LEGO: a novel method for gene set over-representation analysis by incorporating network-based gene weights.

ABSTRACT: Pathway or gene set over-representation analysis (ORA) has become a routine task in functional genomics studies. However, currently widely used ORA tools employ statistical methods such as Fisher's exact test that reduce a pathway into a list of genes, ignoring the constitutive functional non-equivalent roles of genes and the complex gene-gene interactions. Here, we develop a novel method named LEGO (functional Link Enrichment of Gene Ontology or gene sets) that takes into consideration these two types of information by incorporating network-based gene weights in ORA analysis. In three benchmarks, LEGO achieves better performance than Fisher and three other network-based methods. To further evaluate LEGO's usefulness, we compare LEGO with five gene expression-based and three pathway topolo

SUBMITTER: Dong X 

PROVIDER: S-EPMC4707541 | biostudies-literature | 2016 Jan

REPOSITORIES: biostudies-literature