Mapping to ontologies (Gene table) (workflow) - Revision history

WikiBot: Automatic synchronization with BioUML

2019-03-12T09:34:46Z

Automatic synchronization with BioUML

WikiBot: Cosmetic changes in category formatting

2013-05-16T06:28:43Z

Cosmetic changes in category formatting

WikiBot: geneXplain -> GeneXplain in category name

2013-04-19T04:14:22Z

geneXplain -> GeneXplain in category name

WikiBot: Adding provider-specific categories

2013-04-19T04:09:06Z

Adding provider-specific categories

WikiBot: GeneXplain -> geneXplain

2013-04-18T08:47:34Z

GeneXplain -> geneXplain

WikiBot: Protected "Mapping to ontologies (Gene table) (workflow)": Autogenerated page (‎[edit=sysop] (indefinite))

2013-04-18T08:10:51Z

Protected "Mapping to ontologies (Gene table) (workflow)": Autogenerated page (‎[edit=sysop] (indefinite))

WikiBot: Automatic synchronization with BioUML

2013-04-18T08:10:49Z

Automatic synchronization with BioUML

New page

;Workflow title
:Mapping to ontologies (Gene table)
;Provider
:[[GeneXplain GmbH]]
== Workflow overview ==
[[File:Mapping-to-ontologies-Gene-table-workflow-overview.png|400px]]
== Description ==
This workflow is designed to classify an input gene set to several ontologies and to identify terms, hits for which are overrepresented in the input set. The input file can be any gene or protein table.

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 functional classification, which is done in parallel by the following ontologies: GO biological processes, GO cellular components, GO molecular functions, Reactome pathways, HumanCyc pathways, TF classification.

For each ontological term several parameters are calculated, including expected number of hits, actual number of hits, p-value, as well as hit names and the link to the corresponding ontological term.

== Parameters ==
;Input table
;Species
;Results folder

[[Category:Workflows]]
[[Category:Autogenerated pages]]

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		+	[[Category:Autogenerated pages]]

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 [[Category:Workflows]]
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+[[Category:GeneXplain workflows]]

← Older revision		Revision as of 04:09, 19 April 2013
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	[[Category:Workflows]]		[[Category:Workflows]]
	[[Category:Autogenerated pages]]		[[Category:Autogenerated pages]]
		+	[[Category:geneXplain workflows]]

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 [[File:Mapping-to-ontologies-Gene-table-workflow-overview.png|400px]]
 == Description ==
-This workflow is designed to classify an input gene set to several ontologies and to identify terms, hits for which are overrepresented in the input set. The input file can be any gene or protein table.
+ This workflow is designed to classify an input gene set to several ontologies and to identify terms, hits for which are overrepresented in the input set.
-At the first step, the input table is converted into a table with Ensembl Gene IDs.
+The input file can be any gene or protein table.
-This table with Ensembl Gene Ids is subjected to functional classification, which is done in parallel by the following ontologies: GO biological processes, GO cellular components, GO molecular functions, Reactome pathways, HumanCyc pathways, TF classification.
+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 functional classification, which is done in parallel by the following ontologies: GO biological processes, GO cellular components, GO molecular functions, Reactome pathways, HumanCyc pathways, TF classification.
 For each ontological term several parameters are calculated, including expected number of hits, actual number of hits, p-value, as well as hit names and the link to the corresponding ontological term.

@@ Line 2: / Line 2: @@
 :Mapping to ontologies (Gene table)
 ;Provider
-:[[GeneXplain GmbH]]
+:[[geneXplain GmbH]]
 == Workflow overview ==
 [[File:Mapping-to-ontologies-Gene-table-workflow-overview.png|400px]]