Comparative analysis of module-based versus direct methods for reverse-engineering transcriptional regulatory networks

The results indicate that module-based and direct methods retrieve largely distinct parts of the underlying transcriptional regulatory networks, and the choice of algorithm should therefore be based on the particular biological problem of interest and not on global metrics which cannot be transferred between organisms.

Abstract

Our results indicate that module-based and direct methods retrieve largely distinct parts of the underlying transcriptional regulatory networks. The choice of algorithm should therefore be based on the particular biological problem of interest and not on global metrics which cannot be transferred between organisms. The development of sound statistical methods for integrating the predictions of different reverse-engineering strategies emerges as an important challenge for future research.