https://wiki.biouml.org/index.php?action=history&feed=atom&title=Identify_enriched_motifs_in_promoters_%28GTRD%29_%28workflow%29Identify enriched motifs in promoters (GTRD) (workflow) - Revision history2026-04-12T21:33:00ZRevision history for this page on the wikiMediaWiki 1.20.3https://wiki.biouml.org/index.php?title=Identify_enriched_motifs_in_promoters_(GTRD)_(workflow)&diff=7872&oldid=prevWikiBot: Automatic synchronization with BioUML2019-03-12T09:34:52Z<p>Automatic synchronization with BioUML</p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>== Workflow overview ==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>== Workflow overview ==</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[File:Identify-enriched-motifs-in-promoters-GTRD-workflow-overview.png|400px]]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[File:Identify-enriched-motifs-in-promoters-GTRD-workflow-overview.png|400px]]</div></td></tr>
<tr><td colspan="2"> </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"> </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 individual motifs enriched in the promoters of the input gene set as compared with a background set (No set).</ins></div></td></tr>
<tr><td colspan="2"> </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"> </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 '''analyses/Methods/Site analysis/Search for enriched TFBSs (genes)'''. </ins></div></td></tr>
<tr><td colspan="2"> </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"> </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;">Site search is done with the help of the GTRD library of the positional weight matrices, PWMs, namely with the profile moderate threshold. The enriched motifs are filtered with '''Adj_site_FE>1.0''', and a filtered profile is created using the method, ‘Create profile from site model table’. </ins></div></td></tr>
<tr><td colspan="2"> </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"> </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 filtered profile is used to run Site search on gene set on the promoters of the input gene set.</ins></div></td></tr>
<tr><td colspan="2"> </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"> </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 output Sites from this method are converted into Ensembl genes and annotated further with gene description and gene symbol. These Ensembl genes are the Transcription factor genes.</ins></div></td></tr>
<tr><td colspan="2"> </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"> </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 files and folders. The table Enriched Motifs contains those site models, here GTRD matrices, which are enriched in the Yes set in comparison with the No set.</ins></div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>== Parameters ==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>== Parameters ==</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>;Input Yes gene set</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>;Input Yes gene set</div></td></tr>
</table>WikiBothttps://wiki.biouml.org/index.php?title=Identify_enriched_motifs_in_promoters_(GTRD)_(workflow)&diff=6529&oldid=prevWikiBot: Automatic synchronization with BioUML2015-08-25T05:21:52Z<p>Automatic synchronization with BioUML</p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>== Workflow overview ==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>== Workflow overview ==</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[File:Identify-enriched-motifs-in-promoters-GTRD-workflow-overview.png|400px]]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[File:Identify-enriched-motifs-in-promoters-GTRD-workflow-overview.png|400px]]</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;">== Description ==</del></div></td><td colspan="2"> </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;">This workflow finds transcription factor binding sites, TFBS, enriched in the promoters of an input gene set as compared to the promoters of the backgrounds set. Site search is done with the help of the GTRD library of positional weight matrices, PWMs, namely with the profile moderate threshold.</del></div></td><td colspan="2"> </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;"></del></div></td><td colspan="2"> </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;">In the first part of the workflow, the enriched motifs are identified by the method ''Search for enriched TFBSs (genes)''. Filtered enriched motifs serve as a basis to construct a specific profile, and this profile is run on the promoters of the input gene set, method ''Site search on gene set''.</del></div></td><td colspan="2"> </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;"></del></div></td><td colspan="2"> </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;">Yes set and NO set is the gene sets for which you wish to analyse the promoters. By default the workflow uses a subset to 300 genes randomly taken out of the human housekeeping genes as NO set. Filter by TFBS enrichment fold: In this field you can specify the enrichment fold (FE) to filter the motifs. By default it is 1.0, which means all motifs with FE>1.0 will be reported in the resulting table and the same motifs will serve to create a specific profile. If you want to use highly-enriched motifs, you can specify higher thresholds, e.g. 1.1, 1.2 etc, or even 2.0 or 3.0 depending on your Yes and No sets. The promoter region is -1000 to +100 relative to the TSS.</del></div></td><td colspan="2"> </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;"></del></div></td><td colspan="2"> </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;">The result folder contains several files and folders including site search results, annotated transcription factors, Profile table and table with Enriched motifs.</del></div></td><td colspan="2"> </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;"></del></div></td><td colspan="2"> </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;">The table '''Enriched Motifs''' contains those site models, here GTRD matrices, which are enriched in the Yes set in comparison with the No set. Each row of the output table represents the result for one PWM from the input profile. Profile presents only those PWMs with adj. site FE >1. '''Site search analysis output '''serves to visualize enriched motifs in the promoters. The table ''Transcription factors Ensembl genes ''is a list of transcription factors linked to the enriched motifs.</del></div></td><td colspan="2"> </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;"></del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>== Parameters ==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>== Parameters ==</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>;Input Yes gene set</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>;Input Yes gene set</div></td></tr>
</table>WikiBothttps://wiki.biouml.org/index.php?title=Identify_enriched_motifs_in_promoters_(GTRD)_(workflow)&diff=5901&oldid=prevWikiBot: Protected "Identify enriched motifs in promoters (GTRD) (workflow)": Autogenerated page ([edit=sysop] (indefinite))2014-12-11T09:19:06Z<p>Protected "<a href="/index.php/Identify_enriched_motifs_in_promoters_(GTRD)_(workflow)" title="Identify enriched motifs in promoters (GTRD) (workflow)">Identify enriched motifs in promoters (GTRD) (workflow)</a>": Autogenerated page ([edit=sysop] (indefinite))</p>
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<td colspan='1' style="background-color: white; color:black;">← Older revision</td>
<td colspan='1' style="background-color: white; color:black;">Revision as of 09:19, 11 December 2014</td>
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<p><b>New page</b></p><div>;Workflow title<br />
:Identify enriched motifs in promoters (GTRD)<br />
;Provider<br />
:[[geneXplain GmbH]]<br />
== Workflow overview ==<br />
[[File:Identify-enriched-motifs-in-promoters-GTRD-workflow-overview.png|400px]]<br />
== Description ==<br />
This workflow finds transcription factor binding sites, TFBS, enriched in the promoters of an input gene set as compared to the promoters of the backgrounds set. Site search is done with the help of the GTRD library of positional weight matrices, PWMs, namely with the profile moderate threshold.<br />
<br />
In the first part of the workflow, the enriched motifs are identified by the method ''Search for enriched TFBSs (genes)''. Filtered enriched motifs serve as a basis to construct a specific profile, and this profile is run on the promoters of the input gene set, method ''Site search on gene set''.<br />
<br />
Yes set and NO set is the gene sets for which you wish to analyse the promoters. By default the workflow uses a subset to 300 genes randomly taken out of the human housekeeping genes as NO set. Filter by TFBS enrichment fold: In this field you can specify the enrichment fold (FE) to filter the motifs. By default it is 1.0, which means all motifs with FE>1.0 will be reported in the resulting table and the same motifs will serve to create a specific profile. If you want to use highly-enriched motifs, you can specify higher thresholds, e.g. 1.1, 1.2 etc, or even 2.0 or 3.0 depending on your Yes and No sets. The promoter region is -1000 to +100 relative to the TSS.<br />
<br />
The result folder contains several files and folders including site search results, annotated transcription factors, Profile table and table with Enriched motifs.<br />
<br />
The table '''Enriched Motifs''' contains those site models, here GTRD matrices, which are enriched in the Yes set in comparison with the No set. Each row of the output table represents the result for one PWM from the input profile. Profile presents only those PWMs with adj. site FE >1. '''Site search analysis output '''serves to visualize enriched motifs in the promoters. The table ''Transcription factors Ensembl genes ''is a list of transcription factors linked to the enriched motifs.<br />
<br />
== Parameters ==<br />
;Input Yes gene set<br />
;Input No gene set<br />
;Profile<br />
;Species<br />
;Filter by TFBS enrichment fold<br />
:Filter for column Adj. site FE <br />
;Start promoter<br />
;End promoter<br />
;Result folder<br />
<br />
[[Category:Workflows]]<br />
[[Category:GeneXplain workflows]]<br />
[[Category:Autogenerated pages]]</div>WikiBot