https://wiki.biouml.org/index.php?action=history&feed=atom&title=MEALR_%28tracks%29_%28analysis%29 2026-04-13T10:24:45Z Revision history for this page on the wiki MediaWiki 1.20.3 https://wiki.biouml.org/index.php?title=MEALR_(tracks)_(analysis)&diff=8710&oldid=prev 2020-12-09T11:14:36Z

<p>Protected &quot;<a href="/index.php/MEALR_(tracks)_(analysis)" title="MEALR (tracks) (analysis)">MEALR (tracks) (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 11:14, 9 December 2020</td> </tr></table>

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<p>Automatic synchronization with BioUML</p> <p><b>New page</b></p><div>;Analysis title<br /> :[[File:BSA-MEALR-(tracks)-icon.png]] MEALR (tracks)<br /> ;Provider<br /> :[[geneXplain GmbH]]<br /> ;Class<br /> :{{Class|com.genexplain.analyses.MEALR}}<br /> ;Plugin<br /> :[[Com.genexplain.analyses (plugin)|com.genexplain.analyses (geneXplain analyses)]]<br /> <br /> === MEALR - Motif Enrichment Analysis by Logistic Regression ===<br /> <br /> ==== Parameters ====<br /> <br /> * '''Yes set''' - Study track / Track with intervals of interest<br /> * '''No set''' - Background track / Track of non-bound intervals<br /> * '''Sequence source''' - Choose a deployed sequence source from the pull-down list. Selecting '''Custom''' enables setting of a custom sequence collection<br /> * '''Input motif profile''' - Profile of weight matrices<br /> * '''Output path''' - Path in workspace to store output table<br /> <br /> ==== Output ====<br /> <br /> The output contains two columns. The '''ID''' column contains identifiers of motifs to which MEALR assigned a positive coefficient. The coefficients are listed in the column named '''Coefficient'''.<br /> <br /> ==== Description ====<br /> <br /> MEALR searches for a combination of transcription factor binding motifs that discriminate between a positive (Yes) and a negative (No) sequence set. The Yes sequences are the sequences of interest, e.g. as identified in a ChIP-seq experiment.<br /> <br /> Sparse logistic regression assigns non-zero coefficients to only a small subset of motifs specified by an input profile. The coefficients indicate the importance of a motif for discrimination. Hence, MEALR differs from other site enrichment tools by choosing an optimal subset of motifs from a possibly large motif database.<br /> <br /> Currently, the output contains only the set of motifs with positive coefficients. The larger the coefficient, the more important the corresponding motif was for discriminating between Yes and No sequences.<br /> <br /> [[Category:Analyses]]<br /> [[Category:BSA (analyses group)]]<br /> [[Category:GeneXplain analyses]]<br /> [[Category:Autogenerated pages]]</div>

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