MultiDCoX: Multi-factor analysis of differential co-expression

• Main Authors: Liany, Herty, Rajapakse, Jagath Chandana, Karuturi, R. Krishna Murthy
• Other Authors: School of Computer Science and Engineering
• Format: Article
• Language: English
• Published: 2018
• Subjects: Differential Co-expression; Gene Expression
• Online Access: https://hdl.handle.net/10356/89215; http://hdl.handle.net/10220/44821
• Institution: Nanyang Technological University

Background: Differential 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. Results: We 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. Conclusions: MultiDCoX 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.