A Network Inference Workflow Applied to Virulence-Related Processes in Salmonella typhimurium
Book
·
OSTI ID:957364
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 of Biological Interaction Networks (CABIN) tool for further post-analysis 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.
- Research Organization:
- Pacific Northwest National Laboratory (PNNL), Richland, WA (US)
- Sponsoring Organization:
- USDOE
- DOE Contract Number:
- AC05-76RL01830
- OSTI ID:
- 957364
- Report Number(s):
- PNNL-SA-60416
- Country of Publication:
- United States
- Language:
- English
Similar Records
Biological Network Inference and Analysis using SEBINI and CABIN
Bottlenecks and Hubs in Inferred Networks Are Important for Virulence in Salmonella typhimurium
An analysis pipeline for the inference of protein-protein interaction networks
Book
·
Mon Dec 31 23:00:00 EST 2007
·
OSTI ID:965160
Bottlenecks and Hubs in Inferred Networks Are Important for Virulence in Salmonella typhimurium
Journal Article
·
Sat Jan 31 23:00:00 EST 2009
· Journal of Computational Biology, 16(2):169-180
·
OSTI ID:950159
An analysis pipeline for the inference of protein-protein interaction networks
Journal Article
·
Mon Nov 30 23:00:00 EST 2009
· International Journal of Data Mining and Bioinformatics, 3(4) (Sp. Iss. SI):409-430
·
OSTI ID:972552