We describe a powerful analytical method called Gene Set Enrichment Analysis for interpreting gene expression data
2005
Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles
Key concepts
Scholarcy highlights
- Genomewide RNA expression analysis has become a routine tool in biomedical research, extracting biological insight from such information remains a major challenge
- We explored the ability of Gene Set Enrichment Analysis to provide biologically meaningful insights in six examples for which considerable background information is available
- We generated mRNA expression profiles from lymphoblastoid cell lines derived from 15 males and 17 females and sought to identify gene sets correlated with the distinctions ‘‘maleϾfemale’’ and ‘‘femaleϾmale.’’
- We previously introduced GSEA to analyze such data at the level of gene sets
- The method was initially used to discover metabolic pathways altered in human diabetes and was subsequently applied to discover processes involved in diffuse large B cell lymphoma, nutrient-sensing pathways involved in prostate cancer, and in comparing the expression profiles of mouse to those of humans
- We have created an initial molecular signature database consisting of 1,325 gene sets, including ones based on biological pathways, chromosomal location, upstream cis motifs, responses to a drug treatment, or expression profiles in previously generated microarray data sets
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