https://wiki.biouml.org/index.php?action=history&feed=atom&title=Gene_set_enrichment_analysis_HumanPSD_%28Agilent_probes%29_%28workflow%29 2026-04-13T14:17:28Z Revision history for this page on the wiki MediaWiki 1.20.3 https://wiki.biouml.org/index.php?title=Gene_set_enrichment_analysis_HumanPSD_(Agilent_probes)_(workflow)&diff=7880&oldid=prev 2019-03-12T09:34:54Z

<p>Protected &quot;<a href="/index.php/Gene_set_enrichment_analysis_HumanPSD_(Agilent_probes)_(workflow)" title="Gene set enrichment analysis HumanPSD (Agilent probes) (workflow)">Gene set enrichment analysis HumanPSD (Agilent probes) (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 09:34, 12 March 2019</td> </tr></table>

WikiBot https://wiki.biouml.org/index.php?title=Gene_set_enrichment_analysis_HumanPSD_(Agilent_probes)_(workflow)&diff=7876&oldid=prev 2019-03-12T09:34:53Z

<p>Automatic synchronization with BioUML</p> <p><b>New page</b></p><div>;Workflow title<br /> :Gene set enrichment analysis HumanPSD (Agilent probes)<br /> ;Provider<br /> :[[geneXplain GmbH]]<br /> == Workflow overview ==<br /> [[File:Gene-set-enrichment-analysis-HumanPSD-Agilent-probes-workflow-overview.png|400px]]<br /> == Description ==<br /> This workflow is designed to perform Gene Set Enrichment Analysis, GSEA, as it is described at [http://www.broadinstitute.org/gsea/index.jsp http://www.broadinstitute.org/gsea/index.jsp].  As input, the normalized data with Agilent probeset IDs can be submitted. Such normalized files result from the “Normalize data” procedure under “Analyses/Methods/Data normalization/Normalize Agilent experiment and control”.<br /> <br /> First, the input files are subjected to fold-change calculation. The table with probeset IDs and calculated fold change values is converted into a table with Ensembl Gene IDs. In the next step, the Ensembl genes are annotated with additional information, gene descriptions and gene symbols.<br /> <br /> Finally the annotated Ensembl genes are subjected to GSEA using the HumanPSD&lt;sup&gt;TM&lt;/sup&gt; database. Enrichment analysis is performed using the following ontologies: HumanPSD GO biological processes, HumanPSD GO cellular components, HumanPSD GO molecular function, HumanPSD disease and by the TRANSPATH pathways.<br /> <br /> Output files include enrichment analysis results, a list of annotated Ensemble genes and a histogram of log fold change distribution. For each ontological term several parameters are calculated, including nominal p-value, ES, NES, FDR, rank at max, hit names, the link to the corresponding ontological term, and the link to open a visualization plot.<br /> <br /> == Parameters ==<br /> ;Experiment normalized<br /> ;Control normalized<br /> ;Annotation source<br /> ;Species<br /> ;Results folder<br /> <br /> [[Category:Workflows]]<br /> [[Category:GeneXplain workflows]]<br /> [[Category:Autogenerated pages]]</div>

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