MultiDCoX: Multi-factor analysis of differential co-expression

[摘要] BackgroundDifferential co-expression (DCX) signifies change in degree of co-expression of a set of genes among different biological conditions. It has been used to identify differential co-expression networks or interactomes. Many algorithms have been developed for single-factor differential co-expression analysis and applied in a variety of studies. However, in many studies, the samples are characterized by multiple factors such as genetic markers, clinical variables and treatments. No algorithm or methodology is available for multi-factor analysis of differential co-expression.ResultsWe developed a novel formulation and a computationally efficient greedy search algorithm called MultiDCoX to perform multi-factor differential co-expression analysis. Simulated data analysis demonstrates that the algorithm can effectively elicit differentially co-expressed (DCX) gene sets and quantify the influence of each factor on co-expression. MultiDCoX analysis of a breast cancer dataset identified interesting biologically meaningful differentially co-expressed (DCX) gene sets along with genetic and clinical factors that influenced the respective differential co-expression.ConclusionsMultiDCoX is a space and time efficient procedure to identify differentially co-expressed gene sets and successfully identify influence of individual factors on differential co-expression.

[发布日期] 2017-12-28

[关键词] Differential co-expression;Gene expression;MultiDCoX;Multi-factor analysis