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dc.contributor.author
Oliveira, Ana P.
dc.contributor.author
Dimopoulos, Sotiris
dc.contributor.author
Busetto, Alberto G.
dc.contributor.author
Christen, Stefan
dc.contributor.author
Dechant, Reinhard C.
dc.contributor.author
Falter, Laura B.
dc.contributor.author
Haghir Chehreghani, Morteza
dc.contributor.author
Jozefczuk, Szymon
dc.contributor.author
Ludwig, Christina
dc.contributor.author
Rudroff, Florian
dc.contributor.author
Schulz, Juliane C.
dc.contributor.author
González, Asier
dc.contributor.author
Soulard, Alexandre
dc.contributor.author
Stracka, Daniele
dc.contributor.author
Aebersold, Ruedi
dc.contributor.author
Buhmann, Joachim M.
dc.contributor.author
Hall, Michael N.
dc.contributor.author
Peter, Matthias
dc.contributor.author
Sauer, Uwe H.
dc.contributor.author
Stelling, Jörg
dc.date.accessioned
2018-06-07T15:59:00Z
dc.date.available
2017-06-11T17:25:06Z
dc.date.available
2018-06-07T15:59:00Z
dc.date.issued
2015-04
dc.identifier.other
10.15252/msb.20145475
en_US
dc.identifier.uri
http://hdl.handle.net/20.500.11850/100879
dc.identifier.doi
10.3929/ethz-b-000100879
dc.description.abstract
Cells react to nutritional cues in changing environments via the integrated action of signaling, transcriptional, and metabolic networks. Mechanistic insight into signaling processes is often complicated because ubiquitous feedback loops obscure causal relationships. Consequently, the endogenous inputs of many nutrient signaling pathways remain unknown. Recent advances for system‐wide experimental data generation have facilitated the quantification of signaling systems, but the integration of multi‐level dynamic data remains challenging. Here, we co‐designed dynamic experiments and a probabilistic, model‐based method to infer causal relationships between metabolism, signaling, and gene regulation. We analyzed the dynamic regulation of nitrogen metabolism by the target of rapamycin complex 1 (TORC1) pathway in budding yeast. Dynamic transcriptomic, proteomic, and metabolomic measurements along shifts in nitrogen quality yielded a consistent dataset that demonstrated extensive re‐wiring of cellular networks during adaptation. Our inference method identified putative downstream targets of TORC1 and putative metabolic inputs of TORC1, including the hypothesized glutamine signal. The work provides a basis for further mechanistic studies of nitrogen metabolism and a general computational framework to study cellular processes.
en_US
dc.format
application/pdf
en_US
dc.language.iso
en
en_US
dc.publisher
Wiley-Blackwell
en_US
dc.rights.uri
http://creativecommons.org/licenses/by/4.0/
dc.subject
Causal inference
en_US
dc.subject
Network motifs
en_US
dc.subject
Nutrient signaling
en_US
dc.subject
Target of rapamycin pathway
en_US
dc.title
Inferring causal metabolic signals that regulate the dynamic TORC1-dependent transcriptome
en_US
dc.type
Journal Article
dc.rights.license
Creative Commons Attribution 4.0 International
dc.date.published
2015-04-17
ethz.journal.title
Molecular Systems Biology
ethz.journal.volume
11
en_US
ethz.journal.issue
4
en_US
ethz.pages.start
802
en_US
ethz.size
15 p.
en_US
ethz.version.deposit
publishedVersion
en_US
ethz.identifier.wos
ethz.identifier.scopus
ethz.identifier.nebis
004931271
ethz.publication.place
Oxford
en_US
ethz.publication.status
published
en_US
ethz.leitzahl
ETH Zürich::00002 - ETH Zürich::00012 - Lehre und Forschung::00007 - Departemente::02030 - Dep. Biologie / Dep. of Biology::02517 - Institut für Biochemie / Institute of Biochemistry (IBC)::03595 - Peter, Matthias / Peter, Matthias
en_US
ethz.leitzahl
ETH Zürich::00002 - ETH Zürich::00012 - Lehre und Forschung::00007 - Departemente::02060 - Dep. Biosysteme / Dep. of Biosystems Science and Eng.::03699 - Stelling, Jörg / Stelling, Jörg
en_US
ethz.leitzahl
ETH Zürich::00002 - ETH Zürich::00012 - Lehre und Forschung::00007 - Departemente::02030 - Dep. Biologie / Dep. of Biology::02538 - Institut für Molekulare Systembiologie / Institute for Molecular Systems Biology::03713 - Sauer, Uwe / Sauer, Uwe
en_US
ethz.leitzahl
ETH Zürich::00002 - ETH Zürich::00012 - Lehre und Forschung::00007 - Departemente::02030 - Dep. Biologie / Dep. of Biology::02538 - Institut für Molekulare Systembiologie / Institute for Molecular Systems Biology::03663 - Aebersold, Rudolf / Aebersold, Rudolf
en_US
ethz.leitzahl.certified
ETH Zürich::00002 - ETH Zürich::00012 - Lehre und Forschung::00007 - Departemente::02030 - Dep. Biologie / Dep. of Biology::02517 - Institut für Biochemie / Institute of Biochemistry (IBC)::03595 - Peter, Matthias / Peter, Matthias
ethz.leitzahl.certified
ETH Zürich::00002 - ETH Zürich::00012 - Lehre und Forschung::00007 - Departemente::02060 - Dep. Biosysteme / Dep. of Biosystems Science and Eng.::03699 - Stelling, Jörg / Stelling, Jörg
ethz.leitzahl.certified
ETH Zürich::00002 - ETH Zürich::00012 - Lehre und Forschung::00007 - Departemente::02030 - Dep. Biologie / Dep. of Biology::02538 - Institut für Molekulare Systembiologie / Institute for Molecular Systems Biology::03713 - Sauer, Uwe / Sauer, Uwe
ethz.leitzahl.certified
ETH Zürich::00002 - ETH Zürich::00012 - Lehre und Forschung::00007 - Departemente::02030 - Dep. Biologie / Dep. of Biology::02538 - Institut für Molekulare Systembiologie / Institute for Molecular Systems Biology::03663 - Aebersold, Rudolf / Aebersold, Rudolf
ethz.date.deposited
2017-06-11T17:25:13Z
ethz.source
ECIT
ethz.identifier.importid
imp5936532c9511783998
ethz.ecitpid
pub:158388
ethz.eth
yes
en_US
ethz.availability
Open access
en_US
ethz.rosetta.installDate
2017-07-15T10:05:33Z
ethz.rosetta.lastUpdated
2018-11-07T11:31:08Z
ethz.rosetta.versionExported
true
ethz.COinS
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