A network inference workflow applied to virulence-related processes in Salmonella typhimurium

Inference of the structure of mRNA transcriptional regulatory networks, protein regulatory or interaction networks, and protein activation/inactivation-based signal transduction networks are critical tasks in systems biology. In this article we discuss a workflow for the reconstruction of parts of the transcriptional regulatory network of the pathogenic bacterium Salmonella typhimurium based on the information contained in sets of microarray gene-expression data now available for that organism and describe our results obtained by following this workflow. The primary tool is one of the network-inference algorithms deployed in the Software Environment for Biological Network Inference (SEBINI). Specifically, we selected the algorithm called context likelihood of relatedness (CLR), which uses the mutual information contained in the gene-expression data to infer regulatory connections. The associated analysis pipeline automatically stores the inferred edges from the CLR runs within SEBINI and, upon request, transfers the inferred edges into either Cytoscape or the plug-in Collective Analysis of Biological Interaction Networks (CABIN) tool for further postanalysis of the inferred regulatory edges. The following article presents the outcome of this workflow, as well as the protocols followed for microarray data collection, data cleansing, and network inference. Our analysis revealed several interesting interactions, functional groups, metabolic pathways, and regulons in S. typhimurium.