MSigDB v7.0 Release Notes - Revision history https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=MSigDB_v7.0_Release_Notes&action=history Revision history for this page on the wiki en MediaWiki 1.34.4 Thu, 28 Mar 2024 17:11:13 GMT Helga at 20:47, 30 March 2020 https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=MSigDB_v7.0_Release_Notes&diff=4396&oldid=prev https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=MSigDB_v7.0_Release_Notes&diff=4396&oldid=prev <p></p> <table class="diff diff-contentalign-left" data-mw="interface"> <col class="diff-marker" /> <col class="diff-content" /> <col class="diff-marker" /> <col class="diff-content" /> <tr class="diff-title" lang="en"> <td colspan="2" style="background-color: #fff; color: #222; text-align: center;">← Older revision</td> <td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 20:47, 30 March 2020</td> </tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l10" >Line 10:</td> <td colspan="2" class="diff-lineno">Line 10:</td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;b&gt;Note:&lt;/b&gt; Due to substantial changes in MSigDB, it is recommended that users migrate to GSEA 4.0.0+ when utilizing MSigDB 7.0+ resources.&lt;br&gt;</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;b&gt;Note:&lt;/b&gt; Due to substantial changes in MSigDB, it is recommended that users migrate to GSEA 4.0.0+ when utilizing MSigDB 7.0+ resources.&lt;br&gt;</div></td></tr> <tr><td class='diff-marker'>−</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>&lt;b&gt;Advisory&lt;/b&gt;: It is strongly recommended that users of MSigDB7/GSEA4.0 '''always''' use the GSEA &quot;Collapse dataset to gene symbols&quot; feature with the provided Symbol Remapping chip file if your dataset was generated with a transcriptome other than <del class="diffchange diffchange-inline">ENSEMBL97</del>/<del class="diffchange diffchange-inline">GENCODE31</del>.</div></td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>&lt;b&gt;Advisory&lt;/b&gt;: It is strongly recommended that users of MSigDB7/GSEA4.0 '''always''' use the GSEA &quot;Collapse dataset to gene symbols&quot; feature with the provided Symbol Remapping chip file if your dataset was generated with a transcriptome other than <ins class="diffchange diffchange-inline">Ensembl 97</ins>/<ins class="diffchange diffchange-inline">GENCODE 31</ins>.</div></td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;h2&gt;Changes to MSigDB Gene Symbol Mapping Procedures&lt;/h2&gt;</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;h2&gt;Changes to MSigDB Gene Symbol Mapping Procedures&lt;/h2&gt;</div></td></tr> <tr><td class='diff-marker'>−</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>&lt;h3&gt;Now using <del class="diffchange diffchange-inline">ENSEMBL </del>as the platform annotation authority&lt;/h3&gt;</div></td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>&lt;h3&gt;Now using <ins class="diffchange diffchange-inline">Ensembl </ins>as the platform annotation authority&lt;/h3&gt;</div></td></tr> <tr><td class='diff-marker'>−</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>Beginning in MSigDB 7.0, identifiers for genes are mapped to their HGNC approved Gene Symbol and NCBI Gene ID through annotations extracted from <del class="diffchange diffchange-inline">ENSEMBL</del>'s BioMart data service, and will be updated at each MSigDB release with the latest available version of <del class="diffchange diffchange-inline">ENSEMBL</del>. This change mitigates a previous issue where retired gene symbols and symbol aliases that did not reflect the current annotation of the human genome were retained in MSigDB as a result of outdated microarray and transcriptome annotations. This issue resulted in symbols being excluded from some gene sets and GSEA analyses due to the potential presence of multiple symbols for the same gene in different gene sets as a result of differing source annotations for those gene sets, and mismatches between the symbols present in the user supplied dataset and those included in MSigDB.</div></td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>Beginning in MSigDB 7.0, identifiers for genes are mapped to their HGNC approved Gene Symbol and NCBI Gene ID through annotations extracted from <ins class="diffchange diffchange-inline">Ensembl</ins>'s BioMart data service, and will be updated at each MSigDB release with the latest available version of <ins class="diffchange diffchange-inline">Ensembl</ins>. This change mitigates a previous issue where retired gene symbols and symbol aliases that did not reflect the current annotation of the human genome were retained in MSigDB as a result of outdated microarray and transcriptome annotations. This issue resulted in symbols being excluded from some gene sets and GSEA analyses due to the potential presence of multiple symbols for the same gene in different gene sets as a result of differing source annotations for those gene sets, and mismatches between the symbols present in the user supplied dataset and those included in MSigDB.</div></td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;ul&gt;</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;ul&gt;</div></td></tr> <tr><td class='diff-marker'>−</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>     &lt;li&gt;Gene annotations supplied in the MSigDB 7.0 release are derived from '''&lt;span class=&quot;plainlinks&quot;&gt;[http://jul2019.archive.ensembl.org/index.html <del class="diffchange diffchange-inline">ENSEMBL </del>version 97]&lt;/span&gt;''' corresponding to '''GENCODE release 31''' and reflect the HGNC Gene Symbols as of the GENCODE 31 freeze date of February 2019.&lt;/li&gt;</div></td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>     &lt;li&gt;Gene annotations supplied in the MSigDB 7.0 release are derived from '''&lt;span class=&quot;plainlinks&quot;&gt;[http://jul2019.archive.ensembl.org/index.html <ins class="diffchange diffchange-inline">Ensembl </ins>version 97]&lt;/span&gt;''' corresponding to '''GENCODE release 31''' and reflect the HGNC Gene Symbols as of the GENCODE 31 freeze date of February 2019.&lt;/li&gt;</div></td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;/ul&gt;</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;/ul&gt;</div></td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;h3&gt;Change to gene orthology mapping procedure for non-human gene sets&lt;/h3&gt;</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;h3&gt;Change to gene orthology mapping procedure for non-human gene sets&lt;/h3&gt;</div></td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;ul&gt;</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;ul&gt;</div></td></tr> <tr><td class='diff-marker'>−</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>     &lt;li&gt;Mouse and Rat genes were assigned to their corresponding Human orthologues using the gene orthologies provided in <del class="diffchange diffchange-inline">ENSEMBL </del>BioMart for <del class="diffchange diffchange-inline">ENSEMBL </del>version 97.&lt;/li&gt;</div></td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>     &lt;li&gt;Mouse and Rat genes were assigned to their corresponding Human orthologues using the gene orthologies provided in <ins class="diffchange diffchange-inline">Ensembl </ins>BioMart for <ins class="diffchange diffchange-inline">Ensembl </ins>version 97.&lt;/li&gt;</div></td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>     &lt;li&gt;As many Mouse and Rat genes correspond to many possible Human orthologues of various fidelity, a ranking procedure was utilized to match each respective non-human gene to its best orthologue match. Genes were ranked by their dS/dN score, their averaged reciprocal percent identicality, their Human Gene-order conservation score, and their Human Whole-genome alignment coverage. These metrics identify likely best orthologues using a combination of gene coding sequence conservation, gene non-coding sequence conservation, and genomic architecture conservation.&lt;/li&gt;</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>     &lt;li&gt;As many Mouse and Rat genes correspond to many possible Human orthologues of various fidelity, a ranking procedure was utilized to match each respective non-human gene to its best orthologue match. Genes were ranked by their dS/dN score, their averaged reciprocal percent identicality, their Human Gene-order conservation score, and their Human Whole-genome alignment coverage. These metrics identify likely best orthologues using a combination of gene coding sequence conservation, gene non-coding sequence conservation, and genomic architecture conservation.&lt;/li&gt;</div></td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;/ul&gt;</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;/ul&gt;</div></td></tr> <tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l27" >Line 27:</td> <td colspan="2" class="diff-lineno">Line 27:</td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;h3&gt;CHIP file updates&lt;/h3&gt;</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;h3&gt;CHIP file updates&lt;/h3&gt;</div></td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;ul&gt;</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;ul&gt;</div></td></tr> <tr><td class='diff-marker'>−</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>     &lt;li&gt;A new Gene Symbol CHIP file for the GSEA &quot;Collapse dataset&quot; feature will be supplied in order to facilitate remapping data sets which use gene annotations prior to the <del class="diffchange diffchange-inline">ENSEMBL </del>release 97/GENCODE release 31 namespace used in MSigDB 7.0 in to this space for GSEA.&lt;/li&gt;</div></td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>     &lt;li&gt;A new Gene Symbol CHIP file for the GSEA &quot;Collapse dataset&quot; feature will be supplied in order to facilitate remapping data sets which use gene annotations prior to the <ins class="diffchange diffchange-inline">Ensembl </ins>release 97/GENCODE release 31 namespace used in MSigDB 7.0 in to this space for GSEA.&lt;/li&gt;</div></td></tr> <tr><td class='diff-marker'>−</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>     &lt;li&gt;New CHIP files have been provided to enable the use of data sets containing Mouse/Rat gene symbols directly through the use of the GSEA &quot;Collapse dataset&quot; feature. These annotations are derived from <del class="diffchange diffchange-inline">ENSEMBL </del>97's Mouse and Rat databases respectively, and support experiments from pipelines relying on GENCODE annotations up to GENCODE release M22 (Mouse). Mappings to orthologous Human genes were derived by the procedure described above.&lt;/li&gt;  </div></td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>     &lt;li&gt;New CHIP files have been provided to enable the use of data sets containing Mouse/Rat gene symbols directly through the use of the GSEA &quot;Collapse dataset&quot; feature. These annotations are derived from <ins class="diffchange diffchange-inline">Ensembl </ins>97's Mouse and Rat databases respectively, and support experiments from pipelines relying on GENCODE annotations up to GENCODE release M22 (Mouse). Mappings to orthologous Human genes were derived by the procedure described above.&lt;/li&gt;  </div></td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>     &lt;li&gt;Previous symbols and aliases for each current gene were provided by their respective symbol authorities (e.g. HGNC for Human, MGI for Mouse, and RGD for Rat).&lt;/li&gt;</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>     &lt;li&gt;Previous symbols and aliases for each current gene were provided by their respective symbol authorities (e.g. HGNC for Human, MGI for Mouse, and RGD for Rat).&lt;/li&gt;</div></td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>     &lt;li&gt;Previous NCBI IDs for all genes were extracted from the NCBI gene_history file available from the NCBI FTP server.&lt;/li&gt;</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>     &lt;li&gt;Previous NCBI IDs for all genes were extracted from the NCBI gene_history file available from the NCBI FTP server.&lt;/li&gt;</div></td></tr> <tr><td class='diff-marker'>−</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>     &lt;li&gt;Several CHIP files annotating platforms which are not included in <del class="diffchange diffchange-inline">ENSEMBL</del>'s BioMart database have been depreciated.&lt;/li&gt;</div></td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>     &lt;li&gt;Several CHIP files annotating platforms which are not included in <ins class="diffchange diffchange-inline">Ensembl</ins>'s BioMart database have been depreciated.&lt;/li&gt;</div></td></tr> <tr><td class='diff-marker'>−</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>     &lt;li&gt;Annotations for all platforms represented in <del class="diffchange diffchange-inline">ENSEMBL</del>'s BioMart database have been updated to reflect the <del class="diffchange diffchange-inline">ENSEMBL </del>version 97 annotations.&lt;/li&gt;</div></td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>     &lt;li&gt;Annotations for all platforms represented in <ins class="diffchange diffchange-inline">Ensembl</ins>'s BioMart database have been updated to reflect the <ins class="diffchange diffchange-inline">Ensembl </ins>version 97 annotations.&lt;/li&gt;</div></td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;/ul&gt;</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;/ul&gt;</div></td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;h3&gt;Changes to data set handling recommendations&lt;/h3&gt;</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;h3&gt;Changes to data set handling recommendations&lt;/h3&gt;</div></td></tr> <tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l43" >Line 43:</td> <td colspan="2" class="diff-lineno">Line 43:</td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>   &lt;li&gt;Rat_Gene_Symbol_Remapping_MSigDB.v7.0.chip&lt;/li&gt;</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>   &lt;li&gt;Rat_Gene_Symbol_Remapping_MSigDB.v7.0.chip&lt;/li&gt;</div></td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;/ul&gt;</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;/ul&gt;</div></td></tr> <tr><td class='diff-marker'>−</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>This remapping is not necessary if your data set was generated using <del class="diffchange diffchange-inline">ENSEMBL97 </del>or GENCODE 31 transcriptomes. This is a change from our previous recommendation.&lt;/li&gt;</div></td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>This remapping is not necessary if your data set was generated using <ins class="diffchange diffchange-inline">Ensembl 97 </ins>or GENCODE 31 transcriptomes. This is a change from our previous recommendation.&lt;/li&gt;</div></td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;/ul&gt;</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;/ul&gt;</div></td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr> <tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l52" >Line 52:</td> <td colspan="2" class="diff-lineno">Line 52:</td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;h3&gt;C1 (positional gene sets) - Major overhaul &lt;/h3&gt;</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;h3&gt;C1 (positional gene sets) - Major overhaul &lt;/h3&gt;</div></td></tr> <tr><td class='diff-marker'>−</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>C1 has been rebuilt to reflect the primary assembly of the current release of the Human Genome as present in <del class="diffchange diffchange-inline">ENSEMBL </del>97 and GENCODE 31 (GRCh38.p12). Gene annotations for this collection are derived from the ''Chromosome'' and ''Karyotype band'' tracks from the <del class="diffchange diffchange-inline">ENSEMBL </del>BioMart (version 97) and reflect the gene architecture as represented on the primary assembly. This resulted in a small reduction in the number of gene sets (-27), as sets representing complete chromosome arms with few annotated genes were removed.  </div></td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>C1 has been rebuilt to reflect the primary assembly of the current release of the Human Genome as present in <ins class="diffchange diffchange-inline">Ensembl </ins>97 and GENCODE 31 (GRCh38.p12). Gene annotations for this collection are derived from the ''Chromosome'' and ''Karyotype band'' tracks from the <ins class="diffchange diffchange-inline">Ensembl </ins>BioMart (version 97) and reflect the gene architecture as represented on the primary assembly. This resulted in a small reduction in the number of gene sets (-27), as sets representing complete chromosome arms with few annotated genes were removed.  </div></td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;h3&gt;C2:CP:Reactome - Major overhaul &lt;/h3&gt;</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;h3&gt;C2:CP:Reactome - Major overhaul &lt;/h3&gt;</div></td></tr> </table> Mon, 30 Mar 2020 20:47:37 GMT Helga https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Talk:MSigDB_v7.0_Release_Notes Acastanza at 15:58, 18 March 2020 https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=MSigDB_v7.0_Release_Notes&diff=4384&oldid=prev https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=MSigDB_v7.0_Release_Notes&diff=4384&oldid=prev <p></p> <table class="diff diff-contentalign-left" data-mw="interface"> <col class="diff-marker" /> <col class="diff-content" /> <col class="diff-marker" /> <col class="diff-content" /> <tr class="diff-title" lang="en"> <td colspan="2" style="background-color: #fff; color: #222; text-align: center;">← Older revision</td> <td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 15:58, 18 March 2020</td> </tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l7" >Line 7:</td> <td colspan="2" class="diff-lineno">Line 7:</td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;/span&gt;</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;/span&gt;</div></td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr> <tr><td class='diff-marker'>−</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>This page describes the changes made to the gene set collections for Release 7.0 of the Molecular Signatures Database (MSigDB). This is a major release that includes substantial updates to gene set annotations, gene symbol mapping procedures, overhaul of several collections/sub-collections, and corrections to miscellaneous errors .</div></td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>This page describes the changes made to the gene set collections for Release 7.0 of the Molecular Signatures Database (MSigDB). This is a major release that includes substantial updates to gene set annotations, gene symbol mapping procedures, overhaul of several collections/sub-collections, and corrections to miscellaneous errors.</div></td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;b&gt;Note:&lt;/b&gt; Due to substantial changes in MSigDB, it is recommended that users migrate to GSEA 4.0.0+ when utilizing MSigDB 7.0+ resources.&lt;br&gt;</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;b&gt;Note:&lt;/b&gt; Due to substantial changes in MSigDB, it is recommended that users migrate to GSEA 4.0.0+ when utilizing MSigDB 7.0+ resources.&lt;br&gt;</div></td></tr> </table> Wed, 18 Mar 2020 15:58:18 GMT Acastanza https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Talk:MSigDB_v7.0_Release_Notes Helga at 18:57, 14 February 2020 https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=MSigDB_v7.0_Release_Notes&diff=4383&oldid=prev https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=MSigDB_v7.0_Release_Notes&diff=4383&oldid=prev <p></p> <table class="diff diff-contentalign-left" data-mw="interface"> <col class="diff-marker" /> <col class="diff-content" /> <col class="diff-marker" /> <col class="diff-content" /> <tr class="diff-title" lang="en"> <td colspan="2" style="background-color: #fff; color: #222; text-align: center;">← Older revision</td> <td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 18:57, 14 February 2020</td> </tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l57" >Line 57:</td> <td colspan="2" class="diff-lineno">Line 57:</td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;ul&gt;</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;ul&gt;</div></td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>     &lt;li&gt;Reactome gene sets have been updated to reflect the state of the Reactome pathway architecture as of '''Reactome v69''' (+825 gene sets).</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>     &lt;li&gt;Reactome gene sets have been updated to reflect the state of the Reactome pathway architecture as of '''Reactome v69''' (+825 gene sets).</div></td></tr> <tr><td class='diff-marker'>−</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>&lt;li&gt;In order to limit redundancy between gene sets within the Reactome sub-collection we applied a filtering procedure based on <del class="diffchange diffchange-inline">card's </del>coefficients and distance from the top level of the Reactome event hierarchy. This is similar to the procedure applied in the C5 (Gene Ontology) collection (see below). Briefly, we computed Jaccard<del class="diffchange diffchange-inline">'s </del>coefficients for each pair of sets, and marked a pair as highly similar if its Jaccard<del class="diffchange diffchange-inline">'s </del>coefficient was greater than 0.85. We then clustered highly similar sets into &quot;chunks&quot; using the &lt;tt&gt;hclust&lt;/tt&gt; function from the R &lt;tt&gt;stats&lt;/tt&gt; package and applied two rounds of filtering for every &quot;chunk&quot;. First, we kept the largest set in the &quot;chunk&quot; and discarded the smaller sets. This left &quot;chunks&quot; of highly similar sets of identical sizes, which we further pruned by preferentially keeping the more general set (i.e., the set closest to one of the 28 pathways at the top level of the Reactome Event Hierarchy).</div></td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>&lt;li&gt;In order to limit redundancy between gene sets within the Reactome sub-collection we applied a filtering procedure based on <ins class="diffchange diffchange-inline">Jaccard </ins>coefficients and distance from the top level of the Reactome event hierarchy. This is similar to the procedure applied in the C5 (Gene Ontology) collection (see below). Briefly, we computed Jaccard coefficients for each pair of sets, and marked a pair as highly similar if its Jaccard coefficient was greater than 0.85. We then clustered highly similar sets into &quot;chunks&quot; using the &lt;tt&gt;hclust&lt;/tt&gt; function from the R &lt;tt&gt;stats&lt;/tt&gt; package and applied two rounds of filtering for every &quot;chunk&quot;. First, we kept the largest set in the &quot;chunk&quot; and discarded the smaller sets. This left &quot;chunks&quot; of highly similar sets of identical sizes, which we further pruned by preferentially keeping the more general set (i.e., the set closest to one of the 28 pathways at the top level of the Reactome Event Hierarchy).</div></td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;/ul&gt;</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;/ul&gt;</div></td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr> <tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l110" >Line 110:</td> <td colspan="2" class="diff-lineno">Line 110:</td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;p&gt;This file contains the entire GO ontology in &lt;span class=&quot;plainlinks&quot;&gt;[http://owlcollab.github.io/oboformat/doc/GO.format.obo-1_2.html OBO v.1.2 format].&lt;/span&gt;&lt;/p&gt;</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;p&gt;This file contains the entire GO ontology in &lt;span class=&quot;plainlinks&quot;&gt;[http://owlcollab.github.io/oboformat/doc/GO.format.obo-1_2.html OBO v.1.2 format].&lt;/span&gt;&lt;/p&gt;</div></td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;/ul&gt;</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;/ul&gt;</div></td></tr> <tr><td class='diff-marker'>−</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>&lt;p&gt;This procedure has been modified from that described previously for MSigDB v5.2. First, for each GO term we got the corresponding human genes from the gene2go file. Next, we have applied the path rule. Gene products are associated with the most specific GO terms possible. All parent terms up to the root automatically apply to the gene product. Thus, the parent GO term gene sets should include all genes associated with the children GO terms. Then we removed sets with fewer than &lt;b&gt;5&lt;/b&gt; or more than 2,000 Gene IDs. Finally, we resolved redundancies as follows. We computed Jaccard<del class="diffchange diffchange-inline">'s </del>coefficients for each pair of sets, and marked a pair as highly similar if its Jaccard<del class="diffchange diffchange-inline">'s </del>coefficient <del class="diffchange diffchange-inline">waswaseater </del>than 0.85. We then clustered highly similar sets into &quot;chunks&quot; using the &lt;tt&gt;hclust&lt;/tt&gt; function from the R &lt;tt&gt;stats&lt;/tt&gt; package according to their GO terms and applied two rounds of filtering for every &quot;chunk&quot;. First, we kept the largest set in the &quot;chunk&quot; and discarded the smaller sets. This left &quot;chunks&quot; of highly similar sets of identical sizes, which we further pruned by preferentially keeping the more general set (i.e., the set closest to the root of the GO ontology tree).&lt;/p&gt;</div></td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>&lt;p&gt;This procedure has been modified from that described previously for MSigDB v5.2. First, for each GO term we got the corresponding human genes from the gene2go file. Next, we have applied the path rule. Gene products are associated with the most specific GO terms possible. All parent terms up to the root automatically apply to the gene product. Thus, the parent GO term gene sets should include all genes associated with the children GO terms. Then we removed sets with fewer than &lt;b&gt;5&lt;/b&gt; or more than 2,000 Gene IDs. Finally, we resolved redundancies as follows. We computed Jaccard coefficients for each pair of sets, and marked a pair as highly similar if its Jaccard coefficient <ins class="diffchange diffchange-inline">was greater </ins>than 0.85. We then clustered highly similar sets into &quot;chunks&quot; using the &lt;tt&gt;hclust&lt;/tt&gt; function from the R &lt;tt&gt;stats&lt;/tt&gt; package according to their GO terms and applied two rounds of filtering for every &quot;chunk&quot;. First, we kept the largest set in the &quot;chunk&quot; and discarded the smaller sets. This left &quot;chunks&quot; of highly similar sets of identical sizes, which we further pruned by preferentially keeping the more general set (i.e., the set closest to the root of the GO ontology tree).&lt;/p&gt;</div></td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;p&gt;A previous version of the C5 collection contained 864 gene sets that were founder sets for one or more gene set in the MSigDB Hallmark collection. These deprecated C5 sets are included in MSigDB 7.0 as an ARCHIVED collection in order to preserve links to their pages from the hallmark gene set pages.&lt;/p&gt;</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;p&gt;A previous version of the C5 collection contained 864 gene sets that were founder sets for one or more gene set in the MSigDB Hallmark collection. These deprecated C5 sets are included in MSigDB 7.0 as an ARCHIVED collection in order to preserve links to their pages from the hallmark gene set pages.&lt;/p&gt;</div></td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr> </table> Fri, 14 Feb 2020 18:57:57 GMT Helga https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Talk:MSigDB_v7.0_Release_Notes Acastanza: Removed advisory specific to bug present in GSEA 4.0.0 https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=MSigDB_v7.0_Release_Notes&diff=4352&oldid=prev https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=MSigDB_v7.0_Release_Notes&diff=4352&oldid=prev <p>Removed advisory specific to bug present in GSEA 4.0.0</p> <table class="diff diff-contentalign-left" data-mw="interface"> <col class="diff-marker" /> <col class="diff-content" /> <col class="diff-marker" /> <col class="diff-content" /> <tr class="diff-title" lang="en"> <td colspan="2" style="background-color: #fff; color: #222; text-align: center;">← Older revision</td> <td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 22:06, 11 September 2019</td> </tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l10" >Line 10:</td> <td colspan="2" class="diff-lineno">Line 10:</td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;b&gt;Note:&lt;/b&gt; Due to substantial changes in MSigDB, it is recommended that users migrate to GSEA 4.0.0+ when utilizing MSigDB 7.0+ resources.&lt;br&gt;</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;b&gt;Note:&lt;/b&gt; Due to substantial changes in MSigDB, it is recommended that users migrate to GSEA 4.0.0+ when utilizing MSigDB 7.0+ resources.&lt;br&gt;</div></td></tr> <tr><td class='diff-marker'>−</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>&lt;b&gt;Advisory&lt;/b&gt;: It is strongly recommended that users of MSigDB7/GSEA4.0 '''always''' use the GSEA &quot;Collapse dataset to gene symbols&quot; feature with the provided Symbol Remapping chip file if your dataset was generated with a transcriptome other than ENSEMBL97/GENCODE31<del class="diffchange diffchange-inline">. When using this feature for symbol remapping, the &quot;Omit features with no symbol match&quot; flag (in Advanced Fields) &lt;b&gt;MUST be set to false.&lt;/b&gt;  This has been fixed in GSEA 4.0.1 and the &quot;Omit&quot; setting is not longer necessary</del>.</div></td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>&lt;b&gt;Advisory&lt;/b&gt;: It is strongly recommended that users of MSigDB7/GSEA4.0 '''always''' use the GSEA &quot;Collapse dataset to gene symbols&quot; feature with the provided Symbol Remapping chip file if your dataset was generated with a transcriptome other than ENSEMBL97/GENCODE31.</div></td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;h2&gt;Changes to MSigDB Gene Symbol Mapping Procedures&lt;/h2&gt;</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;h2&gt;Changes to MSigDB Gene Symbol Mapping Procedures&lt;/h2&gt;</div></td></tr> <tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l28" >Line 28:</td> <td colspan="2" class="diff-lineno">Line 28:</td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;ul&gt;</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;ul&gt;</div></td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>     &lt;li&gt;A new Gene Symbol CHIP file for the GSEA &quot;Collapse dataset&quot; feature will be supplied in order to facilitate remapping data sets which use gene annotations prior to the ENSEMBL release 97/GENCODE release 31 namespace used in MSigDB 7.0 in to this space for GSEA.&lt;/li&gt;</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>     &lt;li&gt;A new Gene Symbol CHIP file for the GSEA &quot;Collapse dataset&quot; feature will be supplied in order to facilitate remapping data sets which use gene annotations prior to the ENSEMBL release 97/GENCODE release 31 namespace used in MSigDB 7.0 in to this space for GSEA.&lt;/li&gt;</div></td></tr> <tr><td class='diff-marker'>−</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;">    &lt;li&gt;When using this feature for symbol remapping the &quot;Omit features with no symbol match&quot; flag (in Advanced Fields) &lt;b&gt;MUST be set to false.&lt;/b&gt; </del></div></td><td colspan="2"> </td></tr> <tr><td class='diff-marker'>−</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;"> This has been fixed in GSEA 4.0.1 and the &quot;Omit&quot; setting is not longer necessary.&lt;/li&gt;</del></div></td><td colspan="2"> </td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>     &lt;li&gt;New CHIP files have been provided to enable the use of data sets containing Mouse/Rat gene symbols directly through the use of the GSEA &quot;Collapse dataset&quot; feature. These annotations are derived from ENSEMBL 97's Mouse and Rat databases respectively, and support experiments from pipelines relying on GENCODE annotations up to GENCODE release M22 (Mouse). Mappings to orthologous Human genes were derived by the procedure described above.&lt;/li&gt;  </div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>     &lt;li&gt;New CHIP files have been provided to enable the use of data sets containing Mouse/Rat gene symbols directly through the use of the GSEA &quot;Collapse dataset&quot; feature. These annotations are derived from ENSEMBL 97's Mouse and Rat databases respectively, and support experiments from pipelines relying on GENCODE annotations up to GENCODE release M22 (Mouse). Mappings to orthologous Human genes were derived by the procedure described above.&lt;/li&gt;  </div></td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>     &lt;li&gt;Previous symbols and aliases for each current gene were provided by their respective symbol authorities (e.g. HGNC for Human, MGI for Mouse, and RGD for Rat).&lt;/li&gt;</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>     &lt;li&gt;Previous symbols and aliases for each current gene were provided by their respective symbol authorities (e.g. HGNC for Human, MGI for Mouse, and RGD for Rat).&lt;/li&gt;</div></td></tr> <tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l45" >Line 45:</td> <td colspan="2" class="diff-lineno">Line 43:</td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>   &lt;li&gt;Rat_Gene_Symbol_Remapping_MSigDB.v7.0.chip&lt;/li&gt;</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>   &lt;li&gt;Rat_Gene_Symbol_Remapping_MSigDB.v7.0.chip&lt;/li&gt;</div></td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;/ul&gt;</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;/ul&gt;</div></td></tr> <tr><td class='diff-marker'>−</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del class="diffchange diffchange-inline">    &lt;li&gt;&lt;b&gt;When using this feature for symbol remapping the &quot;Omit features with no symbol match&quot; flag (in Advanced Fields) MUST be set to false. &lt;/b&gt;  This has been fixed in GSEA 4.0.1 and the &quot;Omit&quot; setting is not longer necessary.</del></div></td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>This remapping is not necessary if your data set was generated using ENSEMBL97 or GENCODE 31 transcriptomes. This is a change from our previous recommendation.&lt;/li&gt;</div></td></tr> <tr><td class='diff-marker'>−</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del class="diffchange diffchange-inline">&lt;br&gt; </del>This remapping is not necessary if your data set was generated using ENSEMBL97 or GENCODE 31 transcriptomes. This is a change from our previous recommendation.&lt;/li&gt;</div></td><td colspan="2"> </td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;/ul&gt;</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;/ul&gt;</div></td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr> </table> Wed, 11 Sep 2019 22:06:47 GMT Acastanza https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Talk:MSigDB_v7.0_Release_Notes Eby at 08:50, 30 August 2019 https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=MSigDB_v7.0_Release_Notes&diff=4345&oldid=prev https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=MSigDB_v7.0_Release_Notes&diff=4345&oldid=prev <p></p> <table class="diff diff-contentalign-left" data-mw="interface"> <col class="diff-marker" /> <col class="diff-content" /> <col class="diff-marker" /> <col class="diff-content" /> <tr class="diff-title" lang="en"> <td colspan="2" style="background-color: #fff; color: #222; text-align: center;">← Older revision</td> <td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 08:50, 30 August 2019</td> </tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l10" >Line 10:</td> <td colspan="2" class="diff-lineno">Line 10:</td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;b&gt;Note:&lt;/b&gt; Due to substantial changes in MSigDB, it is recommended that users migrate to GSEA 4.0.0+ when utilizing MSigDB 7.0+ resources.&lt;br&gt;</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;b&gt;Note:&lt;/b&gt; Due to substantial changes in MSigDB, it is recommended that users migrate to GSEA 4.0.0+ when utilizing MSigDB 7.0+ resources.&lt;br&gt;</div></td></tr> <tr><td class='diff-marker'>−</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>&lt;b&gt;Advisory&lt;/b&gt;: It is strongly recommended that users of MSigDB7/GSEA4.0 '''always''' use the GSEA &quot;Collapse dataset to gene symbols&quot; feature with the provided Symbol Remapping chip file if your dataset was generated with a transcriptome other than ENSEMBL97/GENCODE31. When using this feature for symbol remapping, the &quot;Omit features with no symbol match&quot; flag (in Advanced Fields) &lt;b&gt;MUST be set to false.&lt;/b&gt;</div></td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>&lt;b&gt;Advisory&lt;/b&gt;: It is strongly recommended that users of MSigDB7/GSEA4.0 '''always''' use the GSEA &quot;Collapse dataset to gene symbols&quot; feature with the provided Symbol Remapping chip file if your dataset was generated with a transcriptome other than ENSEMBL97/GENCODE31. When using this feature for symbol remapping, the &quot;Omit features with no symbol match&quot; flag (in Advanced Fields) &lt;b&gt;MUST be set to false.&lt;/b&gt; <ins class="diffchange diffchange-inline"> This has been fixed in GSEA 4.0.1 and the &quot;Omit&quot; setting is not longer necessary.</ins></div></td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;h2&gt;Changes to MSigDB Gene Symbol Mapping Procedures&lt;/h2&gt;</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;h2&gt;Changes to MSigDB Gene Symbol Mapping Procedures&lt;/h2&gt;</div></td></tr> <tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l28" >Line 28:</td> <td colspan="2" class="diff-lineno">Line 28:</td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;ul&gt;</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;ul&gt;</div></td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>     &lt;li&gt;A new Gene Symbol CHIP file for the GSEA &quot;Collapse dataset&quot; feature will be supplied in order to facilitate remapping data sets which use gene annotations prior to the ENSEMBL release 97/GENCODE release 31 namespace used in MSigDB 7.0 in to this space for GSEA.&lt;/li&gt;</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>     &lt;li&gt;A new Gene Symbol CHIP file for the GSEA &quot;Collapse dataset&quot; feature will be supplied in order to facilitate remapping data sets which use gene annotations prior to the ENSEMBL release 97/GENCODE release 31 namespace used in MSigDB 7.0 in to this space for GSEA.&lt;/li&gt;</div></td></tr> <tr><td class='diff-marker'>−</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>     &lt;li&gt;When using this feature for symbol remapping the &quot;Omit features with no symbol match&quot; flag (in Advanced Fields) &lt;b&gt;MUST be set to false.&lt;/b&gt;&lt;/li&gt;</div></td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>     &lt;li&gt;When using this feature for symbol remapping the &quot;Omit features with no symbol match&quot; flag (in Advanced Fields) &lt;b&gt;MUST be set to false.&lt;/b&gt;  </div></td></tr> <tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins class="diffchange diffchange-inline"> This has been fixed in GSEA 4.0.1 and the &quot;Omit&quot; setting is not longer necessary.</ins>&lt;/li&gt;</div></td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>     &lt;li&gt;New CHIP files have been provided to enable the use of data sets containing Mouse/Rat gene symbols directly through the use of the GSEA &quot;Collapse dataset&quot; feature. These annotations are derived from ENSEMBL 97's Mouse and Rat databases respectively, and support experiments from pipelines relying on GENCODE annotations up to GENCODE release M22 (Mouse). Mappings to orthologous Human genes were derived by the procedure described above.&lt;/li&gt;  </div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>     &lt;li&gt;New CHIP files have been provided to enable the use of data sets containing Mouse/Rat gene symbols directly through the use of the GSEA &quot;Collapse dataset&quot; feature. These annotations are derived from ENSEMBL 97's Mouse and Rat databases respectively, and support experiments from pipelines relying on GENCODE annotations up to GENCODE release M22 (Mouse). Mappings to orthologous Human genes were derived by the procedure described above.&lt;/li&gt;  </div></td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>     &lt;li&gt;Previous symbols and aliases for each current gene were provided by their respective symbol authorities (e.g. HGNC for Human, MGI for Mouse, and RGD for Rat).&lt;/li&gt;</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>     &lt;li&gt;Previous symbols and aliases for each current gene were provided by their respective symbol authorities (e.g. HGNC for Human, MGI for Mouse, and RGD for Rat).&lt;/li&gt;</div></td></tr> <tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l44" >Line 44:</td> <td colspan="2" class="diff-lineno">Line 45:</td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>   &lt;li&gt;Rat_Gene_Symbol_Remapping_MSigDB.v7.0.chip&lt;/li&gt;</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>   &lt;li&gt;Rat_Gene_Symbol_Remapping_MSigDB.v7.0.chip&lt;/li&gt;</div></td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;/ul&gt;</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;/ul&gt;</div></td></tr> <tr><td class='diff-marker'>−</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>     &lt;li&gt;&lt;b&gt;When using this feature for symbol remapping the &quot;Omit features with no symbol match&quot; flag (in Advanced Fields) MUST be set to false. &lt;/b&gt;</div></td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>     &lt;li&gt;&lt;b&gt;When using this feature for symbol remapping the &quot;Omit features with no symbol match&quot; flag (in Advanced Fields) MUST be set to false. &lt;/b&gt; <ins class="diffchange diffchange-inline"> This has been fixed in GSEA 4.0.1 and the &quot;Omit&quot; setting is not longer necessary.</ins></div></td></tr> <tr><td class='diff-marker'>−</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>&lt;br&gt; This is not necessary if your data set was generated using ENSEMBL97 or GENCODE 31 transcriptomes. This is a change from our previous recommendation.&lt;/li&gt;</div></td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>&lt;br&gt; This <ins class="diffchange diffchange-inline">remapping </ins>is not necessary if your data set was generated using ENSEMBL97 or GENCODE 31 transcriptomes. This is a change from our previous recommendation.&lt;/li&gt;</div></td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;/ul&gt;</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;/ul&gt;</div></td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr> </table> Fri, 30 Aug 2019 08:50:00 GMT Eby https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Talk:MSigDB_v7.0_Release_Notes Helga at 19:50, 28 August 2019 https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=MSigDB_v7.0_Release_Notes&diff=4338&oldid=prev https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=MSigDB_v7.0_Release_Notes&diff=4338&oldid=prev <p></p> <table class="diff diff-contentalign-left" data-mw="interface"> <col class="diff-marker" /> <col class="diff-content" /> <col class="diff-marker" /> <col class="diff-content" /> <tr class="diff-title" lang="en"> <td colspan="2" style="background-color: #fff; color: #222; text-align: center;">← Older revision</td> <td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 19:50, 28 August 2019</td> </tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l10" >Line 10:</td> <td colspan="2" class="diff-lineno">Line 10:</td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;b&gt;Note:&lt;/b&gt; Due to substantial changes in MSigDB, it is recommended that users migrate to GSEA 4.0.0+ when utilizing MSigDB 7.0+ resources.&lt;br&gt;</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;b&gt;Note:&lt;/b&gt; Due to substantial changes in MSigDB, it is recommended that users migrate to GSEA 4.0.0+ when utilizing MSigDB 7.0+ resources.&lt;br&gt;</div></td></tr> <tr><td class='diff-marker'>−</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>&lt;b&gt;Advisory&lt;/b&gt;: It is strongly recommended that users of MSigDB7/GSEA4.0 '''always''' use the GSEA &quot;Collapse dataset to gene symbols&quot; feature with the provided Symbol Remapping chip file if your dataset was generated with a transcriptome other than ENSEMBL97/GENCODE31. When using this feature for symbol <del class="diffchange diffchange-inline">remappimng </del>the &quot;Omit features with no symbol match&quot; flag (in Advanced Fields) &lt;b&gt;MUST be set to false.&lt;/b&gt;</div></td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>&lt;b&gt;Advisory&lt;/b&gt;: It is strongly recommended that users of MSigDB7/GSEA4.0 '''always''' use the GSEA &quot;Collapse dataset to gene symbols&quot; feature with the provided Symbol Remapping chip file if your dataset was generated with a transcriptome other than ENSEMBL97/GENCODE31. When using this feature for symbol <ins class="diffchange diffchange-inline">remapping, </ins>the &quot;Omit features with no symbol match&quot; flag (in Advanced Fields) &lt;b&gt;MUST be set to false.&lt;/b&gt;</div></td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;h2&gt;Changes to MSigDB Gene Symbol Mapping Procedures&lt;/h2&gt;</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;h2&gt;Changes to MSigDB Gene Symbol Mapping Procedures&lt;/h2&gt;</div></td></tr> </table> Wed, 28 Aug 2019 19:50:20 GMT Helga https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Talk:MSigDB_v7.0_Release_Notes Acastanza at 23:42, 26 August 2019 https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=MSigDB_v7.0_Release_Notes&diff=4335&oldid=prev https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=MSigDB_v7.0_Release_Notes&diff=4335&oldid=prev <p></p> <table class="diff diff-contentalign-left" data-mw="interface"> <col class="diff-marker" /> <col class="diff-content" /> <col class="diff-marker" /> <col class="diff-content" /> <tr class="diff-title" lang="en"> <td colspan="2" style="background-color: #fff; color: #222; text-align: center;">← Older revision</td> <td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 23:42, 26 August 2019</td> </tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l59" >Line 59:</td> <td colspan="2" class="diff-lineno">Line 59:</td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;ul&gt;</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;ul&gt;</div></td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>     &lt;li&gt;Reactome gene sets have been updated to reflect the state of the Reactome pathway architecture as of '''Reactome v69''' (+825 gene sets).</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>     &lt;li&gt;Reactome gene sets have been updated to reflect the state of the Reactome pathway architecture as of '''Reactome v69''' (+825 gene sets).</div></td></tr> <tr><td class='diff-marker'>−</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>&lt;li&gt;In order to limit redundancy between gene sets within the Reactome sub-collection we applied a filtering procedure based on card's coefficients and distance from the top level of the Reactome event hierarchy. This is similar to the procedure applied in the C5 (Gene Ontology) collection (see below). Briefly, we computed Jaccard's coefficients for each pair of sets, and marked a pair as highly similar if its Jaccard's coefficient was greater than 0.85. We then clustered highly similar sets into &quot;chunks&quot; using the &lt;tt&gt;hclust&lt;/tt&gt; function from the R &lt;tt&gt;stats&lt;/tt&gt; package and applied two rounds of filtering for every &quot;chunk&quot;. First, we kept the largest set in the &quot;chunk&quot; and discarded the smaller sets. This left &quot;chunks&quot; of highly similar sets of identical sizes, which we further pruned by preferentially keeping the more general set (i.e., the set closest to one of the 28 pathways at the top level of the Reactome Event Hierarchy).<del class="diffchange diffchange-inline">&lt;/p&gt;</del></div></td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>&lt;li&gt;In order to limit redundancy between gene sets within the Reactome sub-collection we applied a filtering procedure based on card's coefficients and distance from the top level of the Reactome event hierarchy. This is similar to the procedure applied in the C5 (Gene Ontology) collection (see below). Briefly, we computed Jaccard's coefficients for each pair of sets, and marked a pair as highly similar if its Jaccard's coefficient was greater than 0.85. We then clustered highly similar sets into &quot;chunks&quot; using the &lt;tt&gt;hclust&lt;/tt&gt; function from the R &lt;tt&gt;stats&lt;/tt&gt; package and applied two rounds of filtering for every &quot;chunk&quot;. First, we kept the largest set in the &quot;chunk&quot; and discarded the smaller sets. This left &quot;chunks&quot; of highly similar sets of identical sizes, which we further pruned by preferentially keeping the more general set (i.e., the set closest to one of the 28 pathways at the top level of the Reactome Event Hierarchy).</div></td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;/ul&gt;</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;/ul&gt;</div></td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr> </table> Mon, 26 Aug 2019 23:42:22 GMT Acastanza https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Talk:MSigDB_v7.0_Release_Notes Acastanza at 16:29, 22 August 2019 https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=MSigDB_v7.0_Release_Notes&diff=4334&oldid=prev https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=MSigDB_v7.0_Release_Notes&diff=4334&oldid=prev <p></p> <table class="diff diff-contentalign-left" data-mw="interface"> <col class="diff-marker" /> <col class="diff-content" /> <col class="diff-marker" /> <col class="diff-content" /> <tr class="diff-title" lang="en"> <td colspan="2" style="background-color: #fff; color: #222; text-align: center;">← Older revision</td> <td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 16:29, 22 August 2019</td> </tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l10" >Line 10:</td> <td colspan="2" class="diff-lineno">Line 10:</td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;b&gt;Note:&lt;/b&gt; Due to substantial changes in MSigDB, it is recommended that users migrate to GSEA 4.0.0+ when utilizing MSigDB 7.0+ resources.&lt;br&gt;</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;b&gt;Note:&lt;/b&gt; Due to substantial changes in MSigDB, it is recommended that users migrate to GSEA 4.0.0+ when utilizing MSigDB 7.0+ resources.&lt;br&gt;</div></td></tr> <tr><td class='diff-marker'>−</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>&lt;b&gt;Advisory&lt;/b&gt;: It is strongly recommended that users of MSigDB7/GSEA4.0 '''always''' use the GSEA &quot;Collapse dataset to gene symbols&quot; feature with the provided Symbol Remapping chip file if your dataset was generated with a transcriptome other than ENSEMBL97/GENCODE31. When using this feature the &quot;<del class="diffchange diffchange-inline">omit </del>features with no symbol match&quot; flag (in Advanced Fields) &lt;b&gt;MUST be set to false.&lt;/b&gt;</div></td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>&lt;b&gt;Advisory&lt;/b&gt;: It is strongly recommended that users of MSigDB7/GSEA4.0 '''always''' use the GSEA &quot;Collapse dataset to gene symbols&quot; feature with the provided Symbol Remapping chip file if your dataset was generated with a transcriptome other than ENSEMBL97/GENCODE31. When using this feature <ins class="diffchange diffchange-inline">for symbol remappimng </ins>the &quot;<ins class="diffchange diffchange-inline">Omit </ins>features with no symbol match&quot; flag (in Advanced Fields) &lt;b&gt;MUST be set to false.&lt;/b&gt;</div></td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;h2&gt;Changes to MSigDB Gene Symbol Mapping Procedures&lt;/h2&gt;</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;h2&gt;Changes to MSigDB Gene Symbol Mapping Procedures&lt;/h2&gt;</div></td></tr> <tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l28" >Line 28:</td> <td colspan="2" class="diff-lineno">Line 28:</td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;ul&gt;</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;ul&gt;</div></td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>     &lt;li&gt;A new Gene Symbol CHIP file for the GSEA &quot;Collapse dataset&quot; feature will be supplied in order to facilitate remapping data sets which use gene annotations prior to the ENSEMBL release 97/GENCODE release 31 namespace used in MSigDB 7.0 in to this space for GSEA.&lt;/li&gt;</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>     &lt;li&gt;A new Gene Symbol CHIP file for the GSEA &quot;Collapse dataset&quot; feature will be supplied in order to facilitate remapping data sets which use gene annotations prior to the ENSEMBL release 97/GENCODE release 31 namespace used in MSigDB 7.0 in to this space for GSEA.&lt;/li&gt;</div></td></tr> <tr><td class='diff-marker'>−</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>     &lt;li&gt;When using this feature the &quot;<del class="diffchange diffchange-inline">omit </del>features with no symbol match&quot; flag (in Advanced Fields) &lt;b&gt;MUST be set to false.&lt;/b&gt;&lt;/li&gt;</div></td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>     &lt;li&gt;When using this feature <ins class="diffchange diffchange-inline">for symbol remapping </ins>the &quot;<ins class="diffchange diffchange-inline">Omit </ins>features with no symbol match&quot; flag (in Advanced Fields) &lt;b&gt;MUST be set to false.&lt;/b&gt;&lt;/li&gt;</div></td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>     &lt;li&gt;New CHIP files have been provided to enable the use of data sets containing Mouse/Rat gene symbols directly through the use of the GSEA &quot;Collapse dataset&quot; feature. These annotations are derived from ENSEMBL 97's Mouse and Rat databases respectively, and support experiments from pipelines relying on GENCODE annotations up to GENCODE release M22 (Mouse). Mappings to orthologous Human genes were derived by the procedure described above.&lt;/li&gt;  </div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>     &lt;li&gt;New CHIP files have been provided to enable the use of data sets containing Mouse/Rat gene symbols directly through the use of the GSEA &quot;Collapse dataset&quot; feature. These annotations are derived from ENSEMBL 97's Mouse and Rat databases respectively, and support experiments from pipelines relying on GENCODE annotations up to GENCODE release M22 (Mouse). Mappings to orthologous Human genes were derived by the procedure described above.&lt;/li&gt;  </div></td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>     &lt;li&gt;Previous symbols and aliases for each current gene were provided by their respective symbol authorities (e.g. HGNC for Human, MGI for Mouse, and RGD for Rat).&lt;/li&gt;</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>     &lt;li&gt;Previous symbols and aliases for each current gene were provided by their respective symbol authorities (e.g. HGNC for Human, MGI for Mouse, and RGD for Rat).&lt;/li&gt;</div></td></tr> <tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l44" >Line 44:</td> <td colspan="2" class="diff-lineno">Line 44:</td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>   &lt;li&gt;Rat_Gene_Symbol_Remapping_MSigDB.v7.0.chip&lt;/li&gt;</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>   &lt;li&gt;Rat_Gene_Symbol_Remapping_MSigDB.v7.0.chip&lt;/li&gt;</div></td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;/ul&gt;</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;/ul&gt;</div></td></tr> <tr><td class='diff-marker'>−</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>     &lt;li&gt;&lt;b&gt;When using this feature the &quot;<del class="diffchange diffchange-inline">omit </del>features with no symbol match&quot; flag (in Advanced Fields) MUST be set to false. &lt;/b&gt;</div></td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>     &lt;li&gt;&lt;b&gt;When using this feature <ins class="diffchange diffchange-inline">for symbol remapping </ins>the &quot;<ins class="diffchange diffchange-inline">Omit </ins>features with no symbol match&quot; flag (in Advanced Fields) MUST be set to false. &lt;/b&gt;</div></td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;br&gt; This is not necessary if your data set was generated using ENSEMBL97 or GENCODE 31 transcriptomes. This is a change from our previous recommendation.&lt;/li&gt;</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;br&gt; This is not necessary if your data set was generated using ENSEMBL97 or GENCODE 31 transcriptomes. This is a change from our previous recommendation.&lt;/li&gt;</div></td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;/ul&gt;</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;/ul&gt;</div></td></tr> </table> Thu, 22 Aug 2019 16:29:32 GMT Acastanza https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Talk:MSigDB_v7.0_Release_Notes Acastanza at 15:51, 22 August 2019 https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=MSigDB_v7.0_Release_Notes&diff=4333&oldid=prev https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=MSigDB_v7.0_Release_Notes&diff=4333&oldid=prev <p></p> <table class="diff diff-contentalign-left" data-mw="interface"> <col class="diff-marker" /> <col class="diff-content" /> <col class="diff-marker" /> <col class="diff-content" /> <tr class="diff-title" lang="en"> <td colspan="2" style="background-color: #fff; color: #222; text-align: center;">← Older revision</td> <td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 15:51, 22 August 2019</td> </tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l10" >Line 10:</td> <td colspan="2" class="diff-lineno">Line 10:</td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;b&gt;Note:&lt;/b&gt; Due to substantial changes in MSigDB, it is recommended that users migrate to GSEA 4.0.0+ when utilizing MSigDB 7.0+ resources.&lt;br&gt;</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;b&gt;Note:&lt;/b&gt; Due to substantial changes in MSigDB, it is recommended that users migrate to GSEA 4.0.0+ when utilizing MSigDB 7.0+ resources.&lt;br&gt;</div></td></tr> <tr><td class='diff-marker'>−</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>&lt;b&gt;Advisory&lt;/b&gt;: It is strongly recommended that users of MSigDB7/GSEA4.0 '''always''' use the GSEA &quot;Collapse dataset to gene symbols&quot; feature with the provided Symbol Remapping chip file if your dataset was generated with a transcriptome other than ENSEMBL97/GENCODE31.</div></td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>&lt;b&gt;Advisory&lt;/b&gt;: It is strongly recommended that users of MSigDB7/GSEA4.0 '''always''' use the GSEA &quot;Collapse dataset to gene symbols&quot; feature with the provided Symbol Remapping chip file if your dataset was generated with a transcriptome other than ENSEMBL97/GENCODE31. <ins class="diffchange diffchange-inline">When using this feature the &quot;omit features with no symbol match&quot; flag (in Advanced Fields) &lt;b&gt;MUST be set to false.&lt;/b&gt;</ins></div></td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;h2&gt;Changes to MSigDB Gene Symbol Mapping Procedures&lt;/h2&gt;</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;h2&gt;Changes to MSigDB Gene Symbol Mapping Procedures&lt;/h2&gt;</div></td></tr> <tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l28" >Line 28:</td> <td colspan="2" class="diff-lineno">Line 28:</td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;ul&gt;</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;ul&gt;</div></td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>     &lt;li&gt;A new Gene Symbol CHIP file for the GSEA &quot;Collapse dataset&quot; feature will be supplied in order to facilitate remapping data sets which use gene annotations prior to the ENSEMBL release 97/GENCODE release 31 namespace used in MSigDB 7.0 in to this space for GSEA.&lt;/li&gt;</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>     &lt;li&gt;A new Gene Symbol CHIP file for the GSEA &quot;Collapse dataset&quot; feature will be supplied in order to facilitate remapping data sets which use gene annotations prior to the ENSEMBL release 97/GENCODE release 31 namespace used in MSigDB 7.0 in to this space for GSEA.&lt;/li&gt;</div></td></tr> <tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">    &lt;li&gt;When using this feature the &quot;omit features with no symbol match&quot; flag (in Advanced Fields) &lt;b&gt;MUST be set to false.&lt;/b&gt;&lt;/li&gt;</ins></div></td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>     &lt;li&gt;New CHIP files have been provided to enable the use of data sets containing Mouse/Rat gene symbols directly through the use of the GSEA &quot;Collapse dataset&quot; feature. These annotations are derived from ENSEMBL 97's Mouse and Rat databases respectively, and support experiments from pipelines relying on GENCODE annotations up to GENCODE release M22 (Mouse). Mappings to orthologous Human genes were derived by the procedure described above.&lt;/li&gt;  </div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>     &lt;li&gt;New CHIP files have been provided to enable the use of data sets containing Mouse/Rat gene symbols directly through the use of the GSEA &quot;Collapse dataset&quot; feature. These annotations are derived from ENSEMBL 97's Mouse and Rat databases respectively, and support experiments from pipelines relying on GENCODE annotations up to GENCODE release M22 (Mouse). Mappings to orthologous Human genes were derived by the procedure described above.&lt;/li&gt;  </div></td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>     &lt;li&gt;Previous symbols and aliases for each current gene were provided by their respective symbol authorities (e.g. HGNC for Human, MGI for Mouse, and RGD for Rat).&lt;/li&gt;</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>     &lt;li&gt;Previous symbols and aliases for each current gene were provided by their respective symbol authorities (e.g. HGNC for Human, MGI for Mouse, and RGD for Rat).&lt;/li&gt;</div></td></tr> <tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l37" >Line 37:</td> <td colspan="2" class="diff-lineno">Line 38:</td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;ul&gt;</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;ul&gt;</div></td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>     &lt;li&gt;Due to substantial changes in MSigDB, it is recommended that users '''migrate to GSEA 4.0.0+ when utilizing MSigDB 7.0+''' resources.&lt;/li&gt;</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>     &lt;li&gt;Due to substantial changes in MSigDB, it is recommended that users '''migrate to GSEA 4.0.0+ when utilizing MSigDB 7.0+''' resources.&lt;/li&gt;</div></td></tr> <tr><td class='diff-marker'>−</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>     &lt;li&gt;It is strongly recommended that users of MSigDB7/GSEA4.0 '''always''' use the GSEA &quot;Collapse dataset to gene symbols&quot; feature with the provided Symbol Remapping chip <del class="diffchange diffchange-inline">file </del>'''even if your experiment is already in the gene symbols namespace''' as this will ensure that your gene symbols are matched to those used in MSigDB7<del class="diffchange diffchange-inline">:</del></div></td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>     &lt;li&gt;It is strongly recommended that users of MSigDB7/GSEA4.0 '''always''' use the GSEA &quot;Collapse dataset to gene symbols&quot; feature with <ins class="diffchange diffchange-inline">following </ins>the provided Symbol Remapping chip <ins class="diffchange diffchange-inline">files </ins>'''even if your experiment is already in the gene symbols namespace''' as this will ensure that your gene symbols are matched to those used in MSigDB7<ins class="diffchange diffchange-inline">.</ins></div></td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;ul&gt;</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;ul&gt;</div></td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>   &lt;li&gt;Human_Symbol_with_Remapping_MSigDB.v7.0.chip&lt;/li&gt;</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>   &lt;li&gt;Human_Symbol_with_Remapping_MSigDB.v7.0.chip&lt;/li&gt;</div></td></tr> <tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l43" >Line 43:</td> <td colspan="2" class="diff-lineno">Line 44:</td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>   &lt;li&gt;Rat_Gene_Symbol_Remapping_MSigDB.v7.0.chip&lt;/li&gt;</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>   &lt;li&gt;Rat_Gene_Symbol_Remapping_MSigDB.v7.0.chip&lt;/li&gt;</div></td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;/ul&gt;</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;/ul&gt;</div></td></tr> <tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">    &lt;li&gt;&lt;b&gt;When using this feature the &quot;omit features with no symbol match&quot; flag (in Advanced Fields) MUST be set to false. &lt;/b&gt;</ins></div></td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;br&gt; This is not necessary if your data set was generated using ENSEMBL97 or GENCODE 31 transcriptomes. This is a change from our previous recommendation.&lt;/li&gt;</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;br&gt; This is not necessary if your data set was generated using ENSEMBL97 or GENCODE 31 transcriptomes. This is a change from our previous recommendation.&lt;/li&gt;</div></td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;/ul&gt;</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;/ul&gt;</div></td></tr> </table> Thu, 22 Aug 2019 15:51:15 GMT Acastanza https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Talk:MSigDB_v7.0_Release_Notes Eby at 05:20, 20 August 2019 https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=MSigDB_v7.0_Release_Notes&diff=4323&oldid=prev https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=MSigDB_v7.0_Release_Notes&diff=4323&oldid=prev <p></p> <table class="diff diff-contentalign-left" data-mw="interface"> <col class="diff-marker" /> <col class="diff-content" /> <col class="diff-marker" /> <col class="diff-content" /> <tr class="diff-title" lang="en"> <td colspan="2" style="background-color: #fff; color: #222; text-align: center;">← Older revision</td> <td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 05:20, 20 August 2019</td> </tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l83" >Line 83:</td> <td colspan="2" class="diff-lineno">Line 83:</td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>     &lt;li&gt;The original data source annotation for the gene sets ''HAN_SATB1_TARGETS_UP/DN'' had been inadvertently switched. ''HAN_SATB1_TARGETS_UP'' now correctly refers to Supplementary Table 3-b, and ''HAN_SATB1_TARGETS_DN'' now correctly refers to Supplementary Table 3-c, of the original source publication.&lt;/li&gt;</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>     &lt;li&gt;The original data source annotation for the gene sets ''HAN_SATB1_TARGETS_UP/DN'' had been inadvertently switched. ''HAN_SATB1_TARGETS_UP'' now correctly refers to Supplementary Table 3-b, and ''HAN_SATB1_TARGETS_DN'' now correctly refers to Supplementary Table 3-c, of the original source publication.&lt;/li&gt;</div></td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>     &lt;li&gt;Four gene sets were incorrectly attributed to PubMed ID: 17906691, Author: Mantovani G., et al.: ''MANTOVANI_NFKB_TARGETS_UP, MANTOVANI_NFKB_TARGETS_DN, MANTOVANI_VIRAL_GPCR_SIGNALING_DN, MANTOVANI_VIRAL_GPCR_SIGNALING_UP'' these gene sets have been renamed and reassigned to reflect the correct PMID and author. PMID: 17934524, Author: Martin D., et al. The gene set names have been edited to reflect this correction. See: ''MARTIN_NFKB_TARGETS_UP, MARTIN_NFKB_TARGETS_DN, MARTIN_VIRAL_GPCR_SIGNALING_DN, MARTIN_VIRAL_GPCR_SIGNALING_UP'' &lt;/li&gt;</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>     &lt;li&gt;Four gene sets were incorrectly attributed to PubMed ID: 17906691, Author: Mantovani G., et al.: ''MANTOVANI_NFKB_TARGETS_UP, MANTOVANI_NFKB_TARGETS_DN, MANTOVANI_VIRAL_GPCR_SIGNALING_DN, MANTOVANI_VIRAL_GPCR_SIGNALING_UP'' these gene sets have been renamed and reassigned to reflect the correct PMID and author. PMID: 17934524, Author: Martin D., et al. The gene set names have been edited to reflect this correction. See: ''MARTIN_NFKB_TARGETS_UP, MARTIN_NFKB_TARGETS_DN, MARTIN_VIRAL_GPCR_SIGNALING_DN, MARTIN_VIRAL_GPCR_SIGNALING_UP'' &lt;/li&gt;</div></td></tr> <tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">    &lt;li&gt;Due to an error, the members were incorrect in 17 of the ''GARGALOVIC'' sets (PubMed ID: 16912112).  Likewise, +7 new gene sets that were missed earlier have been added.&lt;/li&gt;</ins></div></td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;/ul&gt;</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;/ul&gt;</div></td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr> </table> Tue, 20 Aug 2019 05:20:44 GMT Eby https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Talk:MSigDB_v7.0_Release_Notes