Difference between revisions of "Mapping to ontologies for multiple gene sets (workflow)"

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[[File:Mapping-to-ontologies-for-multiple-gene-sets-workflow-overview.png|400px]]
 
[[File:Mapping-to-ontologies-for-multiple-gene-sets-workflow-overview.png|400px]]
 
== Description ==
 
== Description ==
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This workflow classifies multiple input gene sets using several ontologies and identifies categories that are over-represented in each of the input sets. The input is a folder containing several gene or protein tables.
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This workflow is designed to classify a multiple set of genes by enrichment analysis using GO, Reactome, HumanCyc  and TF classification databases. Gene sets should be located in one folder.
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In the first step, the first table from the input folder is converted into a gene table with Ensembl IDs.
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In the second step, the table with Ensembl IDs is submitted to the ''Functional classification'' analysis, which is done in parallel using the following ontologies: GO biological processes, GO cellular components, GO molecular functions, Reactome pathways, HumanCyc pathways, and TF classification.
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The first and second steps are repeated for the second table from the input folder, and it is repeatedly performed for each table from the input folder.
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As a result, a new folder is formed with several subfolders corresponding to each input table. Each subfolder contains the results of ''Functional classification.'' For each ontological term several parameters are calculated, including expected number of hits, actual number of hits, p-value as well as the names of genes falling into this category and the link to the corresponding ontological term.
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== Parameters ==
 
== Parameters ==

Revision as of 16:19, 11 December 2014

Workflow title
Mapping to ontologies for multiple gene sets
Provider
geneXplain GmbH

Workflow overview

Mapping-to-ontologies-for-multiple-gene-sets-workflow-overview.png

Description

This workflow is designed to classify a multiple set of genes by enrichment analysis using GO, Reactome, HumanCyc  and TF classification databases. Gene sets should be located in one folder.

Parameters

Input folder
Folder to get input tables from
Species
Results folder
Folder to store results (will be created if not exists yet)
Retrieved from "https://wiki.biouml.org/index.php?title=Mapping_to_ontologies_for_multiple_gene_sets_(workflow)&oldid=5895"
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