View source for Gene set enrichment analysis HumanPSD (Agilent probes) (workflow)

;Workflow title
:Gene set enrichment analysis HumanPSD (Agilent probes)
;Provider
:[[geneXplain GmbH]]
== Workflow overview ==
[[File:Gene-set-enrichment-analysis-HumanPSD-Agilent-probes-workflow-overview.png|400px]]
== 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].  As input, the normalized data with Agilent probeset IDs can be submitted. Such normalized files result 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. 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 HumanPSD<sup>TM</sup> database. Enrichment analysis is performed using the following ontologies: HumanPSD GO biological processes, HumanPSD GO cellular components, HumanPSD GO molecular function, HumanPSD disease and by the TRANSPATH pathways.

Output files include enrichment analysis results, a list of annotated Ensemble genes and a histogram of log fold change 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
;Annotation source
;Species
;Results folder

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