https://wiki.biouml.org/index.php?action=history&feed=atom&title=Identify_enriched_composite_modules_in_promoters_%28GTRD%29_%28workflow%29 2026-04-21T20:14:32Z Revision history for this page on the wiki MediaWiki 1.20.3 https://wiki.biouml.org/index.php?title=Identify_enriched_composite_modules_in_promoters_(GTRD)_(workflow)&diff=7871&oldid=prev 2019-03-12T09:34:52Z

<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 5:</td> <td colspan="2" class="diff-lineno">Line 5:</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:Identify-enriched-composite-modules-in-promoters-GTRD-workflow-overview.png|400px]]</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>[[File:Identify-enriched-composite-modules-in-promoters-GTRD-workflow-overview.png|400px]]</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;">== Description ==</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><ins style="color: red; font-weight: bold; text-decoration: none;">This workflow is designed to find pairs of sites in the promoters of the input gene set. This workflow enables the identification of combinations of several enriched TFBSs in the promoters of the genes under study (Yes-set). The resulting composite module differentiates the Yes-set from a background set (No-set)</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><ins style="color: red; font-weight: bold; text-decoration: none;"></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><ins style="color: red; font-weight: bold; text-decoration: none;">In the first part of the workflow, the enriched motifs are identified by the method Search for enriched TFBSs. The default profile used is the uniprobe profile from GTRD database. Motifs with an '''enrichment of &gt;1.0''' fold serve as a basis for constructing a specific profile, and this profile is used to run site search on the promoters of this input gene set .</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><ins style="color: red; font-weight: bold; text-decoration: none;"></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><ins style="color: red; font-weight: bold; text-decoration: none;">In the second part of this workflow, composite modules are identified based on the enriched TFBSs.</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><ins style="color: red; font-weight: bold; text-decoration: none;"></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><ins style="color: red; font-weight: bold; text-decoration: none;">This workflow identifies pairs of sites. By default, the minimum and maximum numbers of pairs are given as 2 and 8. You can change these parameters according to the number of pairs you aim to identify. The number of iterations of the genetic algorithm is 300 by default, and can be adapted as required.</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><ins style="color: red; font-weight: bold; text-decoration: none;"></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><ins style="color: red; font-weight: bold; text-decoration: none;">The results folder consists of several folders and files including the enriched motifs table, composite modules table and Profile. </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><ins style="color: red; font-weight: bold; text-decoration: none;"></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><ins style="color: red; font-weight: bold; text-decoration: none;">'''Note:''' This workflow may take more time depending on the size of the Yes and No sets and on the number of iterations. The recommended size of the Yes set is 150 genes maximum, and the recommended size of the No set is 300 genes maximum. The maximum recommended number of iterations is 300</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><ins style="color: red; font-weight: bold; text-decoration: none;"></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><ins style="color: red; font-weight: bold; text-decoration: none;">&quot;</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><ins style="color: red; font-weight: bold; text-decoration: none;"></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><ins style="color: red; font-weight: bold; text-decoration: none;"> </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><ins style="color: red; font-weight: bold; text-decoration: none;"></ins></div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>== Parameters ==</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>== Parameters ==</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>;Input Yes gene set</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>;Input Yes gene set</div></td></tr> </table>

WikiBot https://wiki.biouml.org/index.php?title=Identify_enriched_composite_modules_in_promoters_(GTRD)_(workflow)&diff=7103&oldid=prev 2017-02-13T12:02:20Z

<p>Protected &quot;<a href="/index.php/Identify_enriched_composite_modules_in_promoters_(GTRD)_(workflow)" title="Identify enriched composite modules in promoters (GTRD) (workflow)">Identify enriched composite modules in promoters (GTRD) (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 12:02, 13 February 2017</td> </tr></table>

WikiBot https://wiki.biouml.org/index.php?title=Identify_enriched_composite_modules_in_promoters_(GTRD)_(workflow)&diff=7098&oldid=prev 2017-02-13T12:02:17Z

<p>Automatic synchronization with BioUML</p> <p><b>New page</b></p><div>;Workflow title<br /> :Identify enriched composite modules in promoters (GTRD)<br /> ;Provider<br /> :[[geneXplain GmbH]]<br /> == Workflow overview ==<br /> [[File:Identify-enriched-composite-modules-in-promoters-GTRD-workflow-overview.png|400px]]<br /> == Parameters ==<br /> ;Input Yes gene set<br /> ;Input No gene set<br /> ;Species<br /> ;Profile<br /> ;Minimal number of pairs<br /> ;Maximal number of pairs<br /> ;Number of iterations<br /> ;Start promoter<br /> ;End promoter<br /> ;Result folder<br /> <br /> [[Category:Workflows]]<br /> [[Category:GeneXplain workflows]]<br /> [[Category:Autogenerated pages]]</div>

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