Difference between revisions of "Gene set enrichment analysis (Affymetrix probes) (workflow)"
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[[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 result 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. |
| − | + | In the next step, the Ensembl genes are annotated with additional information, gene descriptions and gene symbols. | |
| + | |||
| + | Finally the annotated Ensembl genes are subjected to GSEA using the PROTEOME<sup>TM</sup> database. Enrichment analysis is performed using the following ontologies: PROTEOME GO biological processes, PROTEOME GO cellular components, PROTEOME GO molecular function, PROTEOME disease, and TRANSPATH pathways. | ||
| + | |||
| + | Output files include enrichment analysis results, a list of annotated Ensembl genes and a histogram of LogFoldChange distribution. For each ontological term several parameters are calculated, including nominal p-value, ES, NES, FDR, rank at max, hit names, the link to the corresponding ontological term, and the link to open a visualization plot. | ||
== Parameters == | == Parameters == | ||
Revision as of 16:18, 11 December 2014
- 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 result 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.
In the next step, the Ensembl genes are annotated with additional information, gene descriptions and gene symbols.
Finally the annotated Ensembl genes are subjected to GSEA using the PROTEOMETM database. Enrichment analysis is performed using the following ontologies: PROTEOME GO biological processes, PROTEOME GO cellular components, PROTEOME GO molecular function, PROTEOME disease, and TRANSPATH pathways.
Output files include enrichment analysis results, a list of annotated Ensembl genes and a histogram of LogFoldChange distribution. For each ontological term several parameters are calculated, including nominal p-value, ES, NES, FDR, rank at max, hit names, the link to the corresponding ontological term, and the link to open a visualization plot.
Parameters
- Experiment normalized
- Control normalized
- Species
- Results folder
