Difference between revisions of "Gene set enrichment analysis (Affymetrix probes) (workflow)"
(Automatic synchronization with BioUML) |
(Automatic synchronization with BioUML) |
||
| Line 6: | Line 6: | ||
[[File:Gene-set-enrichment-analysis-Affymetrix-probes-workflow-overview.png|400px]] | [[File:Gene-set-enrichment-analysis-Affymetrix-probes-workflow-overview.png|400px]] | ||
== Description == | == Description == | ||
| − | This workflow is designed to perform Gene Set Enrichment Analysis, GSEA, as it is described | + | 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, the normalized data with Affymetrix probeset IDs can be submitted. |
| − | Such normalized files | + | Such normalized files are resulting from the “Normalize data” procedure under “analyses/Methods/Data normalization/Normalize Affymetrix experiment and control”. |
| − | First, the input files are subjected to fold-change calculation. The table with probeset | + | First, the input files are subjected to fold-change calculation. The table with probeset Ids and calculated fold change values is converted into a table with Ensembl Gene Ids. At the next step, the Ensembl genes are annotated with additional information, gene description and gene symbols. Finally the annotated Ensembl genes are 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. |
| − | + | ||
| − | + | ||
| − | + | ||
| − | + | ||
| − | + | ||
== Parameters == | == Parameters == | ||
Revision as of 11:49, 30 July 2013
- Workflow title
- Gene set enrichment analysis (Affymetrix probes)
- Provider
- geneXplain GmbH
Workflow overview
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, the normalized data with Affymetrix probeset IDs can be submitted.
Such normalized files are resulting from the “Normalize data” procedure under “analyses/Methods/Data normalization/Normalize Affymetrix experiment and control”.
First, the input files are subjected to fold-change calculation. The table with probeset Ids and calculated fold change values is converted into a table with Ensembl Gene Ids. At the next step, the Ensembl genes are annotated with additional information, gene description and gene symbols. Finally the annotated Ensembl genes are 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.
Parameters
- Experiment normalized
- Control normalized
- Species
- Results folder
