https://wiki.biouml.org/index.php?action=history&feed=atom&title=Gene_set_enrichment_analysis_%28Gene_table%29_%28workflow%29 2026-04-13T04:57:17Z Revision history for this page on the wiki MediaWiki 1.20.3 https://wiki.biouml.org/index.php?title=Gene_set_enrichment_analysis_(Gene_table)_(workflow)&diff=7852&oldid=prev 2019-03-12T09:34:44Z

<p>Automatic synchronization with BioUML</p> <table class='diff diff-contentalign-left'> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr style='vertical-align: top;'> <td colspan='2' style="background-color: white; color:black;">← Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 09:34, 12 March 2019</td> </tr><tr><td colspan="2" class="diff-lineno">Line 6:</td> <td colspan="2" class="diff-lineno">Line 6:</td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>[[File:Gene-set-enrichment-analysis-Gene-table-workflow-overview.png|400px]]</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>[[File:Gene-set-enrichment-analysis-Gene-table-workflow-overview.png|400px]]</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>== Description ==</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>== Description ==</div></td></tr> <tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>This workflow is designed to perform Gene Set Enrichment Analysis, GSEA, as it is described at [http://www.broadinstitute.org/gsea/index.jsp http://www.broadinstitute.org/gsea/index.jsp]<del class="diffchange diffchange-inline">. As input, any gene or protein table that includes fold change (or any other numerical value that can be used as a weighted column) can be taken</del>.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>This workflow is designed to perform Gene Set Enrichment Analysis, GSEA, as it is described at [http://www.broadinstitute.org/gsea/index.jsp http://www.broadinstitute.org/gsea/index.jsp].</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline"> At </del>the first step, the input table is converted into a table with Ensembl Gene IDs.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">As input, any gene or protein table that includes fold change (or any other numerical value that can be used as a weighted column) can be taken.</ins></div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>&#160;</div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">At </ins>the first step, the input table is converted into a table with Ensembl Gene IDs.</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>This table with Ensembl Gene IDs is subjected to GSEA. Enrichment analysis is done in parallel by the following ontologies: GO biological processes, GO cellular components, GO molecular functions and by the Reactome pathways.</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>This table with Ensembl Gene IDs is subjected to GSEA. Enrichment analysis is done in parallel by the following ontologies: GO biological processes, GO cellular components, GO molecular functions and by the Reactome pathways.</div></td></tr> </table>

WikiBot https://wiki.biouml.org/index.php?title=Gene_set_enrichment_analysis_(Gene_table)_(workflow)&diff=3501&oldid=prev 2013-05-16T06:28:41Z

<p>Cosmetic changes in category formatting</p> <table class='diff diff-contentalign-left'> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr style='vertical-align: top;'> <td colspan='2' style="background-color: white; color:black;">← Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 06:28, 16 May 2013</td> </tr><tr><td colspan="2" class="diff-lineno">Line 22:</td> <td colspan="2" class="diff-lineno">Line 22:</td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Category:Workflows]]</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Category:Workflows]]</div></td></tr> <tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;">[[Category:Autogenerated pages]]</del></div></td><td colspan="2">&#160;</td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Category:GeneXplain workflows]]</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Category:GeneXplain workflows]]</div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">[[Category:Autogenerated pages]]</ins></div></td></tr> </table>

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<p>geneXplain -&gt; GeneXplain in category name</p> <table class='diff diff-contentalign-left'> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr style='vertical-align: top;'> <td colspan='2' style="background-color: white; color:black;">← Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 04:14, 19 April 2013</td> </tr><tr><td colspan="2" class="diff-lineno">Line 23:</td> <td colspan="2" class="diff-lineno">Line 23:</td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Category:Workflows]]</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Category:Workflows]]</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Category:Autogenerated pages]]</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Category:Autogenerated pages]]</div></td></tr> <tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>[[Category:<del class="diffchange diffchange-inline">geneXplain </del>workflows]]</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>[[Category:<ins class="diffchange diffchange-inline">GeneXplain </ins>workflows]]</div></td></tr> </table>

WikiBot https://wiki.biouml.org/index.php?title=Gene_set_enrichment_analysis_(Gene_table)_(workflow)&diff=1443&oldid=prev 2013-04-19T04:09:04Z

<p>Adding provider-specific categories</p> <table class='diff diff-contentalign-left'> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr style='vertical-align: top;'> <td colspan='2' style="background-color: white; color:black;">← Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 04:09, 19 April 2013</td> </tr><tr><td colspan="2" class="diff-lineno">Line 23:</td> <td colspan="2" class="diff-lineno">Line 23:</td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Category:Workflows]]</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Category:Workflows]]</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Category:Autogenerated pages]]</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Category:Autogenerated pages]]</div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">[[Category:geneXplain workflows]]</ins></div></td></tr> </table>

WikiBot https://wiki.biouml.org/index.php?title=Gene_set_enrichment_analysis_(Gene_table)_(workflow)&diff=1266&oldid=prev 2013-04-18T08:47:35Z

<p>GeneXplain -&gt; geneXplain</p> <table class='diff diff-contentalign-left'> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr style='vertical-align: top;'> <td colspan='2' style="background-color: white; color:black;">← Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 08:47, 18 April 2013</td> </tr><tr><td colspan="2" class="diff-lineno">Line 2:</td> <td colspan="2" class="diff-lineno">Line 2:</td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>:Gene set enrichment analysis (Gene table)</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>:Gene set enrichment analysis (Gene table)</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>;Provider</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>;Provider</div></td></tr> <tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>:[[<del class="diffchange diffchange-inline">GeneXplain </del>GmbH]]</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>:[[<ins class="diffchange diffchange-inline">geneXplain </ins>GmbH]]</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>== Workflow overview ==</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>== Workflow overview ==</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>[[File:Gene-set-enrichment-analysis-Gene-table-workflow-overview.png|400px]]</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>[[File:Gene-set-enrichment-analysis-Gene-table-workflow-overview.png|400px]]</div></td></tr> </table>

WikiBot https://wiki.biouml.org/index.php?title=Gene_set_enrichment_analysis_(Gene_table)_(workflow)&diff=1054&oldid=prev 2013-04-18T08:10:51Z

<p>Protected &quot;<a href="/index.php/Gene_set_enrichment_analysis_(Gene_table)_(workflow)" title="Gene set enrichment analysis (Gene table) (workflow)">Gene set enrichment analysis (Gene table) (workflow)</a>&quot;: Autogenerated page (‎[edit=sysop] (indefinite))</p> <table class='diff diff-contentalign-left'> <tr style='vertical-align: top;'> <td colspan='1' style="background-color: white; color:black;">← Older revision</td> <td colspan='1' style="background-color: white; color:black;">Revision as of 08:10, 18 April 2013</td> </tr></table>

WikiBot https://wiki.biouml.org/index.php?title=Gene_set_enrichment_analysis_(Gene_table)_(workflow)&diff=1051&oldid=prev 2013-04-18T08:10:49Z

<p>Automatic synchronization with BioUML</p> <p><b>New page</b></p><div>;Workflow title<br /> :Gene set enrichment analysis (Gene table)<br /> ;Provider<br /> :[[GeneXplain GmbH]]<br /> == Workflow overview ==<br /> [[File:Gene-set-enrichment-analysis-Gene-table-workflow-overview.png|400px]]<br /> == Description ==<br /> This workflow is designed to perform Gene Set Enrichment Analysis, GSEA, as it is described at [http://www.broadinstitute.org/gsea/index.jsp http://www.broadinstitute.org/gsea/index.jsp]. As input, any gene or protein table that includes fold change (or any other numerical value that can be used as a weighted column) can be taken.<br /> <br />  At the first step, the input table is converted into a table with Ensembl Gene IDs.<br /> <br /> This table with Ensembl Gene IDs is subjected to GSEA. Enrichment analysis is done in parallel by the following ontologies: GO biological processes, GO cellular components, GO molecular functions and by the Reactome pathways.<br /> <br /> For each ontological term several parameters are calculated, including nominal p-value, ES, NES, as well as hit names, the link to the corresponding ontological term, and the link to open a visualization plot.<br /> <br /> == Parameters ==<br /> ;Input table<br /> ;Enrichment Weight Column<br /> :Enter the name of the column from the Input table with numerical values<br /> ;Species<br /> ;Results folder<br /> <br /> [[Category:Workflows]]<br /> [[Category:Autogenerated pages]]</div>

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