https://wiki.biouml.org/index.php?action=history&feed=atom&title=Upstream_analysis_%28TRANSFAC%28R%29_and_GeneWays%29_%28workflow%29 2026-04-13T08:23:35Z Revision history for this page on the wiki MediaWiki 1.20.3 https://wiki.biouml.org/index.php?title=Upstream_analysis_(TRANSFAC(R)_and_GeneWays)_(workflow)&diff=3873&oldid=prev 2013-05-30T06:34:23Z

<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 06:34, 30 May 2013</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:Upstream-analysis-TRANSFAC-R-and-GeneWays-workflow-overview.png|400px]]</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>[[File:Upstream-analysis-TRANSFAC-R-and-GeneWays-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 perform a complete upstream analysis including a search for putative transcription factor binding sites (TFBSs), in the promoters of the input gene set as well as an analysis of the pathways upstream of the suggested TFs. The resulting master regulatory molecules can be considered as new targets, and are candidates for further experimental validations. </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;">As input, any gene or protein table can be submitted. The input consists of two tables, one with the genes under study (Yes set or experiment set), and the other with a background set, or 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 step, both input tables are converted into the corresponding tables with Ensembl Gene IDs applying the “Convert table” analysis.</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 next step, the promoters of the specified gene sets are searched for TFBSs with the help of the “Site search on gene set” analysis. Promoters in this workflow are by default defined as sequences from -1000 to +100 relative to the transcription start sites, as they are annotated in Ensembl. Promoter regions can be specified differently in the input form.  The site search is performed using the TRANSFAC® library of positional weight matrices, PWMs, with the profile vertebrate_non_redundant_minSUM as default. Any other TRANSFAC® profile or user-specific profile can be chosen in the input form.</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 same step, frequencies of putative TFBS are compared between Yes set and No set to identify sites that are enriched in Yes set versus 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;">The output of this step is a list of PWMs the hits of which are enriched in Yes set versus 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;">Next, the list of PWMs is converted into a table of transcription factors with GeneWays IDs using the“Matrices to molecules” analysis. The resulting table is subjected to the “Regulator search” analysis to identify master regulatory molecules in the GeneWays network. For each potential master regulator, FDR, Score, Z-score and Rank sum are calculated.</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 are filtered by Z_Score&gt;1 and Score&gt;0.2 and sorted by the Rank sum column to select statistically significant master regulators.</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 table with the resulting master regulatory molecules is converted into the table Ensembl Gene IDs applying the “Convert table” analysis and further annotated with additional information, gene descriptions and gene symbols via the “Annotate table” analysis. </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;">Finally, networks for the three top master regulatory molecules are visualized as diagrams in the hierarchical layout , via the “Visualize results” method.</ins></div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="background: #cfc; 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color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">:Position relative to TSS, bp</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;">;End of promoter</ins></div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>:Position relative to TSS, bp</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>:Position relative to TSS, bp</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>;Results Folder</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>;Results Folder</div></td></tr> </table>

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<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 18:</td> <td colspan="2" class="diff-lineno">Line 18:</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>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 04:15, 7 May 2013</td> </tr><tr><td colspan="2" class="diff-lineno">Line 10:</td> <td colspan="2" class="diff-lineno">Line 10:</td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>;Input No gene set</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>;Input No gene set</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>;Profile</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>;Profile</div></td></tr> <tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>;<del class="diffchange diffchange-inline">Start </del>of <del class="diffchange diffchange-inline">promotor</del></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>;<ins class="diffchange diffchange-inline">End </ins>of <ins class="diffchange diffchange-inline">promoter</ins></div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>:Position relative to TSS, bp</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>:Position relative to TSS, bp</div></td></tr> <tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>;<del class="diffchange diffchange-inline">End </del>of <del class="diffchange diffchange-inline">promotor</del></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>;<ins class="diffchange diffchange-inline">Start </ins>of <ins class="diffchange diffchange-inline">promoter</ins></div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>:Position relative to TSS, bp</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>:Position relative to TSS, bp</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>;Results Folder</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>;Results Folder</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 19:</td> <td colspan="2" class="diff-lineno">Line 19:</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>

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<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 19:</td> <td colspan="2" class="diff-lineno">Line 19:</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>

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<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>:Upstream analysis (TRANSFAC(R) and GeneWays)</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>:Upstream analysis (TRANSFAC(R) and GeneWays)</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:Upstream-analysis-TRANSFAC-R-and-GeneWays-workflow-overview.png|400px]]</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>[[File:Upstream-analysis-TRANSFAC-R-and-GeneWays-workflow-overview.png|400px]]</div></td></tr> </table>

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<p>Protected &quot;<a href="/index.php/Upstream_analysis_(TRANSFAC(R)_and_GeneWays)_(workflow)" title="Upstream analysis (TRANSFAC(R) and GeneWays) (workflow)">Upstream analysis (TRANSFAC(R) and GeneWays) (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 08:11, 18 April 2013</td> </tr></table>

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<p>Automatic synchronization with BioUML</p> <p><b>New page</b></p><div>;Workflow title<br /> :Upstream analysis (TRANSFAC(R) and GeneWays)<br /> ;Provider<br /> :[[GeneXplain GmbH]]<br /> == Workflow overview ==<br /> [[File:Upstream-analysis-TRANSFAC-R-and-GeneWays-workflow-overview.png|400px]]<br /> == Parameters ==<br /> ;Input Yes gene set<br /> ;Species<br /> ;Input No gene set<br /> ;Profile<br /> ;Start of promotor<br /> :Position relative to TSS, bp<br /> ;End of promotor<br /> :Position relative to TSS, bp<br /> ;Results Folder<br /> :Folder to store results (will be created if not exists)<br /> <br /> [[Category:Workflows]]<br /> [[Category:Autogenerated pages]]</div>

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