br /> &lt;li&gt;MSigDB 7.5 gene annotations and gene mapping CHIP files have been updated to data from Ensembl 105.&lt;/li&gt;<br /> &lt;li&gt;MSigDB 7.5 includes new handling for deprecated Ensembl Gene IDs thanks to work by &lt;span class=&quot;plainlinks&quot;&gt;[https://github.com/dhimmel Daniel Himmelstein]&lt;/span&gt;. Briefly, historical IDs that map uniquely to one &quot;newest&quot; ensembl gene ID were extracted from the &quot;old_to_newest.tsv&quot; file from the respective Human, Mouse, and Rat repositories generated for Ensembl 105 &lt;span class=&quot;plainlinks&quot;&gt;[https://github.com/related-sciences/ensembl-genes (see: Github repository)]&lt;/span&gt; and then merged into the species specific Ensembl_Gene_ID chip file.&lt;/li&gt;<br /> &lt;li&gt;Gene orthology annotations for mapping mouse and rat genes to their best match human orthologs have been updated to &lt;span class=&quot;plainlinks&quot;&gt;[https://www.alliancegenome.org/ Alliance of Genome Resources]&lt;/span&gt; orthology database release 4.2.&lt;/li&gt;<br /> &lt;li&gt;&lt;b&gt;Warning:&lt;/b&gt; Rat Microarray derived annotations. Ensembl 105 brought a major update to the rat genome assembly transitioning from the deprecated Rnor_6.0 assembly to the modern mRatBN7.2 assembly. However, Ensembl has not yet released updated microarray probe mappings for the mRatBN7.2 assembly. In order to continue to provide CHIP files and internal mappings in MSigDB for experiments derived from these platforms, we have carried forward the historical Probe-to-Gene mappings from Ensembl 103/MSigDB v7.4 and remapped the target genes to the current assembly using the Ensembl_Gene_ID_MSigDB.v7.5 chip. However, until Ensembl releases updated probe to gene mappings derived directly from the mRatBN7.2 assembly the quality of MSigDB's rat microarray chip files may be impacted. Rat CHIP files affected by this have recieved the suffix the temporary suffix &lt;b&gt;_REMAPPED&lt;/b&gt; after the MSigDB version number.&lt;/li&gt;<br /> &lt;/ul&gt;</div> Acastanza https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=MSigDB_Latest_Release_Notes&diff=4481 MSigDB Latest Release Notes 2022-01-20T01:48:55Z <p>Acastanza: Redirected page to MSigDB v7.5.1 Release Notes</p> <hr /> <div>#REDIRECT [[MSigDB_v7.5.1_Release_Notes]]</div> Acastanza https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=MSigDB_v7.5.1_Release_Notes&diff=4480 MSigDB v7.5.1 Release Notes 2022-01-20T01:48:10Z <p>Acastanza: Patch note</p> <hr /> <div>&lt;span class=&quot;plainlinks&quot;&gt;<br /> [http://www.broadinstitute.org/gsea/ GSEA Home] |<br /> [http://www.broadinstitute.org/gsea/downloads.jsp Downloads] | <br /> [http://www.broadinstitute.org/gsea/msigdb/ Molecular Signatures Database] | <br /> [http://www.broadinstitute.org/cancer/software/gsea/wiki/index.php/Main_Page Documentation] |<br /> [http://www.broadinstitute.org/gsea/contact.jsp Contact]<br /> &lt;/span&gt;<br /> <br /> This page describes the changes made to the gene set collections for Release 7.5.x of the Molecular Signatures Database (MSigDB). This release contains updates to: C1, GO, HPO, and Reactome, as well as the addition of curated sets to C8 and user submitted sets to C2:CGP. This update incorporates the removal of clone based gene IDs introduced in Ensembl 104. <br /> <br /> <br /> &lt;b&gt;Note:&lt;/b&gt; Due to substantial changes introduced in MSigDB 7.0, using GSEA 4.0.0+ is recommended when utilizing MSigDB 7.0+ resources.&lt;br&gt;<br /> &lt;b&gt;Advisory&lt;/b&gt;: It is strongly recommended that users of MSigDB 7.5 '''always''' use the GSEA &quot;Collapse/Remap to gene symbols&quot; feature with the provided Symbol Remapping chip file if your dataset was generated with a transcriptome other than '''Ensembl v105/GENCODE v39'''.<br /> <br /> &lt;h1&gt;Specific Updates in the MSigDB 7.5.1 Patch Release&lt;/h1&gt;<br /> &lt;h3&gt;C2:CGP and C2:CP:WikiPathways&lt;/h3&gt;<br /> &lt;ul&gt;<br /> &lt;li&gt;SATOH_COLORECTAL_CANCER_MYC_DN contributed by Rintaro Saito, Institute for Advanced Biosciences, Keio University (+1 gene set) from [https://pubmed.ncbi.nlm.nih.gov/28847964 (PMID:28847964)] was inadvertently omitted from MSigDB 7.5, this has been corrected&lt;/li&gt;<br /> &lt;li&gt;In C2:CP:WikiPathways duplicate WP_ARYL_HYDROCARBON_RECEPTOR_PATHWAY gene sets have been disambiguated by using the specific WikiPathways ID number as a suffix; the two sets are now indicated as &lt;span class=&quot;plainlinks&quot;&gt;[https://www.gsea-msigdb.org/gsea/msigdb/cards/WP_ARYL_HYDROCARBON_RECEPTOR_PATHWAY_WP2586.html WP_ARYL_HYDROCARBON_RECEPTOR_PATHWAY_WP2586]&lt;/span&gt; and &lt;span class=&quot;plainlinks&quot;&gt;[https://www.gsea-msigdb.org/gsea/msigdb/cards/WP_ARYL_HYDROCARBON_RECEPTOR_PATHWAY_WP2873 WP_ARYL_HYDROCARBON_RECEPTOR_PATHWAY_WP2873]&lt;/span&gt;&lt;/li&gt;<br /> &lt;li&gt;In C2:CP:WikiPathways duplicate WP_HEDGEHOG_SIGNALING_PATHWAYgene sets have been disambiguated by using the specific WikiPathways ID number as a suffix; the two sets are now indicated as &lt;span class=&quot;plainlinks&quot;&gt;[https://www.gsea-msigdb.org/gsea/msigdb/cards/WP_HEDGEHOG_SIGNALING_PATHWAY_WP4249.html WP_HEDGEHOG_SIGNALING_PATHWAY_WP4249]&lt;/span&gt; and &lt;span class=&quot;plainlinks&quot;&gt;[https://www.gsea-msigdb.org/gsea/msigdb/cards/WP_HEDGEHOG_SIGNALING_PATHWAY_WP47 WP_HEDGEHOG_SIGNALING_PATHWAY_WP47]&lt;/span&gt;&lt;/li&gt;<br /> &lt;li&gt;MSigDB version numbers in CHIP files and other collection GMTs have also been incremented to MSigDB 7.5.1.<br /> &lt;/ul&gt;<br /> <br /> <br /> &lt;h1&gt;MSigDB 7.5 Initial Release&lt;/h1&gt;<br /> <br /> &lt;h2&gt;Updates to Collections&lt;/h2&gt;<br /> <br /> &lt;h3&gt;C1&lt;/h3&gt;<br /> Updated human gene annotations to Ensembl 105 (+21 gene sets).<br /> &lt;h3&gt;C2:CGP&lt;/h3&gt;<br /> Gene sets contributed by the following individuals have been added to C2:CGP<br /> &lt;ul&gt;<br /> &lt;li&gt;NRF response gene sets contributed by Lara Ibrahim, The Scripps Research Institute (+6 gene sets) from [https://pubmed.ncbi.nlm.nih.gov/33096892/ (PMID:33096892)]&lt;/li&gt;<br /> &lt;li&gt;Gene sets describing the epithelial-mesenchymal transition (EMT) upon transforming growth factor beta (TGFb) stimulation contributed by Dharmesh D. Bhuva, Walter and Eliza Hall Institute of Medical Research (+6 gene sets) from [https://pubmed.ncbi.nlm.nih.gov/28119430 (PMID:28119430)]&lt;/li&gt;<br /> &lt;li&gt;SEAVEY_EPITHELIOID_HEMANGIOENDOTHELIOMA contributed by Caleb Seavey, Cleveland Clinic Foundation (+1 gene set) from [https://pubmed.ncbi.nlm.nih.gov/33766982 (PMID:33766982)]&lt;/li&gt;<br /> &lt;li&gt;SATOH_COLORECTAL_CANCER_MYC_UP contributed by Rintaro Saito, Institute for Advanced Biosciences, Keio University (+1 gene set) from [https://pubmed.ncbi.nlm.nih.gov/28847964 (PMID:28847964)]&lt;/li&gt;<br /> &lt;li&gt;GLASS_IGF2BP1_CLIP_TARGETS_KNOCKDOWN_DN contributed by Markus Gla&amp;szlig;, Martin Luther University Halle-Wittenberg (+1 gene set) from [https://pubmed.ncbi.nlm.nih.gov/33829040 (PMID:33829040)]&lt;/li&gt;<br /> <br /> &lt;/ul&gt;<br /> <br /> &lt;h3&gt;C2:CP:Reactome&lt;/h3&gt;<br /> <br /> &lt;ul&gt;<br /> &lt;li&gt;Reactome gene sets have been updated to reflect the state of the Reactome pathway architecture as of '''Reactome v78''' (+11 gene sets).&lt;/li&gt;<br /> &lt;li&gt;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.&lt;/li&gt;<br /> &lt;/ul&gt;<br /> <br /> &lt;h3&gt;C2:CP:WikiPathways&lt;/h3&gt;<br /> WikiPathways gene sets have been updated to the January 10, 2022 release (+47 gene sets).<br /> <br /> &lt;h3&gt;C3:TFT:GTRD&lt;/h3&gt;<br /> As a result of Ensembl gene annotations, 5 gene sets were removed from GTRD as they no fall below the the maximum number genes threshold (&lt;2000 genes). (-5)<br /> <br /> &lt;h3&gt;C5:GO (Gene Ontology)&lt;/h3&gt;<br /> &lt;p&gt; 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 (&lt;span class=&quot;plainlinks&quot;&gt;[http://www.geneontology.org Nature Genet 2000]&lt;/span&gt;). 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 2021-12-15 and NCBI gene2go annotations downloaded on 2022-01-03.&lt;/p&gt;<br /> &lt;p&gt;This collection is divided into three sub-collections:&lt;/p&gt;<br /> &lt;ul&gt;<br /> &lt;li&gt;&lt;strong&gt;BP&lt;/strong&gt;: GO Biological process (+177 gene sets). Gene sets derived from the Biological Process Ontology.&lt;/li&gt;<br /> &lt;li&gt;&lt;strong&gt;CC&lt;/strong&gt;: GO Cellular component (+10 gene sets). Gene sets derived from the Cellular Component Ontology.&lt;/li&gt;<br /> &lt;li&gt;&lt;strong&gt;MF&lt;/strong&gt;: GO Molecular function (+30 gene sets). Gene sets derived from the Molecular Function Ontology.&lt;/li&gt;<br /> &lt;/ul&gt;<br /> <br /> &lt;p&gt;These updates were generated in accordance with the procedure described in the [[MSigDB_v7.0_Release_Notes#C5_.28Gene_Ontology_collection.29_-_Major_overhaul | GO release notes for MSigDB 7.0.]]<br /> <br /> &lt;h3&gt;C5:HPO (Human Phenotype Ontology)&lt;/h3&gt;<br /> <br /> Gene sets in this sub-collection have been updated to reflect the 2021-10-10 release of the Human Phenotype Ontology database (+258 gene sets). This sub-collection has been redundancy filtered through a procedure comparable to that of the GO and Reactome sub-collections.<br /> <br /> &lt;h3&gt;C8: cell type signature gene sets&lt;/h3&gt;<br /> Added eye gene sets from &lt;span class=&quot;plainlinks&quot;&gt;[https://www.ncbi.nlm.nih.gov/labs/pmc/articles/PMC8478974/ Gautam and Hamashima et al. 2021. Multi-species single-cell transcriptomic analysis of ocular compartment regulons.]&lt;/span&gt; (+29 gene sets)<br /> <br /> &lt;h3&gt;CHIP file updates&lt;/h3&gt;<br /> &lt;ul&gt;<br /> &lt;li&gt;MSigDB 7.5 gene annotations and gene mapping CHIP files have been updated to data from Ensembl 105.&lt;/li&gt;<br /> &lt;li&gt;MSigDB 7.5 includes new handling for deprecated Ensembl Gene IDs thanks to work by &lt;span class=&quot;plainlinks&quot;&gt;[https://github.com/dhimmel Daniel Himmelstein]&lt;/span&gt;. Briefly, historical IDs that map uniquely to one &quot;newest&quot; ensembl gene ID were extracted from the &quot;old_to_newest.tsv&quot; file from the respective Human, Mouse, and Rat repositories generated for Ensembl 105 &lt;span class=&quot;plainlinks&quot;&gt;[https://github.com/related-sciences/ensembl-genes (see: Github repository)]&lt;/span&gt; and then merged into the species specific Ensembl_Gene_ID chip file.&lt;/li&gt;<br /> &lt;li&gt;Gene orthology annotations for mapping mouse and rat genes to their best match human orthologs have been updated to &lt;span class=&quot;plainlinks&quot;&gt;[https://www.alliancegenome.org/ Alliance of Genome Resources]&lt;/span&gt; orthology database release 4.2.&lt;/li&gt;<br /> &lt;li&gt;&lt;b&gt;Warning:&lt;/b&gt; Rat Microarray derived annotations. Ensembl 105 brought a major update to the rat genome assembly transitioning from the deprecated Rnor_6.0 assembly to the modern mRatBN7.2 assembly. However, Ensembl has not yet released updated microarray probe mappings for the mRatBN7.2 assembly. In order to continue to provide CHIP files and internal mappings in MSigDB for experiments derived from these platforms, we have carried forward the historical Probe-to-Gene mappings from Ensembl 103/MSigDB v7.4 and remapped the target genes to the current assembly using the Ensembl_Gene_ID_MSigDB.v7.5 chip. However, until Ensembl releases updated probe to gene mappings derived directly from the mRatBN7.2 assembly the quality of MSigDB's rat microarray chip files may be impacted. Rat CHIP files affected by this have recieved the suffix the temporary suffix &lt;b&gt;_REMAPPED&lt;/b&gt; after the MSigDB version number.&lt;/li&gt;<br /> &lt;/ul&gt;</div> Acastanza https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=MSigDB_v7.5.1_Release_Notes&diff=4478 MSigDB v7.5.1 Release Notes 2022-01-20T01:35:45Z <p>Acastanza: moved MSigDB v7.5 Release Notes to MSigDB v7.5.1 Release Notes:&amp;#32;Add patch version notes</p> <hr /> <div>&lt;span class=&quot;plainlinks&quot;&gt;<br /> [http://www.broadinstitute.org/gsea/ GSEA Home] |<br /> [http://www.broadinstitute.org/gsea/downloads.jsp Downloads] | <br /> [http://www.broadinstitute.org/gsea/msigdb/ Molecular Signatures Database] | <br /> [http://www.broadinstitute.org/cancer/software/gsea/wiki/index.php/Main_Page Documentation] |<br /> [http://www.broadinstitute.org/gsea/contact.jsp Contact]<br /> &lt;/span&gt;<br /> <br /> This page describes the changes made to the gene set collections for Release 7.5 of the Molecular Signatures Database (MSigDB). This release contains updates to: C1, GO, HPO, and Reactome, as well as the addition of curated sets to C8 and user submitted sets to C2:CGP. This update incorporates the removal of clone based gene IDs introduced in Ensembl 104. <br /> <br /> <br /> &lt;b&gt;Note:&lt;/b&gt; Due to substantial changes introduced in MSigDB 7.0, using GSEA 4.0.0+ is recommended when utilizing MSigDB 7.0+ resources.&lt;br&gt;<br /> &lt;b&gt;Advisory&lt;/b&gt;: It is strongly recommended that users of MSigDB 7.5 '''always''' use the GSEA &quot;Collapse/Remap to gene symbols&quot; feature with the provided Symbol Remapping chip file if your dataset was generated with a transcriptome other than '''Ensembl v105/GENCODE v39'''.<br /> <br /> &lt;h2&gt;Updates to Collections&lt;/h2&gt;<br /> <br /> &lt;h3&gt;C1&lt;/h3&gt;<br /> Updated human gene annotations to Ensembl 105 (+21 gene sets).<br /> &lt;h3&gt;C2:CGP&lt;/h3&gt;<br /> Gene sets contributed by the following individuals have been added to C2:CGP<br /> &lt;ul&gt;<br /> &lt;li&gt;NRF response gene sets contributed by Lara Ibrahim, The Scripps Research Institute (+6 gene sets) from [https://pubmed.ncbi.nlm.nih.gov/33096892/ (PMID:33096892)]&lt;/li&gt;<br /> &lt;li&gt;Gene sets describing the epithelial-mesenchymal transition (EMT) upon transforming growth factor beta (TGFb) stimulation contributed by Dharmesh D. Bhuva, Walter and Eliza Hall Institute of Medical Research (+6 gene sets) from [https://pubmed.ncbi.nlm.nih.gov/28119430 (PMID:28119430)]&lt;/li&gt;<br /> &lt;li&gt;SEAVEY_EPITHELIOID_HEMANGIOENDOTHELIOMA contributed by Caleb Seavey, Cleveland Clinic Foundation (+1 gene set) from [https://pubmed.ncbi.nlm.nih.gov/33766982 (PMID:33766982)]&lt;/li&gt;<br /> &lt;li&gt;SATOH_COLORECTAL_CANCER_MYC_UP contributed by Rintaro Saito, Institute for Advanced Biosciences, Keio University (+1 gene set) from [https://pubmed.ncbi.nlm.nih.gov/28847964 (PMID:28847964)]&lt;/li&gt;<br /> &lt;li&gt;GLASS_IGF2BP1_CLIP_TARGETS_KNOCKDOWN_DN contributed by Markus Gla&amp;szlig;, Martin Luther University Halle-Wittenberg (+1 gene set) from [https://pubmed.ncbi.nlm.nih.gov/33829040 (PMID:33829040)]&lt;/li&gt;<br /> <br /> &lt;/ul&gt;<br /> <br /> &lt;h3&gt;C2:CP:Reactome&lt;/h3&gt;<br /> <br /> &lt;ul&gt;<br /> &lt;li&gt;Reactome gene sets have been updated to reflect the state of the Reactome pathway architecture as of '''Reactome v78''' (+11 gene sets).&lt;/li&gt;<br /> &lt;li&gt;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.&lt;/li&gt;<br /> &lt;/ul&gt;<br /> <br /> &lt;h3&gt;C2:CP:WikiPathways&lt;/h3&gt;<br /> WikiPathways gene sets have been updated to the January 10, 2022 release (+47 gene sets).<br /> <br /> &lt;h3&gt;C3:TFT:GTRD&lt;/h3&gt;<br /> As a result of Ensembl gene annotations, 5 gene sets were removed from GTRD as they no fall below the the maximum number genes threshold (&lt;2000 genes). (-5)<br /> <br /> &lt;h3&gt;C5:GO (Gene Ontology)&lt;/h3&gt;<br /> &lt;p&gt; 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 (&lt;span class=&quot;plainlinks&quot;&gt;[http://www.geneontology.org Nature Genet 2000]&lt;/span&gt;). 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 2021-12-15 and NCBI gene2go annotations downloaded on 2022-01-03.&lt;/p&gt;<br /> &lt;p&gt;This collection is divided into three sub-collections:&lt;/p&gt;<br /> &lt;ul&gt;<br /> &lt;li&gt;&lt;strong&gt;BP&lt;/strong&gt;: GO Biological process (+177 gene sets). Gene sets derived from the Biological Process Ontology.&lt;/li&gt;<br /> &lt;li&gt;&lt;strong&gt;CC&lt;/strong&gt;: GO Cellular component (+10 gene sets). Gene sets derived from the Cellular Component Ontology.&lt;/li&gt;<br /> &lt;li&gt;&lt;strong&gt;MF&lt;/strong&gt;: GO Molecular function (+30 gene sets). Gene sets derived from the Molecular Function Ontology.&lt;/li&gt;<br /> &lt;/ul&gt;<br /> <br /> &lt;p&gt;These updates were generated in accordance with the procedure described in the [[MSigDB_v7.0_Release_Notes#C5_.28Gene_Ontology_collection.29_-_Major_overhaul | GO release notes for MSigDB 7.0.]]<br /> <br /> &lt;h3&gt;C5:HPO (Human Phenotype Ontology)&lt;/h3&gt;<br /> <br /> Gene sets in this sub-collection have been updated to reflect the 2021-10-10 release of the Human Phenotype Ontology database (+258 gene sets). This sub-collection has been redundancy filtered through a procedure comparable to that of the GO and Reactome sub-collections.<br /> <br /> &lt;h3&gt;C8: cell type signature gene sets&lt;/h3&gt;<br /> Added eye gene sets from &lt;span class=&quot;plainlinks&quot;&gt;[https://www.ncbi.nlm.nih.gov/labs/pmc/articles/PMC8478974/ Gautam and Hamashima et al. 2021. Multi-species single-cell transcriptomic analysis of ocular compartment regulons.]&lt;/span&gt; (+29 gene sets)<br /> <br /> &lt;h3&gt;CHIP file updates&lt;/h3&gt;<br /> &lt;ul&gt;<br /> &lt;li&gt;MSigDB 7.5 gene annotations and gene mapping CHIP files have been updated to data from Ensembl 105.&lt;/li&gt;<br /> &lt;li&gt;MSigDB 7.5 includes new handling for deprecated Ensembl Gene IDs thanks to work by &lt;span class=&quot;plainlinks&quot;&gt;[https://github.com/dhimmel Daniel Himmelstein]&lt;/span&gt;. Briefly, historical IDs that map uniquely to one &quot;newest&quot; ensembl gene ID were extracted from the &quot;old_to_newest.tsv&quot; file from the respective Human, Mouse, and Rat repositories generated for Ensembl 105 &lt;span class=&quot;plainlinks&quot;&gt;[https://github.com/related-sciences/ensembl-genes (see: Github repository)]&lt;/span&gt; and then merged into the species specific Ensembl_Gene_ID chip file.&lt;/li&gt;<br /> &lt;li&gt;Gene orthology annotations for mapping mouse and rat genes to their best match human orthologs have been updated to &lt;span class=&quot;plainlinks&quot;&gt;[https://www.alliancegenome.org/ Alliance of Genome Resources]&lt;/span&gt; orthology database release 4.2.&lt;/li&gt;<br /> &lt;li&gt;&lt;b&gt;Warning:&lt;/b&gt; Rat Microarray derived annotations. Ensembl 105 brought a major update to the rat genome assembly transitioning from the deprecated Rnor_6.0 assembly to the modern mRatBN7.2 assembly. However, Ensembl has not yet released updated microarray probe mappings for the mRatBN7.2 assembly. In order to continue to provide CHIP files and internal mappings in MSigDB for experiments derived from these platforms, we have carried forward the historical Probe-to-Gene mappings from Ensembl 103/MSigDB v7.4 and remapped the target genes to the current assembly using the Ensembl_Gene_ID_MSigDB.v7.5 chip. However, until Ensembl releases updated probe to gene mappings derived directly from the mRatBN7.2 assembly the quality of MSigDB's rat microarray chip files may be impacted. Rat CHIP files affected by this have recieved the suffix the temporary suffix &lt;b&gt;_REMAPPED&lt;/b&gt; after the MSigDB version number.&lt;/li&gt;<br /> &lt;/ul&gt;</div> Acastanza https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=MSigDB_v7.5_Release_Notes&diff=4479 MSigDB v7.5 Release Notes 2022-01-20T01:35:45Z <p>Acastanza: moved MSigDB v7.5 Release Notes to MSigDB v7.5.1 Release Notes:&amp;#32;Add patch version notes</p> <hr /> <div>#REDIRECT [[MSigDB v7.5.1 Release Notes]]</div> Acastanza https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=MSigDB_v7.5.1_Release_Notes&diff=4477 MSigDB v7.5.1 Release Notes 2022-01-14T19:58:34Z <p>Acastanza: Formatting fix</p> <hr /> <div>&lt;span class=&quot;plainlinks&quot;&gt;<br /> [http://www.broadinstitute.org/gsea/ GSEA Home] |<br /> [http://www.broadinstitute.org/gsea/downloads.jsp Downloads] | <br /> [http://www.broadinstitute.org/gsea/msigdb/ Molecular Signatures Database] | <br /> [http://www.broadinstitute.org/cancer/software/gsea/wiki/index.php/Main_Page Documentation] |<br /> [http://www.broadinstitute.org/gsea/contact.jsp Contact]<br /> &lt;/span&gt;<br /> <br /> This page describes the changes made to the gene set collections for Release 7.5 of the Molecular Signatures Database (MSigDB). This release contains updates to: C1, GO, HPO, and Reactome, as well as the addition of curated sets to C8 and user submitted sets to C2:CGP. This update incorporates the removal of clone based gene IDs introduced in Ensembl 104. <br /> <br /> <br /> &lt;b&gt;Note:&lt;/b&gt; Due to substantial changes introduced in MSigDB 7.0, using GSEA 4.0.0+ is recommended when utilizing MSigDB 7.0+ resources.&lt;br&gt;<br /> &lt;b&gt;Advisory&lt;/b&gt;: It is strongly recommended that users of MSigDB 7.5 '''always''' use the GSEA &quot;Collapse/Remap to gene symbols&quot; feature with the provided Symbol Remapping chip file if your dataset was generated with a transcriptome other than '''Ensembl v105/GENCODE v39'''.<br /> <br /> &lt;h2&gt;Updates to Collections&lt;/h2&gt;<br /> <br /> &lt;h3&gt;C1&lt;/h3&gt;<br /> Updated human gene annotations to Ensembl 105 (+21 gene sets).<br /> &lt;h3&gt;C2:CGP&lt;/h3&gt;<br /> Gene sets contributed by the following individuals have been added to C2:CGP<br /> &lt;ul&gt;<br /> &lt;li&gt;NRF response gene sets contributed by Lara Ibrahim, The Scripps Research Institute (+6 gene sets) from [https://pubmed.ncbi.nlm.nih.gov/33096892/ (PMID:33096892)]&lt;/li&gt;<br /> &lt;li&gt;Gene sets describing the epithelial-mesenchymal transition (EMT) upon transforming growth factor beta (TGFb) stimulation contributed by Dharmesh D. Bhuva, Walter and Eliza Hall Institute of Medical Research (+6 gene sets) from [https://pubmed.ncbi.nlm.nih.gov/28119430 (PMID:28119430)]&lt;/li&gt;<br /> &lt;li&gt;SEAVEY_EPITHELIOID_HEMANGIOENDOTHELIOMA contributed by Caleb Seavey, Cleveland Clinic Foundation (+1 gene set) from [https://pubmed.ncbi.nlm.nih.gov/33766982 (PMID:33766982)]&lt;/li&gt;<br /> &lt;li&gt;SATOH_COLORECTAL_CANCER_MYC_UP contributed by Rintaro Saito, Institute for Advanced Biosciences, Keio University (+1 gene set) from [https://pubmed.ncbi.nlm.nih.gov/28847964 (PMID:28847964)]&lt;/li&gt;<br /> &lt;li&gt;GLASS_IGF2BP1_CLIP_TARGETS_KNOCKDOWN_DN contributed by Markus Gla&amp;szlig;, Martin Luther University Halle-Wittenberg (+1 gene set) from [https://pubmed.ncbi.nlm.nih.gov/33829040 (PMID:33829040)]&lt;/li&gt;<br /> <br /> &lt;/ul&gt;<br /> <br /> &lt;h3&gt;C2:CP:Reactome&lt;/h3&gt;<br /> <br /> &lt;ul&gt;<br /> &lt;li&gt;Reactome gene sets have been updated to reflect the state of the Reactome pathway architecture as of '''Reactome v78''' (+11 gene sets).&lt;/li&gt;<br /> &lt;li&gt;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.&lt;/li&gt;<br /> &lt;/ul&gt;<br /> <br /> &lt;h3&gt;C2:CP:WikiPathways&lt;/h3&gt;<br /> WikiPathways gene sets have been updated to the January 10, 2022 release (+47 gene sets).<br /> <br /> &lt;h3&gt;C3:TFT:GTRD&lt;/h3&gt;<br /> As a result of Ensembl gene annotations, 5 gene sets were removed from GTRD as they no fall below the the maximum number genes threshold (&lt;2000 genes). (-5)<br /> <br /> &lt;h3&gt;C5:GO (Gene Ontology)&lt;/h3&gt;<br /> &lt;p&gt; 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 (&lt;span class=&quot;plainlinks&quot;&gt;[http://www.geneontology.org Nature Genet 2000]&lt;/span&gt;). 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 2021-12-15 and NCBI gene2go annotations downloaded on 2022-01-03.&lt;/p&gt;<br /> &lt;p&gt;This collection is divided into three sub-collections:&lt;/p&gt;<br /> &lt;ul&gt;<br /> &lt;li&gt;&lt;strong&gt;BP&lt;/strong&gt;: GO Biological process (+177 gene sets). Gene sets derived from the Biological Process Ontology.&lt;/li&gt;<br /> &lt;li&gt;&lt;strong&gt;CC&lt;/strong&gt;: GO Cellular component (+10 gene sets). Gene sets derived from the Cellular Component Ontology.&lt;/li&gt;<br /> &lt;li&gt;&lt;strong&gt;MF&lt;/strong&gt;: GO Molecular function (+30 gene sets). Gene sets derived from the Molecular Function Ontology.&lt;/li&gt;<br /> &lt;/ul&gt;<br /> <br /> &lt;p&gt;These updates were generated in accordance with the procedure described in the [[MSigDB_v7.0_Release_Notes#C5_.28Gene_Ontology_collection.29_-_Major_overhaul | GO release notes for MSigDB 7.0.]]<br /> <br /> &lt;h3&gt;C5:HPO (Human Phenotype Ontology)&lt;/h3&gt;<br /> <br /> Gene sets in this sub-collection have been updated to reflect the 2021-10-10 release of the Human Phenotype Ontology database (+258 gene sets). This sub-collection has been redundancy filtered through a procedure comparable to that of the GO and Reactome sub-collections.<br /> <br /> &lt;h3&gt;C8: cell type signature gene sets&lt;/h3&gt;<br /> Added eye gene sets from &lt;span class=&quot;plainlinks&quot;&gt;[https://www.ncbi.nlm.nih.gov/labs/pmc/articles/PMC8478974/ Gautam and Hamashima et al. 2021. Multi-species single-cell transcriptomic analysis of ocular compartment regulons.]&lt;/span&gt; (+29 gene sets)<br /> <br /> &lt;h3&gt;CHIP file updates&lt;/h3&gt;<br /> &lt;ul&gt;<br /> &lt;li&gt;MSigDB 7.5 gene annotations and gene mapping CHIP files have been updated to data from Ensembl 105.&lt;/li&gt;<br /> &lt;li&gt;MSigDB 7.5 includes new handling for deprecated Ensembl Gene IDs thanks to work by &lt;span class=&quot;plainlinks&quot;&gt;[https://github.com/dhimmel Daniel Himmelstein]&lt;/span&gt;. Briefly, historical IDs that map uniquely to one &quot;newest&quot; ensembl gene ID were extracted from the &quot;old_to_newest.tsv&quot; file from the respective Human, Mouse, and Rat repositories generated for Ensembl 105 &lt;span class=&quot;plainlinks&quot;&gt;[https://github.com/related-sciences/ensembl-genes (see: Github repository)]&lt;/span&gt; and then merged into the species specific Ensembl_Gene_ID chip file.&lt;/li&gt;<br /> &lt;li&gt;Gene orthology annotations for mapping mouse and rat genes to their best match human orthologs have been updated to &lt;span class=&quot;plainlinks&quot;&gt;[https://www.alliancegenome.org/ Alliance of Genome Resources]&lt;/span&gt; orthology database release 4.2.&lt;/li&gt;<br /> &lt;li&gt;&lt;b&gt;Warning:&lt;/b&gt; Rat Microarray derived annotations. Ensembl 105 brought a major update to the rat genome assembly transitioning from the deprecated Rnor_6.0 assembly to the modern mRatBN7.2 assembly. However, Ensembl has not yet released updated microarray probe mappings for the mRatBN7.2 assembly. In order to continue to provide CHIP files and internal mappings in MSigDB for experiments derived from these platforms, we have carried forward the historical Probe-to-Gene mappings from Ensembl 103/MSigDB v7.4 and remapped the target genes to the current assembly using the Ensembl_Gene_ID_MSigDB.v7.5 chip. However, until Ensembl releases updated probe to gene mappings derived directly from the mRatBN7.2 assembly the quality of MSigDB's rat microarray chip files may be impacted. Rat CHIP files affected by this have recieved the suffix the temporary suffix &lt;b&gt;_REMAPPED&lt;/b&gt; after the MSigDB version number.&lt;/li&gt;<br /> &lt;/ul&gt;</div> Acastanza https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=MSigDB_v7.5.1_Release_Notes&diff=4474 MSigDB v7.5.1 Release Notes 2022-01-12T01:13:01Z <p>Acastanza: </p> <hr /> <div>&lt;span class=&quot;plainlinks&quot;&gt;<br /> [http://www.broadinstitute.org/gsea/ GSEA Home] |<br /> [http://www.broadinstitute.org/gsea/downloads.jsp Downloads] | <br /> [http://www.broadinstitute.org/gsea/msigdb/ Molecular Signatures Database] | <br /> [http://www.broadinstitute.org/cancer/software/gsea/wiki/index.php/Main_Page Documentation] |<br /> [http://www.broadinstitute.org/gsea/contact.jsp Contact]<br /> &lt;/span&gt;<br /> <br /> This page describes the changes made to the gene set collections for Release 7.5 of the Molecular Signatures Database (MSigDB). This release contains updates to: C1, GO, HPO, and Reactome, as well as the addition of curated sets to C8 and user submitted sets to C2:CGP. This update incorporates the removal of clone based gene IDs introduced in Ensembl 104. <br /> <br /> <br /> &lt;b&gt;Note:&lt;/b&gt; Due to substantial changes introduced in MSigDB 7.0, using GSEA 4.0.0+ is recommended when utilizing MSigDB 7.0+ resources.&lt;br&gt;<br /> &lt;b&gt;Advisory&lt;/b&gt;: It is strongly recommended that users of MSigDB 7.5 '''always''' use the GSEA &quot;Collapse/Remap to gene symbols&quot; feature with the provided Symbol Remapping chip file if your dataset was generated with a transcriptome other than '''Ensembl v105/GENCODE v39'''.<br /> <br /> &lt;h2&gt;Updates to Collections&lt;/h2&gt;<br /> <br /> &lt;h3&gt;C1&lt;/h3&gt;<br /> Updated human gene annotations to Ensembl 105 (+21 gene sets).<br /> &lt;h3&gt;C2:CGP&lt;/h3&gt;<br /> Gene sets contributed by the following individuals have been added to C2:CGP<br /> &lt;ul&gt;<br /> &lt;li&gt;NRF response gene sets contributed by Lara Ibrahim, The Scripps Research Institute (+6 gene sets) from [https://pubmed.ncbi.nlm.nih.gov/33096892/ (PMID:33096892)]<br /> &lt;li&gt;Gene sets describing the epithelial-mesenchymal transition (EMT) upon transforming growth factor beta (TGFb) stimulation contributed by Dharmesh D. Bhuva, Walter and Eliza Hall Institute of Medical Research (+6 gene sets) from [https://pubmed.ncbi.nlm.nih.gov/28119430 (PMID:28119430)]<br /> &lt;li&gt;SEAVEY_EPITHELIOID_HEMANGIOENDOTHELIOMA contributed by Caleb Seavey, Cleveland Clinic Foundation (+1 gene set) from [https://pubmed.ncbi.nlm.nih.gov/33766982 (PMID:33766982)]<br /> &lt;li&gt;SATOH_COLORECTAL_CANCER_MYC_UP contributed by Rintaro Saito, Institute for Advanced Biosciences, Keio University (+1 gene set) from [https://pubmed.ncbi.nlm.nih.gov/28847964 (PMID:28847964)]<br /> &lt;li&gt;GLASS_IGF2BP1_CLIP_TARGETS_KNOCKDOWN_DN contributed by Markus Gla&amp;szlig;, Martin Luther University Halle-Wittenberg (+1 gene set) from [https://pubmed.ncbi.nlm.nih.gov/33829040 (PMID:33829040)]<br /> <br /> &lt;/ul&gt;<br /> <br /> &lt;h3&gt;C2:CP:Reactome&lt;/h3&gt;<br /> &lt;ul&gt;<br /> &lt;li&gt;Reactome gene sets have been updated to reflect the state of the Reactome pathway architecture as of '''Reactome v78''' (+11 gene sets).<br /> &lt;li&gt;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.<br /> &lt;/ul&gt;<br /> &lt;h3&gt;C2:CP:WikiPathways&lt;/h3&gt;<br /> WikiPathways gene sets have been updated to the January 10, 2022 release (+47 gene sets).<br /> <br /> &lt;h3&gt;C3:TFT:GTRD&lt;/h3&gt;<br /> As a result of Ensembl gene annotations, 5 gene sets were removed from GTRD as they no fall below the the maximum number genes threshold (&lt;2000 genes). (-5)<br /> <br /> &lt;h3&gt;C5:GO (Gene Ontology)&lt;/h3&gt;<br /> &lt;p&gt; 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 (&lt;span class=&quot;plainlinks&quot;&gt;[http://www.geneontology.org Nature Genet 2000]&lt;/span&gt;). 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 2021-12-15 and NCBI gene2go annotations downloaded on 2022-01-03.&lt;/p&gt;<br /> &lt;p&gt;This collection is divided into three sub-collections:&lt;/p&gt;<br /> &lt;ul&gt;<br /> &lt;li&gt;&lt;strong&gt;BP&lt;/strong&gt;: GO Biological process (+177 gene sets). Gene sets derived from the Biological Process Ontology.&lt;/li&gt;<br /> &lt;li&gt;&lt;strong&gt;CC&lt;/strong&gt;: GO Cellular component (+10 gene sets). Gene sets derived from the Cellular Component Ontology.&lt;/li&gt;<br /> &lt;li&gt;&lt;strong&gt;MF&lt;/strong&gt;: GO Molecular function (+30 gene sets). Gene sets derived from the Molecular Function Ontology.&lt;/li&gt;<br /> &lt;/ul&gt;<br /> <br /> &lt;p&gt;These updates were generated in accordance with the procedure described in the [[MSigDB_v7.0_Release_Notes#C5_.28Gene_Ontology_collection.29_-_Major_overhaul | GO release notes for MSigDB 7.0.]]<br /> <br /> &lt;h3&gt;C5:HPO (Human Phenotype Ontology)&lt;/h3&gt;<br /> <br /> Gene sets in this sub-collection have been updated to reflect the 2021-10-10 release of the Human Phenotype Ontology database (+258 gene sets). This sub-collection has been redundancy filtered through a procedure comparable to that of the GO and Reactome sub-collections.<br /> <br /> &lt;h3&gt;C8: cell type signature gene sets&lt;/h3&gt;<br /> Added eye gene sets from &lt;span class=&quot;plainlinks&quot;&gt;[https://www.ncbi.nlm.nih.gov/labs/pmc/articles/PMC8478974/ Gautam and Hamashima et al. 2021. Multi-species single-cell transcriptomic analysis of ocular compartment regulons.] (+29 gene sets)<br /> <br /> &lt;h3&gt;CHIP file updates&lt;/h3&gt;<br /> <br /> &lt;ul&gt;<br /> &lt;li&gt;MSigDB 7.5 includes new handling for deprecated Ensembl Gene IDs thanks to work by &lt;span class=&quot;plainlinks&quot;&gt;[https://github.com/dhimmel Daniel Himmelstein]. Briefly, historical IDs that map uniquely to one &quot;newest&quot; ensembl gene ID were extracted from the &quot;old_to_newest.tsv&quot; file from the respective Human, Mouse, and Rat repositories generated for Ensembl 105 &lt;span class=&quot;plainlinks&quot;&gt;[https://github.com/related-sciences/ensembl-genes (see: Github repository)] and then merged into the species specific Ensembl_Gene_ID chip file.<br /> &lt;li&gt;&lt;b&gt;Warning:&lt;/b&gt; Rat Microarray derived annotations. Ensembl 105 brought a major update to the rat genome assembly transitioning from the deprecated Rnor_6.0 assembly to the modern mRatBN7.2 assembly. However, Ensembl has not yet released updated microarray probe mappings for the mRatBN7.2 assembly. In order to continue to provide CHIP files and internal mappings in MSigDB for experiments derived from these platforms, we have carried forward the historical Probe-to-Gene mappings from Ensembl 103/MSigDB v7.4 and remapped the target genes to the current assembly using the Ensembl_Gene_ID_MSigDB.v7.5 chip. However, until Ensembl releases updated probe to gene mappings derived directly from the mRatBN7.2 assembly the quality of MSigDB's rat microarray chip files may be impacted. Rat CHIP files affected by this have recieved the suffix the temporary suffix &lt;b&gt;_REMAPPED&lt;/b&gt; after the MSigDB version number.<br /> &lt;li&gt;Gene orthology annotations for mapping mouse and rat genes to their best match human orthologs have been updated to &lt;span class=&quot;plainlinks&quot;&gt;[https://www.alliancegenome.org/ Alliance of Genome Resources] orthology database release 4.2.</div> Acastanza