Difference between revisions of "Mapping to ontologies (TRANSPATH(R)) (workflow)"
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[[File:Mapping-to-ontologies-TRANSPATH-R-workflow-overview.png|400px]] | [[File:Mapping-to-ontologies-TRANSPATH-R-workflow-overview.png|400px]] | ||
== Description == | == 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. | |
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At the first step, the input table is converted into a table with Ensembl Gene IDs. | At the first step, the input table is converted into a table with Ensembl Gene IDs. | ||
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Mapping to ontologies for multiple gene sets | 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 | + | 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 | + | 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 | + | 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. | 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. | ||
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This workflow is available together with a valid TRANSPATH® license. | This workflow is available together with a valid TRANSPATH® license. | ||
Latest revision as of 16:35, 12 March 2019
- Workflow title
- Mapping to ontologies (TRANSPATH(R))
- Provider
- geneXplain GmbH
[edit] Workflow overview
[edit] 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 can be a gene or protein table.
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, 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.
[edit] Parameters
- Input gene set
- Species
- Results folder
