Show simple item record

dc.contributor.author
Zamboni, Nicola
dc.contributor.author
Kümmel, Anne
dc.contributor.author
Heinemann, Matthias
dc.date.accessioned
2018-09-05T07:44:21Z
dc.date.available
2018-09-05T07:44:21Z
dc.date.issued
2008-04
dc.identifier.issn
1471-2105
dc.identifier.other
10.1186/1471-2105-9-199
en_US
dc.identifier.uri
http://hdl.handle.net/20.500.11850/286996
dc.identifier.doi
10.3929/ethz-a-005751784
dc.description.abstract
Background Compared to other omics techniques, quantitative metabolomics is still at its infancy. Complex sample preparation and analytical procedures render exact quantification extremely difficult. Furthermore, not only the actual measurement but also the subsequent interpretation of quantitative metabolome data to obtain mechanistic insights is still lacking behind the current expectations. Recently, the method of network-embedded thermodynamic (NET) analysis was introduced to address some of these open issues. Building upon principles of thermodynamics, this method allows for a quality check of measured metabolite concentrations and enables to spot metabolic reactions where active regulation potentially controls metabolic flux. So far, however, widespread application of NET analysis in metabolomics labs was hindered by the absence of suitable software. Results We have developed in Matlab a generalized software called 'anNET' that affords a user-friendly implementation of the NET analysis algorithm. anNET supports the analysis of any metabolic network for which a stoichiometric model can be compiled. The model size can span from a single reaction to a complete genome-wide network reconstruction including compartments. anNET can (i) test quantitative data sets for thermodynamic consistency, (ii) predict metabolite concentrations beyond the actually measured data, (iii) identify putative sites of active regulation in the metabolic reaction network, and (iv) help in localizing errors in data sets that were found to be thermodynamically infeasible. We demonstrate the application of anNET with three published Escherichia coli metabolome data sets. Conclusion Our user-friendly and generalized implementation of the NET analysis method in the software anNET allows users to rapidly integrate quantitative metabolome data obtained from virtually any organism. We envision that use of anNET in labs working on quantitative metabolomics will provide the systems biology and metabolic engineering communities with a mean to proof the quality of metabolome data sets and with all further benefits of the NET analysis approach.
en_US
dc.format
application/pdf
en_US
dc.language.iso
en
en_US
dc.publisher
BioMed Central
en_US
dc.rights.uri
http://creativecommons.org/licenses/by/2.0/
dc.subject
METABOLISMUS (MIKROORGANISMEN)
en_US
dc.subject
SYSTEMBIOLOGIE
en_US
dc.subject
BIOLOGISCHE THERMODYNAMIK
en_US
dc.subject
BIOLOGISCHE INFORMATIK UND COMPUTERANWENDUNG IN DER BIOLOGIE
en_US
dc.subject
METABOLISM (MICROORGANISMS)
en_US
dc.subject
SYSTEMS BIOLOGY
en_US
dc.subject
BIOLOGICAL THERMODYNAMICS
en_US
dc.subject
BIOLOGICAL INFORMATICS AND COMPUTER APPLICATIONS IN BIOLOGY
en_US
dc.subject
Metabolite Concentration
en_US
dc.subject
Metabolome Data
en_US
dc.subject
Central Carbon Metabolism
en_US
dc.subject
Feasible Range
en_US
dc.subject
Flux Direction
en_US
dc.title
anNET: a tool for network-embedded thermodynamic analysis of quantitative metabolome data
en_US
dc.type
Journal Article
dc.rights.license
Creative Commons Attribution 2.0 Generic
ethz.journal.title
BMC Bioinformatics
ethz.journal.volume
9
en_US
ethz.journal.issue
199
en_US
ethz.journal.abbreviated
BMC bioinformatics
ethz.pages.start
199
en_US
ethz.size
11 p.
en_US
ethz.version.deposit
publishedVersion
en_US
ethz.code.ddc
5 - Science::570 - Life sciences
en_US
ethz.identifier.wos
ethz.publication.place
London
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::02538 - Institut für Molekulare Systembiologie / Institute for Molecular Systems Biology
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::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
2017-06-08T21:26:25Z
ethz.source
ECOL
ethz.source
ECIT
ethz.identifier.importid
imp59366acd9436012792
ethz.identifier.importid
imp59364c425f28028769
ethz.ecolpid
eth:41378
ethz.ecitpid
pub:26291
ethz.eth
yes
en_US
ethz.availability
Open access
en_US
ethz.rosetta.installDate
2018-09-05T07:44:30Z
ethz.rosetta.lastUpdated
2018-11-08T01:35:52Z
ethz.rosetta.versionExported
true
dc.identifier.olduri
http://hdl.handle.net/20.500.11850/150961
dc.identifier.olduri
http://hdl.handle.net/20.500.11850/14629
ethz.COinS
ctx_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.atitle=anNET:%20a%20tool%20for%20network-embedded%20thermodynamic%20analysis%20of%20quantitative%20metabolome%20data&rft.jtitle=BMC%20Bioinformatics&rft.date=2008-04&rft.volume=9&rft.issue=199&rft.spage=199&rft.issn=1471-2105&rft.au=Zamboni,%20Nicola&K%C3%BCmmel,%20Anne&Heinemann,%20Matthias&rft.genre=article&
 Search via SFX

Files in this item

Thumbnail

Publication type

Show simple item record