64 A Practical Guide to Cancer Systems Biology
Preparation
— Download GSEA Java desktop application from the website: http://
http://www.broadinstitute.org/gsea/index.jsp.
— Download and install Cytoscape from the website: http://www.cyto
scape.org.
— Download and install the EnrichmentMap, a Cytoscape plugin, from the
website: http://www.baderlab.org/Software/EnrichmentMap.
Data preparation for GSEA
To apply GSEA for enrichment analysis of proteome data, expression data
and description of data are required.
— Expression data: TXT file (*.txt).
GSEA supports expression data in four formats: res, gct, pcl, or txt. For
proteome data preparation, we recommend to create the expression data
in tab delimited txt file format, which contains name (Gene Symbol),
description, and expression value (the peak area of extracted ion current
or log 2 transformed value) in columns (Fig. 1). Convert the identifier of
Figure 1. The organization of the text file format for expression dataset. The first line
contains the NAME and DESCRIPTION followed by the identifiers for each sample in the
dataset. DESCRIPTION is optional; fill in it with “NA” if the description is not available.
We use the Gene Symbol as the NAME, and the identified UniProt protein accession
number as the DESCRIPTION for each expression value.