Gene regulatory networks provide insight into the mechanisms of differential gene expression at a system level. However, the methods for inference, functional analysis and visualization of regulatory modules and networks require the user to collect heterogeneous data from many sources using numerous bioinformatics tools. This makes the analysis expensive and time-consuming. In this work, the BiologicalNetworks application -the data integration and network visualization environment – was extended with tools for inference and analysis of gene regulatory modules and networks. The backend database of the application integrates public data on gene expression, pathways, transcription factor binding sites, gene and protein sequences, and functional annotations. Thus, all data essential for the analysis can be mined publicly. In addition, the user’s data can either be integrated in the database and become public, or kept private within the application. The capabilities to analyze multiple gene expression experiments are also provided. The generated network, regulatory modules and binding sites can be visualized and further analyzed within this same application.
The developed tools were applied to the OCT4 regulatory network in embryonic stem cells.