Integration of transcription and flux data reveals molecular paths associated with differences in oxygen-dependent phenotypes of Saccharomyces cerevisiae

Erno Lindfors, Paula Jouhten, Merja Oja, Eija Rintala, Matej Orešič, Merja Penttilä

Research output: Contribution to journalArticleScientificpeer-review

1 Citation (Scopus)

Abstract

Background: Saccharomyces cerevisiae is able to adapt to a wide range of external oxygen conditions. Previously, oxygen-dependent phenotypes have been studied individually at the transcriptional, metabolite, and flux level. However, the regulation of cell phenotype occurs across the different levels of cell function. Integrative analysis of data from multiple levels of cell function in the context of a network of several known biochemical interaction types could enable identification of active regulatory paths not limited to a single level of cell function.Results: The graph theoretical method called Enriched Molecular Path detection (EMPath) was extended to enable integrative utilization of transcription and flux data. The utility of the method was demonstrated by detecting paths associated with phenotype differences of S. cerevisiae under three different conditions of oxygen provision: 20.9%, 2.8% and 0.5%. The detection of molecular paths was performed in an integrated genome-scale metabolic and protein-protein interaction network.Conclusions: The molecular paths associated with the phenotype differences of S. cerevisiae under conditions of different oxygen provisions revealed paths of molecular interactions that could potentially mediate information transfer between processes that respond to the particular oxygen availabilities.

Original languageEnglish
Article number16
JournalBMC Systems Biology
Volume8
Issue number1
DOIs
Publication statusPublished - 14 Feb 2014
MoE publication typeA1 Journal article-refereed

Fingerprint

Saccharomyces Cerevisiae
Transcription
Phenotype
Yeast
Saccharomyces cerevisiae
Oxygen
Fluxes
Path
Dependent
Cell
Proteins
Protein Interaction Maps
Molecular interactions
Metabolites
Information Transfer
Protein Interaction Networks
Protein-protein Interaction
Interaction
Genes
Cells

Keywords

  • Constraint-based modeling
  • Data integration
  • Molecular path finding
  • Network biology
  • Oxygen
  • Saccharomyces cerevisiae

Cite this

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title = "Integration of transcription and flux data reveals molecular paths associated with differences in oxygen-dependent phenotypes of Saccharomyces cerevisiae",
abstract = "Background: Saccharomyces cerevisiae is able to adapt to a wide range of external oxygen conditions. Previously, oxygen-dependent phenotypes have been studied individually at the transcriptional, metabolite, and flux level. However, the regulation of cell phenotype occurs across the different levels of cell function. Integrative analysis of data from multiple levels of cell function in the context of a network of several known biochemical interaction types could enable identification of active regulatory paths not limited to a single level of cell function.Results: The graph theoretical method called Enriched Molecular Path detection (EMPath) was extended to enable integrative utilization of transcription and flux data. The utility of the method was demonstrated by detecting paths associated with phenotype differences of S. cerevisiae under three different conditions of oxygen provision: 20.9{\%}, 2.8{\%} and 0.5{\%}. The detection of molecular paths was performed in an integrated genome-scale metabolic and protein-protein interaction network.Conclusions: The molecular paths associated with the phenotype differences of S. cerevisiae under conditions of different oxygen provisions revealed paths of molecular interactions that could potentially mediate information transfer between processes that respond to the particular oxygen availabilities.",
keywords = "Constraint-based modeling, Data integration, Molecular path finding, Network biology, Oxygen, Saccharomyces cerevisiae",
author = "Erno Lindfors and Paula Jouhten and Merja Oja and Eija Rintala and Matej Orešič and Merja Penttil{\"a}",
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Integration of transcription and flux data reveals molecular paths associated with differences in oxygen-dependent phenotypes of Saccharomyces cerevisiae. / Lindfors, Erno; Jouhten, Paula; Oja, Merja; Rintala, Eija; Orešič, Matej; Penttilä, Merja.

In: BMC Systems Biology, Vol. 8, No. 1, 16, 14.02.2014.

Research output: Contribution to journalArticleScientificpeer-review

TY - JOUR

T1 - Integration of transcription and flux data reveals molecular paths associated with differences in oxygen-dependent phenotypes of Saccharomyces cerevisiae

AU - Lindfors, Erno

AU - Jouhten, Paula

AU - Oja, Merja

AU - Rintala, Eija

AU - Orešič, Matej

AU - Penttilä, Merja

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PY - 2014/2/14

Y1 - 2014/2/14

N2 - Background: Saccharomyces cerevisiae is able to adapt to a wide range of external oxygen conditions. Previously, oxygen-dependent phenotypes have been studied individually at the transcriptional, metabolite, and flux level. However, the regulation of cell phenotype occurs across the different levels of cell function. Integrative analysis of data from multiple levels of cell function in the context of a network of several known biochemical interaction types could enable identification of active regulatory paths not limited to a single level of cell function.Results: The graph theoretical method called Enriched Molecular Path detection (EMPath) was extended to enable integrative utilization of transcription and flux data. The utility of the method was demonstrated by detecting paths associated with phenotype differences of S. cerevisiae under three different conditions of oxygen provision: 20.9%, 2.8% and 0.5%. The detection of molecular paths was performed in an integrated genome-scale metabolic and protein-protein interaction network.Conclusions: The molecular paths associated with the phenotype differences of S. cerevisiae under conditions of different oxygen provisions revealed paths of molecular interactions that could potentially mediate information transfer between processes that respond to the particular oxygen availabilities.

AB - Background: Saccharomyces cerevisiae is able to adapt to a wide range of external oxygen conditions. Previously, oxygen-dependent phenotypes have been studied individually at the transcriptional, metabolite, and flux level. However, the regulation of cell phenotype occurs across the different levels of cell function. Integrative analysis of data from multiple levels of cell function in the context of a network of several known biochemical interaction types could enable identification of active regulatory paths not limited to a single level of cell function.Results: The graph theoretical method called Enriched Molecular Path detection (EMPath) was extended to enable integrative utilization of transcription and flux data. The utility of the method was demonstrated by detecting paths associated with phenotype differences of S. cerevisiae under three different conditions of oxygen provision: 20.9%, 2.8% and 0.5%. The detection of molecular paths was performed in an integrated genome-scale metabolic and protein-protein interaction network.Conclusions: The molecular paths associated with the phenotype differences of S. cerevisiae under conditions of different oxygen provisions revealed paths of molecular interactions that could potentially mediate information transfer between processes that respond to the particular oxygen availabilities.

KW - Constraint-based modeling

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