Mapping to ontologies (TRANSPATH(R)) (workflow) - Revision history

WikiBot: Automatic synchronization with BioUML

2019-03-12T09:35:14Z

Automatic synchronization with BioUML

WikiBot: Automatic synchronization with BioUML

2014-12-11T09:19:15Z

Automatic synchronization with BioUML

WikiBot: Automatic synchronization with BioUML

2013-07-30T04:49:33Z

Automatic synchronization with BioUML

WikiBot: Cosmetic changes in category formatting

2013-05-16T06:28:53Z

Cosmetic changes in category formatting

WikiBot: geneXplain -> GeneXplain in category name

2013-04-19T04:14:32Z

geneXplain -> GeneXplain in category name

WikiBot: Adding provider-specific categories

2013-04-19T04:09:15Z

Adding provider-specific categories

WikiBot: GeneXplain -> geneXplain

2013-04-18T08:47:54Z

GeneXplain -> geneXplain

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

2013-04-18T08:11:12Z

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

WikiBot: Automatic synchronization with BioUML

2013-04-18T08:11:10Z

Automatic synchronization with BioUML

New page

;Workflow title
:Mapping to ontologies (TRANSPATH(R))
;Provider
:[[GeneXplain GmbH]]
== Workflow overview ==
[[File:Mapping-to-ontologies-TRANSPATH-R-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, Transpath 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.

Mapping to ontologies for multiple gene sets

This workflow is designed to classify input gene set to several ontologies and to identify terms, hits for which are overrepresented in the input set. The input is a folder containing several gene or protein tables, and these tables are taken automatically by the workflow, one input table after another, in a cycle.

At the first step, one of the input tables from the input folder 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.

The same steps are repeated for the next input table, and several cycles are performed automatically corresponding to the number of tables in the input folder.

This workflow is available together with a valid TRANSPATH® license.

== Parameters ==
;Input gene set
;Species
;Results folder

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

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 [[File:Mapping-to-ontologies-TRANSPATH-R-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. 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.
@@ Line 18: / Line 16: @@
 Mapping to ontologies for multiple gene sets
-This workflow is designed to classify input gene set to several ontologies and to identify terms, hits for which are overrepresented in the input set. The input is a folder containing several gene or protein tables, and these tables are taken automatically by the workflow, one input table after another, in a cycle.
+This workflow is designed to classify input gene set to several ontologies and to identify terms, hits for which are overrepresented in the input set. The Input can be a gene or protein table.
-At the first step, one of the input tables from the input folder is converted into a table with Ensembl Gene IDs.
+At the first step, one of 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.
+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, TF classification, and Transpath pathways
 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.
 This workflow is available together with a valid TRANSPATH® license.

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