https://wiki.biouml.org/index.php?action=history&feed=atom&title=Find_regulatory_regions_%28analysis%29 2026-04-15T14:03:06Z Revision history for this page on the wiki MediaWiki 1.20.3 https://wiki.biouml.org/index.php?title=Find_regulatory_regions_(analysis)&diff=8873&oldid=prev 2020-12-09T11:15:02Z

<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 11:15, 9 December 2020</td> </tr><tr><td colspan="2" class="diff-lineno">Line 1:</td> <td colspan="2" class="diff-lineno">Line 1:</td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>;Analysis title</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>;Analysis title</div></td></tr> <tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>:[[File:<del class="diffchange diffchange-inline">Default</del>-<del class="diffchange diffchange-inline">analysis</del>-icon.png]] Find regulatory regions</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>:[[File:<ins class="diffchange diffchange-inline">Genome</ins>-<ins class="diffchange diffchange-inline">enhancer-Find-regulatory-regions</ins>-icon.png]] Find regulatory regions</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'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>:[[Biosoft]]</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>:[[Biosoft]]</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>;Class</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>;Class</div></td></tr> <tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>:{{Class|biouml.plugins.genomeenhancer.FindRegulatoryRegions}}</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>:{{Class|biouml.plugins.genomeenhancer<ins class="diffchange diffchange-inline">.analysis</ins>.FindRegulatoryRegions}}</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>;Plugin</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>;Plugin</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>:[[Biouml.plugins.genomeenhancer (plugin)|biouml.plugins.genomeenhancer (Genome Enhancer)]]</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>:[[Biouml.plugins.genomeenhancer (plugin)|biouml.plugins.genomeenhancer (Genome Enhancer)]]</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;">==== 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 method creates a track of regulatory regions for input genes. These regulatory regions can be used in &quot;[[Site search on track (analysis)|Site search on track]]&quot;. If ChIP-seq peaks were selected, regulatory regions will tend to cover peaks intervals. The analysis will first select the peaks inside the input genes extended with flanks. Then intervals around the peak centers will be created, overlapped, and cut to input size (promoter from and promoter to, 1100bp by default). Finally, the closest to TSS interval will be selected as the result. The TSS is taken from Fantom/TSS database (CAGE TSS database parameter). If no peaks are found around the gene, Fantom promoter will be used if tissue type was selected and Ensembl promoter will be used if no tissue type was selected.</ins></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>==== Parameters: ====</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>==== Parameters: ====</div></td></tr> </table>

WikiBot https://wiki.biouml.org/index.php?title=Find_regulatory_regions_(analysis)&diff=7776&oldid=prev 2019-03-12T09:33:28Z

<p>Protected &quot;<a href="/index.php/Find_regulatory_regions_(analysis)" title="Find regulatory regions (analysis)">Find regulatory regions (analysis)</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 09:33, 12 March 2019</td> </tr></table>

WikiBot https://wiki.biouml.org/index.php?title=Find_regulatory_regions_(analysis)&diff=7772&oldid=prev 2019-03-12T09:33:25Z

<p>Automatic synchronization with BioUML</p> <p><b>New page</b></p><div>;Analysis title<br /> :[[File:Default-analysis-icon.png]] Find regulatory regions<br /> ;Provider<br /> :[[Biosoft]]<br /> ;Class<br /> :{{Class|biouml.plugins.genomeenhancer.FindRegulatoryRegions}}<br /> ;Plugin<br /> :[[Biouml.plugins.genomeenhancer (plugin)|biouml.plugins.genomeenhancer (Genome Enhancer)]]<br /> <br /> ==== Parameters: ====<br /> <br /> * '''Input genes''' – Input genes<br /> * '''ChIP-seq peaks''' – ChIP-seq peaks<br /> * '''Ensembl database''' – Ensembl database<br /> * '''CAGE TSS database''' – Select type of database to extract TSSs<br /> * '''Cell/Tissue condition''' – Cell/Tissue condition<br /> * '''TSS selection''' – Selection of TSS if multiple TSSs are known<br /> * '''Promoter from''' – Promoter from<br /> * '''Promoter to''' – Promoter to<br /> * '''Shift of left gene bound position''' (expert) – Shift of left gene bound position<br /> * '''Shift of right gene bound position''' (expert) – Shift of right gene bound position<br /> * '''Regulatory region from''' (expert) – Regulatory region from<br /> * '''Regulatory region to''' (expert) – Regulatory region to<br /> * '''Output path''' – Path for the output track<br /> <br /> [[Category:Analyses]]<br /> [[Category:Genome enhancer (analyses group)]]<br /> [[Category:Biosoft analyses]]<br /> [[Category:Autogenerated pages]]</div>

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