https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=GSEA_v2.1.0._Release_Notes&feed=atom&action=history GSEA v2.1.0. Release Notes - Revision history 2024-03-28T14:29:23Z Revision history for this page on the wiki MediaWiki 1.34.4 https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=GSEA_v2.1.0._Release_Notes&diff=3844&oldid=prev Liberzon at 18:46, 12 March 2015 2015-03-12T18:46:17Z <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 18:46, 12 March 2015</td> </tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l2" >Line 2:</td> <td colspan="2" class="diff-lineno">Line 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;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;</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>In collaboration with the [http://www.baderlab.org/ Bader lab] at the University of Toronto, we have added Enrichment Map visualization as one of the steps in a GSEA analysis.  Enrichment Map visualization organizes gene sets into a network work two gene sets are connected in the enrichment map if they have high overlap, i.e., if they share many of the same genes.  Applying automatic layout techniques, groups of inter-related gene sets will tend to cluster together, providing a much easier and intuitive visualization of the enrichment results.  For example, the resulting enrichment map might reveal distinct clusters of gene sets associated with the Cell Cycle, Transcription, Translation, DNA Metabolism, etc.&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>In collaboration with the [http://www.baderlab.org/ Bader lab] at the University of Toronto, we have added Enrichment Map visualization as one of the steps in a GSEA analysis.  Enrichment Map visualization organizes gene sets into a network work two gene sets are connected in the enrichment map if they have high overlap, i.e., if they share many of the same genes.  Applying automatic layout techniques, groups of inter-related gene sets will tend to cluster together, providing a much easier and intuitive visualization of the enrichment results.  For example, the resulting enrichment map might reveal distinct clusters of gene sets associated with the Cell Cycle, Transcription, Translation, DNA Metabolism, etc.&lt;/p&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;p&gt;There is now a button on GSEA's main user interface for initiating the creation of an enrichment map of GSEA results directly from the GSEA desktop application.  Users can create multiple enrichment maps from this interface; they can also compare two different enrichment results within a single map.&lt;/p&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;p&gt;Further information on this feature, along with guided, step-by-step tutorial, is available [http://www.baderlab.org/Software/EnrichmentMap/AutoEMFromGSEA here].&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;Further information on this feature, along with guided, step-by-step tutorial, is available [http://www.baderlab.org/Software/EnrichmentMap/AutoEMFromGSEA here].&lt;/p&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;p&gt;There is now a button on GSEA's main user interface for initiating the creation of an enrichment map of GSEA results directly from the GSEA desktop application.  Users can create multiple enrichment maps from this interface; they can also compare two different enrichment results within a single map.&lt;/p&gt;</del></div></td><td colspan="2"> </td></tr> </table> Liberzon https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=GSEA_v2.1.0._Release_Notes&diff=3843&oldid=prev Liberzon at 18:13, 12 March 2015 2015-03-12T18:13:39Z <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 18:13, 12 March 2015</td> </tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l1" >Line 1:</td> <td colspan="2" class="diff-lineno">Line 1:</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>GSEA v2.1.0 has the following upgrades:</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>GSEA v2.1.0 has the following upgrades:</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;<del class="diffchange diffchange-inline">ol</del>&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;<ins class="diffchange diffchange-inline">p</ins>&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;</del>In collaboration with the [http://www.baderlab.org/ Bader lab] at the University of Toronto, we have added Enrichment Map visualization as one of the steps in a GSEA analysis.  Enrichment Map visualization organizes gene sets into a network work two gene sets are connected in the enrichment map if they have high overlap, i.e., if they share many of the same genes.  Applying automatic layout techniques, groups of inter-related gene sets will tend to cluster together, providing a much easier and intuitive visualization of the enrichment results.  For example, the resulting enrichment map might reveal distinct clusters of gene sets associated with the Cell Cycle, Transcription, Translation, DNA Metabolism, etc.</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>In collaboration with the [http://www.baderlab.org/ Bader lab] at the University of Toronto, we have added Enrichment Map visualization as one of the steps in a GSEA analysis.  Enrichment Map visualization organizes gene sets into a network work two gene sets are connected in the enrichment map if they have high overlap, i.e., if they share many of the same genes.  Applying automatic layout techniques, groups of inter-related gene sets will tend to cluster together, providing a much easier and intuitive visualization of the enrichment results.  For example, the resulting enrichment map might reveal distinct clusters of gene sets associated with the Cell Cycle, Transcription, Translation, DNA Metabolism, etc.<ins class="diffchange diffchange-inline">&lt;/p&gt;</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>Further information on this feature, along with guided, step-by-step tutorial, is available [http://www.baderlab.org/Software/EnrichmentMap/AutoEMFromGSEA here]<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><ins class="diffchange diffchange-inline">&lt;p&gt;</ins>Further information on this feature, along with guided, step-by-step tutorial, is available [http://www.baderlab.org/Software/EnrichmentMap/AutoEMFromGSEA here].&lt;/<ins class="diffchange diffchange-inline">p</ins>&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;</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;<ins class="diffchange diffchange-inline">p</ins>&gt;There is now a button on GSEA's main user interface for initiating the creation of an enrichment map of GSEA results directly from the GSEA desktop application.  Users can create multiple enrichment maps from this interface; they can also compare two different enrichment results within a single map.&lt;/<ins class="diffchange diffchange-inline">p</ins>&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;Improved text describing error 1001.  Now reads &quot;After pruning, none of the gene sets passed size thresholds&quot;.  This communicates that tests to determine whether gene sets pass size threshold are done AFTER gene sets have been pruned to remove genes that do not appear in the gebe expression data file or ranked gene list file</del>.&lt;/<del class="diffchange diffchange-inline">li</del>&gt;</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>&lt;<del class="diffchange diffchange-inline">li</del>&gt;There is now a button on GSEA's main user interface for initiating the creation of an enrichment map of GSEA results directly from the GSEA desktop application.  Users can create multiple enrichment maps from this interface; they can also compare two different enrichment results within a single map.&lt;/<del class="diffchange diffchange-inline">li&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 class="diffchange diffchange-inline">&lt;/ol</del>&gt;</div></td><td colspan="2"> </td></tr> </table> Liberzon https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=GSEA_v2.1.0._Release_Notes&diff=3842&oldid=prev Liberzon at 16:50, 12 March 2015 2015-03-12T16:50:42Z <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 16:50, 12 March 2015</td> </tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l1" >Line 1:</td> <td colspan="2" class="diff-lineno">Line 1:</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>GSEA v2.1.0 has the following upgrades:</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>GSEA v2.1.0 has the following upgrades:</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;ol&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;ol&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;In collaboration with the [http://www.baderlab.org/ Bader lab] at the University of Toronto, we have added Enrichment Map visualization as one of the steps in a GSEA analysis.  Enrichment Map visualization organizes gene sets into a network work two gene sets are connected in the enrichment map if they have high overlap, i.e., if they share many of the same genes.  Applying automatic layout techniques, groups of inter-related gene sets will tend to cluster together, providing a much easier and intuitive visualization of the enrichment results.  For example, the resulting enrichment map might reveal distinct clusters of gene sets associated with the Cell Cycle, Transcription, Translation, DNA Metabolism, etc.&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;In collaboration with the [http://www.baderlab.org/ Bader lab] at the University of Toronto, we have added Enrichment Map visualization as one of the steps in a GSEA analysis.  Enrichment Map visualization organizes gene sets into a network work two gene sets are connected in the enrichment map if they have high overlap, i.e., if they share many of the same genes.  Applying automatic layout techniques, groups of inter-related gene sets will tend to cluster together, providing a much easier and intuitive visualization of the enrichment results.  For example, the resulting enrichment map might reveal distinct clusters of gene sets associated with the Cell Cycle, Transcription, Translation, DNA Metabolism, etc.</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">Further information on this feature, along with guided, step-by-step tutorial, is available [http://www.baderlab.org/Software/EnrichmentMap/AutoEMFromGSEA here].</ins></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>&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;Improved text describing error 1001.  Now reads &quot;After pruning, none of the gene sets passed size thresholds&quot;.  This communicates that tests to determine whether gene sets pass size threshold are done AFTER gene sets have been pruned to remove genes that do not appear in the gebe expression data file or ranked gene list file.&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;Improved text describing error 1001.  Now reads &quot;After pruning, none of the gene sets passed size thresholds&quot;.  This communicates that tests to determine whether gene sets pass size threshold are done AFTER gene sets have been pruned to remove genes that do not appear in the gebe expression data file or ranked gene list file.&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;There is now a button on GSEA's main user interface for initiating the creation of an enrichment map of GSEA results directly from the GSEA desktop application.  Users can create multiple enrichment maps from this interface; they can also compare two different enrichment results within a single map.&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;There is now a button on GSEA's main user interface for initiating the creation of an enrichment map of GSEA results directly from the GSEA desktop application.  Users can create multiple enrichment maps from this interface; they can also compare two different enrichment results within a single map.&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;Further information on this feature, along with guided, step-by-step tutorial, is available [http://www.baderlab.org/Software/EnrichmentMap/AutoEMFromGSEA here]&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;/ol&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;/ol&gt;</div></td></tr> </table> Liberzon https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=GSEA_v2.1.0._Release_Notes&diff=3841&oldid=prev Liberzon at 16:29, 12 March 2015 2015-03-12T16:29:59Z <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, 12 March 2015</td> </tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l1" >Line 1:</td> <td colspan="2" class="diff-lineno">Line 1:</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>GSEA v2.1.0 has the following upgrades:</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>GSEA v2.1.0 has the following upgrades:</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;<del class="diffchange diffchange-inline">ul</del>&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;<ins class="diffchange diffchange-inline">ol</ins>&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;In collaboration with the [http://www.baderlab.org/ Bader lab] at the University of Toronto, we have added Enrichment Map visualization as one of the steps in a GSEA analysis.  Enrichment Map visualization organizes gene sets into a network work two gene sets are connected in the enrichment map if they have high overlap, i.e., if they share many of the same genes.  Applying automatic layout techniques, groups of inter-related gene sets will tend to cluster together, providing a much easier and intuitive visualization of the enrichment results.  For example, the resulting enrichment map might reveal distinct clusters of gene sets associated with the Cell Cycle, Transcription, Translation, DNA Metabolism, etc.&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;In collaboration with the [http://www.baderlab.org/ Bader lab] at the University of Toronto, we have added Enrichment Map visualization as one of the steps in a GSEA analysis.  Enrichment Map visualization organizes gene sets into a network work two gene sets are connected in the enrichment map if they have high overlap, i.e., if they share many of the same genes.  Applying automatic layout techniques, groups of inter-related gene sets will tend to cluster together, providing a much easier and intuitive visualization of the enrichment results.  For example, the resulting enrichment map might reveal distinct clusters of gene sets associated with the Cell Cycle, Transcription, Translation, DNA Metabolism, etc.&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;Improved text describing error 1001.  Now reads &quot;After pruning, none of the gene sets passed size thresholds&quot;.  This communicates that tests to determine whether gene sets pass size threshold are done AFTER gene sets have been pruned to remove genes that do not appear in the gebe expression data file or ranked gene list file.&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;Improved text describing error 1001.  Now reads &quot;After pruning, none of the gene sets passed size thresholds&quot;.  This communicates that tests to determine whether gene sets pass size threshold are done AFTER gene sets have been pruned to remove genes that do not appear in the gebe expression data file or ranked gene list file.&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;There is now a button on GSEA's main user interface for initiating the creation of an enrichment map of GSEA results directly from the GSEA desktop application.  Users can create multiple enrichment maps from this interface; they can also compare two different enrichment results within a single map.&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;There is now a button on GSEA's main user interface for initiating the creation of an enrichment map of GSEA results directly from the GSEA desktop application.  Users can create multiple enrichment maps from this interface; they can also compare two different enrichment results within a single map.&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;Further information on this feature, along with guided, step-by-step tutorial, is available [http://www.baderlab.org/Software/EnrichmentMap/AutoEMFromGSEA here]&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;Further information on this feature, along with guided, step-by-step tutorial, is available [http://www.baderlab.org/Software/EnrichmentMap/AutoEMFromGSEA here]&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;/<del class="diffchange diffchange-inline">ul</del>&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;/<ins class="diffchange diffchange-inline">ol</ins>&gt;</div></td></tr> </table> Liberzon https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=GSEA_v2.1.0._Release_Notes&diff=3838&oldid=prev Liberzon at 16:28, 12 March 2015 2015-03-12T16:28:16Z <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 16:28, 12 March 2015</td> </tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l1" >Line 1:</td> <td colspan="2" class="diff-lineno">Line 1:</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>GSEA v2.1.0 has the following upgrades:</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>GSEA v2.1.0 has the following upgrades:</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;<del class="diffchange diffchange-inline">ol</del>&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;<ins class="diffchange diffchange-inline">ul</ins>&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;In collaboration with the [http://www.baderlab.org/ Bader lab] at the University of Toronto, we have added Enrichment Map visualization as one of the steps in a GSEA analysis.  Enrichment Map visualization organizes gene sets into a network work two gene sets are connected in the enrichment map if they have high overlap, i.e., if they share many of the same genes.  Applying automatic layout techniques, groups of inter-related gene sets will tend to cluster together, providing a much easier and intuitive visualization of the enrichment results.  For example, the resulting enrichment map might reveal distinct clusters of gene sets associated with the Cell Cycle, Transcription, Translation, DNA Metabolism, etc.&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;In collaboration with the [http://www.baderlab.org/ Bader lab] at the University of Toronto, we have added Enrichment Map visualization as one of the steps in a GSEA analysis.  Enrichment Map visualization organizes gene sets into a network work two gene sets are connected in the enrichment map if they have high overlap, i.e., if they share many of the same genes.  Applying automatic layout techniques, groups of inter-related gene sets will tend to cluster together, providing a much easier and intuitive visualization of the enrichment results.  For example, the resulting enrichment map might reveal distinct clusters of gene sets associated with the Cell Cycle, Transcription, Translation, DNA Metabolism, etc.&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;Improved text describing error 1001.  Now reads &quot;After pruning, none of the gene sets passed size thresholds&quot;.  This communicates that tests to determine whether gene sets pass size threshold are done AFTER gene sets have been pruned to remove genes that do not appear in the gebe expression data file or ranked gene list file.&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;Improved text describing error 1001.  Now reads &quot;After pruning, none of the gene sets passed size thresholds&quot;.  This communicates that tests to determine whether gene sets pass size threshold are done AFTER gene sets have been pruned to remove genes that do not appear in the gebe expression data file or ranked gene list file.&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;There is now a button on GSEA's main user interface for initiating the creation of an enrichment map of GSEA results directly from the GSEA desktop application.  Users can create multiple enrichment maps from this interface; they can also compare two different enrichment results within a single map.&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;There is now a button on GSEA's main user interface for initiating the creation of an enrichment map of GSEA results directly from the GSEA desktop application.  Users can create multiple enrichment maps from this interface; they can also compare two different enrichment results within a single map.&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;Further information on this feature, along with guided, step-by-step tutorial, is available [http://www.baderlab.org/Software/EnrichmentMap/AutoEMFromGSEA here]&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;Further information on this feature, along with guided, step-by-step tutorial, is available [http://www.baderlab.org/Software/EnrichmentMap/AutoEMFromGSEA here]&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;/<del class="diffchange diffchange-inline">ol</del>&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;/<ins class="diffchange diffchange-inline">ul</ins>&gt;</div></td></tr> </table> Liberzon https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=GSEA_v2.1.0._Release_Notes&diff=3835&oldid=prev Liberzon at 16:18, 12 March 2015 2015-03-12T16:18:38Z <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 16:18, 12 March 2015</td> </tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l4" >Line 4:</td> <td colspan="2" class="diff-lineno">Line 4:</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;Improved text describing error 1001.  Now reads &quot;After pruning, none of the gene sets passed size thresholds&quot;.  This communicates that tests to determine whether gene sets pass size threshold are done AFTER gene sets have been pruned to remove genes that do not appear in the gebe expression data file or ranked gene list file.&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;Improved text describing error 1001.  Now reads &quot;After pruning, none of the gene sets passed size thresholds&quot;.  This communicates that tests to determine whether gene sets pass size threshold are done AFTER gene sets have been pruned to remove genes that do not appear in the gebe expression data file or ranked gene list file.&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;There is now a button on GSEA's main user interface for initiating the creation of an enrichment map of GSEA results directly from the GSEA desktop application.  Users can create multiple enrichment maps from this interface; they can also compare two different enrichment results within a single map.&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;There is now a button on GSEA's main user interface for initiating the creation of an enrichment map of GSEA results directly from the GSEA desktop application.  Users can create multiple enrichment maps from this interface; they can also compare two different enrichment results within a single map.&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;Further information on this feature, along with guided, step-by-step tutorial, is available <del class="diffchange diffchange-inline">at </del>http://www.baderlab.org/Software/EnrichmentMap/AutoEMFromGSEA&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;Further information on this feature, along with guided, step-by-step tutorial, is available <ins class="diffchange diffchange-inline">[</ins>http://www.baderlab.org/Software/EnrichmentMap/AutoEMFromGSEA <ins class="diffchange diffchange-inline">here]</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;/ol&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;/ol&gt;</div></td></tr> </table> Liberzon https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=GSEA_v2.1.0._Release_Notes&diff=3834&oldid=prev Liberzon at 16:17, 12 March 2015 2015-03-12T16:17:38Z <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 16:17, 12 March 2015</td> </tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l1" >Line 1:</td> <td colspan="2" class="diff-lineno">Line 1:</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>GSEA v2.1.0 has the following upgrades:</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>GSEA v2.1.0 has the following upgrades:</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;ol&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;ol&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;<del class="diffchange diffchange-inline">We </del>have added Enrichment Map visualization as one of the steps in a GSEA analysis.  Enrichment Map visualization organizes gene sets into a network work two gene sets are connected in the enrichment map if they have high overlap, i.e., if they share many of the same genes.  Applying automatic layout techniques, groups of inter-related gene sets will tend to cluster together, providing a much easier and intuitive visualization of the enrichment results.  For example, the resulting enrichment map might reveal distinct clusters of gene sets associated with the Cell Cycle, Transcription, Translation, DNA Metabolism, etc.&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;<ins class="diffchange diffchange-inline">In collaboration with the [http://www.baderlab.org/ Bader lab] at the University of Toronto, we </ins>have added Enrichment Map visualization as one of the steps in a GSEA analysis.  Enrichment Map visualization organizes gene sets into a network work two gene sets are connected in the enrichment map if they have high overlap, i.e., if they share many of the same genes.  Applying automatic layout techniques, groups of inter-related gene sets will tend to cluster together, providing a much easier and intuitive visualization of the enrichment results.  For example, the resulting enrichment map might reveal distinct clusters of gene sets associated with the Cell Cycle, Transcription, Translation, DNA Metabolism, etc.&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;Improved text describing error 1001.  Now reads &quot;After pruning, none of the gene sets passed size thresholds&quot;.  This communicates that tests to determine whether gene sets pass size threshold are done AFTER gene sets have been pruned to remove genes that do not appear in the gebe expression data file or ranked gene list file.&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;Improved text describing error 1001.  Now reads &quot;After pruning, none of the gene sets passed size thresholds&quot;.  This communicates that tests to determine whether gene sets pass size threshold are done AFTER gene sets have been pruned to remove genes that do not appear in the gebe expression data file or ranked gene list file.&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;There is now a button on GSEA's main user interface for initiating the creation of an enrichment map of GSEA results directly from the GSEA desktop application.  Users can create multiple enrichment maps from this interface; they can also compare two different enrichment results within a single map.&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;There is now a button on GSEA's main user interface for initiating the creation of an enrichment map of GSEA results directly from the GSEA desktop application.  Users can create multiple enrichment maps from this interface; they can also compare two different enrichment results within a single map.&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;Further information on this feature, along with guided, step-by-step tutorial, is available at http://www.baderlab.org/Software/EnrichmentMap/AutoEMFromGSEA&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;Further information on this feature, along with guided, step-by-step tutorial, is available at http://www.baderlab.org/Software/EnrichmentMap/AutoEMFromGSEA&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;/ol&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;/ol&gt;</div></td></tr> </table> Liberzon https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=GSEA_v2.1.0._Release_Notes&diff=3832&oldid=prev Liberzon at 16:11, 12 March 2015 2015-03-12T16:11:21Z <p></p> <p><b>New page</b></p><div>GSEA v2.1.0 has the following upgrades:<br /> &lt;ol&gt;<br /> &lt;li&gt;We have added Enrichment Map visualization as one of the steps in a GSEA analysis. Enrichment Map visualization organizes gene sets into a network work two gene sets are connected in the enrichment map if they have high overlap, i.e., if they share many of the same genes. Applying automatic layout techniques, groups of inter-related gene sets will tend to cluster together, providing a much easier and intuitive visualization of the enrichment results. For example, the resulting enrichment map might reveal distinct clusters of gene sets associated with the Cell Cycle, Transcription, Translation, DNA Metabolism, etc.&lt;/li&gt;<br /> &lt;li&gt;Improved text describing error 1001. Now reads &quot;After pruning, none of the gene sets passed size thresholds&quot;. This communicates that tests to determine whether gene sets pass size threshold are done AFTER gene sets have been pruned to remove genes that do not appear in the gebe expression data file or ranked gene list file.&lt;/li&gt;<br /> &lt;li&gt;There is now a button on GSEA's main user interface for initiating the creation of an enrichment map of GSEA results directly from the GSEA desktop application. Users can create multiple enrichment maps from this interface; they can also compare two different enrichment results within a single map.&lt;/li&gt;<br /> &lt;li&gt;Further information on this feature, along with guided, step-by-step tutorial, is available at http://www.baderlab.org/Software/EnrichmentMap/AutoEMFromGSEA&lt;/li&gt;<br /> &lt;/ol&gt;</div> Liberzon