https://wiki.biouml.org/index.php?action=history&feed=atom&title=Find_common_effectors_in_networks_%28TRANSPATH%28R%29%29_%28workflow%29 2026-04-12T21:10:55Z Revision history for this page on the wiki MediaWiki 1.20.3 https://wiki.biouml.org/index.php?title=Find_common_effectors_in_networks_(TRANSPATH(R))_(workflow)&diff=3512&oldid=prev 2013-05-16T06:28:50Z

<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 30:</td> <td colspan="2" class="diff-lineno">Line 30:</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 31:</td> <td colspan="2" class="diff-lineno">Line 31:</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 31:</td> <td colspan="2" class="diff-lineno">Line 31:</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>:Find common effectors in networks (TRANSPATH(R))</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>:Find common effectors in networks (TRANSPATH(R))</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:Find-common-effectors-in-networks-TRANSPATH-R-workflow-overview.png|400px]]</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>[[File:Find-common-effectors-in-networks-TRANSPATH-R-workflow-overview.png|400px]]</div></td></tr> </table>

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<p>Protected &quot;<a href="/index.php/Find_common_effectors_in_networks_(TRANSPATH(R))_(workflow)" title="Find common effectors in networks (TRANSPATH(R)) (workflow)">Find common effectors in networks (TRANSPATH(R)) (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 /> :Find common effectors in networks (TRANSPATH(R))<br /> ;Provider<br /> :[[GeneXplain GmbH]]<br /> == Workflow overview ==<br /> [[File:Find-common-effectors-in-networks-TRANSPATH-R-workflow-overview.png|400px]]<br /> == Description ==<br /> This workflow is designed to find effector molecules downstream of an input list of genes. Input file is any gene or protein table.<br /> <br /> At the first step, the input table is converted into a table with TRANSPATH® peptides which is later also present in the output folder.<br /> <br /> This table is annotated with additional information, gene description and gene symbols.<br /> <br /> The annotated table is subjected to Effector search in TRANSPATH® network. For each potential Effector molecule, FDR, Score, and Z-score are calculated.<br /> <br /> The results are filtered by Z_Score&gt;1 and Score&gt;0.2 to select statistically significant Effector nodes.<br /> <br /> Further, the filtered effector molecules are converted to both Ensembl Gene IDs and a list of UniProt protein IDs.<br /> <br /> The table with Ensembl Gene Ids is annotated with additional information, gene description and gene symbols.<br /> <br /> Finally, the table with the effector molecules is sorted by Score and networks for the three top master regulators are visualized as diagrams in the hierarchical layout.<br /> <br /> This workflow is available together with a valid TRANSPATH® license.<br /> <br /> == Parameters ==<br /> ;Input gene set<br /> ;Species<br /> ;Results folder<br /> <br /> [[Category:Workflows]]<br /> [[Category:Autogenerated pages]]</div>

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