Difference between revisions of "Gene set enrichment analysis (Gene table) (workflow)"
(GeneXplain -> geneXplain) |
(Automatic synchronization with BioUML) |
||
| (3 intermediate revisions by one user not shown) | |||
| Line 6: | Line 6: | ||
[[File:Gene-set-enrichment-analysis-Gene-table-workflow-overview.png|400px]] | [[File:Gene-set-enrichment-analysis-Gene-table-workflow-overview.png|400px]] | ||
== Description == | == Description == | ||
| − | This workflow is designed to perform Gene Set Enrichment Analysis, GSEA, as it is described at [http://www.broadinstitute.org/gsea/index.jsp http://www.broadinstitute.org/gsea/index.jsp] | + | This workflow is designed to perform Gene Set Enrichment Analysis, GSEA, as it is described at [http://www.broadinstitute.org/gsea/index.jsp 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. | 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. | ||
| Line 22: | Line 24: | ||
[[Category:Workflows]] | [[Category:Workflows]] | ||
| + | [[Category:GeneXplain workflows]] | ||
[[Category:Autogenerated pages]] | [[Category:Autogenerated pages]] | ||
Latest revision as of 16:34, 12 March 2019
- Workflow title
- Gene set enrichment analysis (Gene table)
- Provider
- geneXplain GmbH
[edit] Workflow overview
[edit] 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.
[edit] Parameters
- Input table
- Enrichment Weight Column
- Enter the name of the column from the Input table with numerical values
- Species
- Results folder
