The propagation of perturbations in rewired bacterial gene networks.

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• dc.contributor.author Baumstark, Rebeccaca
• dc.contributor.author Hänzelmann, Sonja, 1981-ca
• dc.contributor.author Tsuru, Saburoca
• dc.contributor.author Schaerli, Yolandaca
• dc.contributor.author Francesconi, Mirkoca
• dc.contributor.author Mancuso, Francesco M.ca
• dc.contributor.author Castelo Valdueza, Robertca
• dc.contributor.author Isalan, Markca
• dc.date.accessioned 2016-02-01T08:21:06Z
• dc.date.available 2016-02-01T08:21:06Z
• dc.date.issued 2015
• dc.description.abstract What happens to gene expression when you add new links to a gene regulatory network? To answer this question, we profile 85 network rewirings in E. coli. Here we report that concerted patterns of differential expression propagate from reconnected hub genes. The rewirings link promoter regions to different transcription factor and σ-factor genes, resulting in perturbations that span four orders of magnitude, changing up to ∼70% of the transcriptome. Importantly, factor connectivity and promoter activity both associate with perturbation size. Perturbations from related rewirings have more similar transcription profiles and a statistical analysis reveals ∼20 underlying states of the system, associating particular gene groups with rewiring constructs. We examine two large clusters (ribosomal and flagellar genes) in detail. These represent alternative global outcomes from different rewirings because of antagonism between these major cell states. This data set of systematically related perturbations enables reverse engineering and discovery of underlying network interactions.ca
• dc.description.sponsorship Funding was provided by FP7 ERC 201249 ZINC-HUBS (R.B.), Spanish grants MICINNBFU2010-17953 (M.I.), MINECO TIN2011-22826 (R.C., S.H.), ISCIII COMBIOMEDRD07/0067/0001 (R.C., S.H.). Y.S. was funded by a Swiss National Science FoundationFellowship (PBSKP3_134331/1) and by the Marie Curie Action (FP7 PIEF-GA-2011-298348). M.I. was funded by New Investigator Award No. WT102944 from theWellcome Trust UK
• dc.format.mimetype application/pdfca
• dc.identifier.citation Baumstark R, Hänzelmann S, Tsuru S, Schaerli Y, Francesconi M, Mancuso FM. et al. The propagation of perturbations in rewired bacterial gene networks. Nat Commun. 2015 Dec 16;6:10105. DOI: 10.1038/ncomms10105.ca
• dc.identifier.doi http://dx.doi.org/10.1038/ncomms10105
• dc.identifier.issn 2041-1723
• dc.identifier.uri http://hdl.handle.net/10230/25702
• dc.language.iso engca
• dc.publisher Nature Publishing Groupca
• dc.relation.ispartof Nature Communications. 2015 Dec 16;6:10105
• dc.relation.projectID info:eu-repo/grantAgreement/EC/FP7/201249
• dc.relation.projectID info:eu-repo/grantAgreement/EC/FP7/298348
• dc.relation.projectID info:eu-repo/grantAgreement/ES/3PN/BFU2010-17953
• dc.relation.projectID info:eu-repo/grantAgreement/ES/3PN/TIN2011-22826
• dc.rights This work is licensed under a http://creativecommons.org/licenses/by/4.0/. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ca
• dc.rights.accessRights info:eu-repo/semantics/openAccessca
• dc.rights.uri http://creativecommons.org/licenses/by/4.0/ca
• dc.subject.other Gens -- Anàlisi -- Informàticaca
• dc.title The propagation of perturbations in rewired bacterial gene networks.ca
• dc.type info:eu-repo/semantics/articleca
• dc.type.version info:eu-repo/semantics/publishedVersionca