Testing gene set enrichment for subset of genes: Sub-GSE.

ABSTRACT:

Background

Many methods have been developed to test the enrichment of genes related to certain phenotypes or cell states in gene sets. These approaches usually combine gene expression data with functionally related gene sets as defined in databases such as GeneOntology (GO), KEGG, or BioCarta. The results based on gene set analysis are generally more biologically interpretable, accurate and robust than the results based on individual gene analysis. However, while most available methods for gene set enrichment analysis test the enrichment of the entire gene set, it is more likely that only a subset of the genes in the gene set may be related to the phenotypes of interest.

Results

In this paper, we develop a novel method, termed Sub-GSE, which measures the enrichment of a pred

SUBMITTER: Yan X 

PROVIDER: S-EPMC2543030 | biostudies-literature | 2008 Sep

REPOSITORIES: biostudies-literature