title: Comparative microbial modules resource: generation and visualization of multi-species biclusters.
abstract: The increasing abundance of large-scale, high-throughput datasets for many closely related organisms provides opportunities for comparative analysis via the simultaneous biclustering of datasets from multiple species. These analyses require a reformulation of how to organize multi-species datasets and visualize comparative genomics data analyses results. Recently, we developed a method, multi-species cMonkey, which integrates heterogeneous high-throughput datatypes from multiple species to identify conserved regulatory modules. Here we present an integrated data visualization system, built upon the Gaggle, enabling exploration of our method's results (available at http://meatwad.bio.nyu.edu/cmmr.html). The system can also be used to explore other comparative genomics datasets and outputs from other data analysis procedures - results from other multiple-species clustering programs or from independent clustering of different single-species datasets. We provide an example use of our system for two bacteria, Escherichia coli and Salmonella Typhimurium. We illustrate the use of our system by exploring conserved biclusters involved in nitrogen metabolism, uncovering a putative function for yjjI, a currently uncharacterized gene that we predict to be involved in nitrogen assimilation.
authors.affiliation: Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York, USA.
authors.forename: Thadeous
authors.initials: T
authors.lastname: Kacmarczyk
authors.forename: Peter
authors.initials: P
authors.lastname: Waltman
authors.forename: Ashley
authors.initials: A
authors.lastname: Bate
authors.forename: Patrick
authors.initials: P
authors.lastname: Eichenberger
authors.forename: Richard
authors.initials: R
authors.lastname: Bonneau
mesh_terms: D000465:Algorithms; D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods*; D016208:Databases, Factual; D004926:Escherichia coli / Q000235:genetics / Q000378:metabolism / Q000502:physiology; D016680:Genome, Bacterial; D009584:Nitrogen / Q000378:metabolism; D012486:Salmonella typhimurium / Q000235:genetics / Q000378:metabolism / Q000502:physiology; D012984:Software; D049490:Systems Biology; D014584:User-Computer Interface
chemical_list: D009584:Nitrogen