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Research Article

Model-Based Deconvolution of Cell Cycle Time-Series Data Reveals Gene Expression Details at High Resolution

  • Dan Siegal-Gaskins equal contributor mail,

    equal contributor Contributed equally to this work with: Dan Siegal-Gaskins, Joshua N. Ash

    dsg@mbi.osu.edu

    Affiliations: Mathematical Biosciences Institute, Ohio State University, Columbus, Ohio, United States of America, Department of Plant Cellular and Molecular Biology, Ohio State University, Columbus, Ohio, United States of America, Plant Biotechnology Center, Ohio State University, Columbus, Ohio, United States of America

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  • Joshua N. Ash equal contributor,

    equal contributor Contributed equally to this work with: Dan Siegal-Gaskins, Joshua N. Ash

    Affiliation: Department of Electrical and Computer Engineering, Ohio State University, Columbus, Ohio, United States of America

    X
  • Sean Crosson

    Affiliations: Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois, United States of America, The Committee on Microbiology, University of Chicago, Chicago, Illinois, United States of America

    X
  • Published: August 14, 2009
  • DOI: 10.1371/journal.pcbi.1000460

Reader Comments (2)

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Deconvolution done right

Posted by mfero on 07 Oct 2009 at 21:02 GMT

A very nice job getting deconvolved RNA expression data out of the raw expression data using a simple cell cycle model. I have tried gaussians with dispersion, but this looks like a better and well thought out approach. When will you have a MATLAB based tool for us to use? Somthing that could do simple time corrections of any kind of time course data would be nice. I think your method will benefit from better, more closely time-spaced expression data. I don't trust much of the expression data we have to give us much more than a qualitative look at expression regulation. I am skeptical of most of the high frequency wiggles given that there is no acknowlegement of errors, however I do believe you might be seeing a real effect in the step in CtrA expression. Nice Work.

No competing interests declared.