Pathway correlation profile of gene-gene co-expression for identifying pathway perturbation.

ABSTRACT: Identifying perturbed or dysregulated pathways is critical to understanding the biological processes that change within an experiment. Previous methods identified important pathways that are significantly enriched among differentially expressed genes; however, these methods cannot account for small, coordinated changes in gene expression that amass across a whole pathway. In order to overcome this limitation, we use microarray gene expression data to identify pathway perturbation based on pathway correlation profiles. By identifying the distribution of gene-gene pair correlations within a pathway, we can rank the pathways based on the level of perturbation and dysregulation. We have shown this successfully for differences between two experimental conditions in Escherichia coli and changes

SUBMITTER: Tegge AN 

PROVIDER: S-EPMC3527387 | biostudies-literature | 2012

REPOSITORIES: biostudies-literature