Gene set enrichment analysis (Affymetrix probes) (workflow)

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 PROTEOME^TM 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