EMDomics: a robust and powerful method for the identification of genes differentially expressed between heterogeneous classes.

ABSTRACT:

Motivation

A major goal of biomedical research is to identify molecular features associated with a biological or clinical class of interest. Differential expression analysis has long been used for this purpose; however, conventional methods perform poorly when applied to data with high within class heterogeneity.

Results

To address this challenge, we developed EMDomics, a new method that uses the Earth mover's distance to measure the overall difference between the distributions of a gene's expression in two classes of samples and uses permutations to obtain q-values for each gene. We applied EMDomics to the challenging problem of identifying genes associated with drug resistance in ovarian cancer. We also used simulated data to evaluate the performance of EMDomics, in terms

SUBMITTER: Nabavi S 

PROVIDER: S-EPMC4743632 | biostudies-literature | 2016 Feb

REPOSITORIES: biostudies-literature