This code is for running GSEA file in PHP. User can incarporate GSEA in their application and use for enrichment analysis.
Introduction: Gene Set Enrichment Analysis (GSEA) is a computational method that determines whether an a priori defined set of genes shows statistically significant, concordant differences between two biological states (e.g. phenotypes) (http://software.broadinstitute.org/gsea/index.jsp).
Steps:
Step-1: Download folder in your localhost or server.
Step-2: Run "PHP_gsea.php" in your server/browser.
Step-3: Change the data with your data (replace temporary .rnk and geneset.gmt files)
Step-4: Find your results in the same folder named as Output.
##For Expression matrix (or microarray) type of data use "PHP_ExpressionMatrix_gsea.php" script.
Example: For leukemia Phenotype(Leukemia.cls) and Expression matrix (Leukemia.gct).
Step-1: Download folder in your localhost or server.
Step-2: Run "PHP_ExpressionMatrix_gsea.php" in your server/browser.
Step-3: Change the data with your data (replace example data or geneset.gmt files)
Step-4: Find your results in the same folder named as Output.
Acknowledgement and Citation: Subramanian, Tamayo, et al. (2005, PNAS 102, 15545-15550) and Mootha, Lindgren, et al. (2003, Nat Genet 34, 267-273).
Licence : Please follow license agreement from http://software.broadinstitute.org/gsea/license_terms_list.jsp here.
Enjoy