CABeRNET: a Cytoscape app for augmented Boolean models of gene regulatory NETworks

BMC Bioinformatics

Software

Andrea Paroni¹  Alex Graudenzi²  Giancarlo Mauri³  Marco Antoniotti⁴  Chiara Damiani⁵  Giulio Caravagna⁶ 

[1] Department of Informatics, Systems and Communication, University of Milan-Bicocca, Viale Sarca 336, I-20126, Milan, Italy;Department of Informatics, Systems and Communication, University of Milan-Bicocca, Viale Sarca 336, I-20126, Milan, Italy;Institute of Molecular Bioimaging and Physiology of the Italian National Research Council (IBFM-CNR), Via F.lli Cervi, 93, I-20090, Segrate, (MI), Italy;Department of Informatics, Systems and Communication, University of Milan-Bicocca, Viale Sarca 336, I-20126, Milan, Italy;Institute of Molecular Bioimaging and Physiology of the Italian National Research Council (IBFM-CNR), Via F.lli Cervi, 93, I-20090, Segrate, (MI), Italy;SYSBIO Centre of Systems Biology, Piazza della Scienza 2, 20126 Milano, Italy, Viale Sarca 336, I-20126, Milan, Italy;Department of Informatics, Systems and Communication, University of Milan-Bicocca, Viale Sarca 336, I-20126, Milan, Italy;Milan Center for Neuroscience, University of Milan-Bicocca, Milan, Italy;Department of Informatics, Systems and Communication, University of Milan-Bicocca, Viale Sarca 336, I-20126, Milan, Italy;SYSBIO Centre of Systems Biology, Piazza della Scienza 2, 20126 Milano, Italy, Viale Sarca 336, I-20126, Milan, Italy;Department of Informatics, Systems and Communication, University of Milan-Bicocca, Viale Sarca 336, I-20126, Milan, Italy;School of Informatics, University of Edinburgh, 10 Crichton St, EH8 9AB, Edinburgh, UK;

关键词: Gene regulatory networks;    Cell differentiation;    Attractors;    Cancer development;    Network augmentation;    Robustness analysis;   

DOI  :  10.1186/s12859-016-0914-z

 received in 2015-05-20, accepted in 2016-01-27,  发布年份 2016

来源: Springer

【 摘 要 】

BackgroundDynamical models of gene regulatory networks (GRNs) are highly effective in describing complex biological phenomena and processes, such as cell differentiation and cancer development. Yet, the topological and functional characterization of real GRNs is often still partial and an exhaustive picture of their functioning is missing.ResultsWe here introduce CABeRNET, a Cytoscape app for the generation, simulation and analysis of Boolean models of GRNs, specifically focused on their augmentation when a only partial topological and functional characterization of the network is available. By generating large ensembles of networks in which user-defined entities and relations are added to the original core, CABeRNET allows to formulate hypotheses on the missing portions of real networks, as well to investigate their generic properties, in the spirit of complexity science.ConclusionsCABeRNET offers a series of innovative simulation and modeling functions and tools, including (but not being limited to) the dynamical characterization of the gene activation patterns ruling cell types and differentiation fates, and sophisticated robustness assessments, as in the case of gene knockouts. The integration within the widely used Cytoscape framework for the visualization and analysis of biological networks, makes CABeRNET a new essential instrument for both the bioinformatician and the computational biologist, as well as a computational support for the experimentalist. An example application concerning the analysis of an augmented T-helper cell GRN is provided.

【 授权许可】

CC BY   
© Paroni et al. 2016

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