IDEAS home Printed from https://ideas.repec.org/a/eee/phsmap/v430y2015icp224-235.html
   My bibliography  Save this article

Effect of environmental stress on regulation of gene expression in the yeast

Author

Listed:
  • Gross, Eitan

Abstract

Several mathematical models have been proposed to predict the activation state of a transcription factor (TF) from the expression levels of its target genes. This inference problem is complicated however due to the fact that different genes may be regulated by different activation schemes (linear, exponential, sigmoidal, etc.). In addition to transcription regulation, the rate of gene expression at any instantaneous point in time is also determined by the independent rates of baseline production and degradation. Consequently, the set of solutions to any model equations describe an infinite number of trajectories in probability space, thus rendering the problem NP-hard. In the current study we used a Gaussian process (GP) approach to address this inverse problem. Experimental gene expression data were modeled by a putative linear activation scheme and discrepancy between theory and experiment was modeled by a GP. Model hyperparameters were calculated using maximum likelihood estimates to generate continuous TF state-space profiles. Identifiability of model parameters was optimized by obtaining TF state-space functions for multiple genes simultaneously. We found that model parameters were sensitive to environmental stress conditions, producing different state-space profiles for different stresses.

Suggested Citation

  • Gross, Eitan, 2015. "Effect of environmental stress on regulation of gene expression in the yeast," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 430(C), pages 224-235.
  • Handle: RePEc:eee:phsmap:v:430:y:2015:i:c:p:224-235
    DOI: 10.1016/j.physa.2015.02.076
    as

    Download full text from publisher

    File URL: http://www.sciencedirect.com/science/article/pii/S0378437115001995
    Download Restriction: Full text for ScienceDirect subscribers only. Journal offers the option of making the article available online on Science direct for a fee of $3,000

    File URL: https://libkey.io/10.1016/j.physa.2015.02.076?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    As the access to this document is restricted, you may want to search for a different version of it.

    References listed on IDEAS

    as
    1. R. Khanin & V. Vinciotti & V. Mersinias & C. P. Smith & E. Wit, 2007. "Statistical Reconstruction of Transcription Factor Activity Using Michaelis–Menten Kinetics," Biometrics, The International Biometric Society, vol. 63(3), pages 816-823, September.
    2. Vincent J. Lynch & Gemma May & Günter P. Wagner, 2011. "Regulatory evolution through divergence of a phosphoswitch in the transcription factor CEBPB," Nature, Nature, vol. 480(7377), pages 383-386, December.
    3. S. Conti & J. P. Gosling & J. E. Oakley & A. O'Hagan, 2009. "Gaussian process emulation of dynamic computer codes," Biometrika, Biometrika Trust, vol. 96(3), pages 663-676.
    4. Marc C. Kennedy & Anthony O'Hagan, 2001. "Bayesian calibration of computer models," Journal of the Royal Statistical Society Series B, Royal Statistical Society, vol. 63(3), pages 425-464.
    5. Christopher T. Harbison & D. Benjamin Gordon & Tong Ihn Lee & Nicola J. Rinaldi & Kenzie D. Macisaac & Timothy W. Danford & Nancy M. Hannett & Jean-Bosco Tagne & David B. Reynolds & Jane Yoo & Ezra G., 2004. "Transcriptional regulatory code of a eukaryotic genome," Nature, Nature, vol. 431(7004), pages 99-104, September.
    6. Stephan B. Schawalder & Mehdi Kabani & Isabelle Howald & Urmila Choudhury & Michel Werner & David Shore, 2004. "Growth-regulated recruitment of the essential yeast ribosomal protein gene activator Ifh1," Nature, Nature, vol. 432(7020), pages 1058-1061, December.
    Full references (including those not matched with items on IDEAS)

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Mohammadi, Hossein & Challenor, Peter & Goodfellow, Marc, 2019. "Emulating dynamic non-linear simulators using Gaussian processes," Computational Statistics & Data Analysis, Elsevier, vol. 139(C), pages 178-196.
    2. Bozağaç, Doruk & Batmaz, İnci & Oğuztüzün, Halit, 2016. "Dynamic simulation metamodeling using MARS: A case of radar simulation," Mathematics and Computers in Simulation (MATCOM), Elsevier, vol. 124(C), pages 69-86.
    3. Raymond K. W. Wong & Curtis B. Storlie & Thomas C. M. Lee, 2017. "A frequentist approach to computer model calibration," Journal of the Royal Statistical Society Series B, Royal Statistical Society, vol. 79(2), pages 635-648, March.
    4. Nott, David J. & Marshall, Lucy & Fielding, Mark & Liong, Shie-Yui, 2014. "Mixtures of experts for understanding model discrepancy in dynamic computer models," Computational Statistics & Data Analysis, Elsevier, vol. 71(C), pages 491-505.
    5. Reichert, P. & White, G. & Bayarri, M.J. & Pitman, E.B., 2011. "Mechanism-based emulation of dynamic simulation models: Concept and application in hydrology," Computational Statistics & Data Analysis, Elsevier, vol. 55(4), pages 1638-1655, April.
    6. Jackson Samuel E. & Vernon Ian & Liu Junli & Lindsey Keith, 2020. "Understanding hormonal crosstalk in Arabidopsis root development via emulation and history matching," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 19(2), pages 1-33, April.
    7. Priscilla Avegliano & Jaime Simão Sichman, 2023. "Equation-Based Versus Agent-Based Models: Why Not Embrace Both for an Efficient Parameter Calibration?," Journal of Artificial Societies and Social Simulation, Journal of Artificial Societies and Social Simulation, vol. 26(4), pages 1-3.
    8. Yawen Guan & Christian Sampson & J. Derek Tucker & Won Chang & Anirban Mondal & Murali Haran & Deborah Sulsky, 2019. "Computer Model Calibration Based on Image Warping Metrics: An Application for Sea Ice Deformation," Journal of Agricultural, Biological and Environmental Statistics, Springer;The International Biometric Society;American Statistical Association, vol. 24(3), pages 444-463, September.
    9. Matthias Katzfuss & Joseph Guinness & Wenlong Gong & Daniel Zilber, 2020. "Vecchia Approximations of Gaussian-Process Predictions," Journal of Agricultural, Biological and Environmental Statistics, Springer;The International Biometric Society;American Statistical Association, vol. 25(3), pages 383-414, September.
    10. Hao Wu & Michael Browne, 2015. "Random Model Discrepancy: Interpretations and Technicalities (A Rejoinder)," Psychometrika, Springer;The Psychometric Society, vol. 80(3), pages 619-624, September.
    11. Xiaoyu Xiong & Benjamin D. Youngman & Theodoros Economou, 2021. "Data fusion with Gaussian processes for estimation of environmental hazard events," Environmetrics, John Wiley & Sons, Ltd., vol. 32(3), May.
    12. Matvei Khoroshkin & Andrey Buyan & Martin Dodel & Albertas Navickas & Johnny Yu & Fathima Trejo & Anthony Doty & Rithvik Baratam & Shaopu Zhou & Sean B. Lee & Tanvi Joshi & Kristle Garcia & Benedict C, 2024. "Systematic identification of post-transcriptional regulatory modules," Nature Communications, Nature, vol. 15(1), pages 1-21, December.
    13. Petropoulos, G. & Wooster, M.J. & Carlson, T.N. & Kennedy, M.C. & Scholze, M., 2009. "A global Bayesian sensitivity analysis of the 1d SimSphere soil–vegetation–atmospheric transfer (SVAT) model using Gaussian model emulation," Ecological Modelling, Elsevier, vol. 220(19), pages 2427-2440.
    14. Drignei, Dorin, 2011. "A general statistical model for computer experiments with time series output," Reliability Engineering and System Safety, Elsevier, vol. 96(4), pages 460-467.
    15. Yuan, Jun & Ng, Szu Hui, 2013. "A sequential approach for stochastic computer model calibration and prediction," Reliability Engineering and System Safety, Elsevier, vol. 111(C), pages 273-286.
    16. Edward Boone & Jan Hannig & Ryad Ghanam & Sujit Ghosh & Fabrizio Ruggeri & Serge Prudhomme, 2022. "Model Validation of a Single Degree-of-Freedom Oscillator: A Case Study," Stats, MDPI, vol. 5(4), pages 1-17, November.
    17. Abokersh, Mohamed Hany & Vallès, Manel & Cabeza, Luisa F. & Boer, Dieter, 2020. "A framework for the optimal integration of solar assisted district heating in different urban sized communities: A robust machine learning approach incorporating global sensitivity analysis," Applied Energy, Elsevier, vol. 267(C).
    18. Campbell, Katherine, 2006. "Statistical calibration of computer simulations," Reliability Engineering and System Safety, Elsevier, vol. 91(10), pages 1358-1363.
    19. Perrin, G., 2016. "Active learning surrogate models for the conception of systems with multiple failure modes," Reliability Engineering and System Safety, Elsevier, vol. 149(C), pages 130-136.
    20. Antony M. Overstall & David C. Woods, 2016. "Multivariate emulation of computer simulators: model selection and diagnostics with application to a humanitarian relief model," Journal of the Royal Statistical Society Series C, Royal Statistical Society, vol. 65(4), pages 483-505, August.

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:eee:phsmap:v:430:y:2015:i:c:p:224-235. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Catherine Liu (email available below). General contact details of provider: http://www.journals.elsevier.com/physica-a-statistical-mechpplications/ .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.