Difference between revisions of "Gene set enrichment analysis (Gene table) (workflow)"

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:Gene set enrichment analysis (Gene table)
 
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== Workflow overview ==
 
== Workflow overview ==
 
[[File:Gene-set-enrichment-analysis-Gene-table-workflow-overview.png|400px]]
 
[[File:Gene-set-enrichment-analysis-Gene-table-workflow-overview.png|400px]]

Revision as of 15:47, 18 April 2013

Workflow title
Gene set enrichment analysis (Gene table)
Provider
geneXplain GmbH

Workflow overview

Gene-set-enrichment-analysis-Gene-table-workflow-overview.png

Description

This workflow is designed to perform Gene Set Enrichment Analysis, GSEA, as it is described at http://www.broadinstitute.org/gsea/index.jsp. As input, any gene or protein table that includes fold change (or any other numerical value that can be used as a weighted column) can be taken.

 At the first step, the input table is converted into a table with Ensembl Gene IDs.

This table with Ensembl Gene IDs is subjected to GSEA. Enrichment analysis is done in parallel by the following ontologies: GO biological processes, GO cellular components, GO molecular functions and by the Reactome pathways.

For each ontological term several parameters are calculated, including nominal p-value, ES, NES, as well as hit names, the link to the corresponding ontological term, and the link to open a visualization plot.

Parameters

Input table
Enrichment Weight Column
Enter the name of the column from the Input table with numerical values
Species
Results folder
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