Difference between revisions of "Gene set enrichment analysis (Agilent probes) (workflow)"

Latest revision as of 16:34, 12 March 2019

Workflow title

Gene set enrichment analysis (Agilent probes)

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, the normalized data with Agilent probeset IDs can be submitted.

Such normalized files are resulting from the “Normalize data” procedure under “analyses/Methods/Data normalization/Normalize Agilent 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.

For each ontological item 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

Experiment normalized

Control normalized

Annotation source

Species

Results folder