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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 within time series data in Saccharomyces cerevisiae, as well as two estrogen receptor response classes of breast cancer. Overall, our method made significant predictions as to the pathway perturbations that are involved in the experimental conditions.

SUBMITTER: Tegge AN 

PROVIDER: S-EPMC3527387 | biostudies-literature | 2012

REPOSITORIES: biostudies-literature

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

Tegge Allison N AN   Caldwell Charles W CW   Xu Dong D  

PloS one 20121220 12


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 pathwa  ...[more]

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