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Analysis of Time-Resolved Gene Expression Measurements across Individuals

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  • Laura L Elo
  • Benno Schwikowski

Abstract

Genetic and environmental determinants of altered cellular function, disease state, and drug response are increasingly studied using time-resolved transcriptomic profiles. While it is widely acknowledged that the rate of biological processes may vary between individuals, data analysis approaches that go beyond evaluating differential expression of single genes have so far not taken this variability into account. To this end, we introduce here a robust multi-gene data analysis approach and evaluate it in a biomarker discovery scenario across four publicly available datasets. In our evaluation, existing methods perform surprisingly poorly on time-resolved data; only the approach taking the variability into account yields reproducible and biologically plausible results. Our results indicate the need to capture gene expression between potentially heterogeneous individuals at multiple time points, and highlight the importance of robust data analysis in the presence of heterogeneous gene expression responses.

Suggested Citation

  • Laura L Elo & Benno Schwikowski, 2013. "Analysis of Time-Resolved Gene Expression Measurements across Individuals," PLOS ONE, Public Library of Science, vol. 8(12), pages 1-8, December.
  • Handle: RePEc:plo:pone00:0082340
    DOI: 10.1371/journal.pone.0082340
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    1. Miriam F. Moffatt & Michael Kabesch & Liming Liang & Anna L. Dixon & David Strachan & Simon Heath & Martin Depner & Andrea von Berg & Albrecht Bufe & Ernst Rietschel & Andrea Heinzmann & Burkard Simma, 2007. "Genetic variants regulating ORMDL3 expression contribute to the risk of childhood asthma," Nature, Nature, vol. 448(7152), pages 470-473, July.
    2. Valur Emilsson & Gudmar Thorleifsson & Bin Zhang & Amy S. Leonardson & Florian Zink & Jun Zhu & Sonia Carlson & Agnar Helgason & G. Bragi Walters & Steinunn Gunnarsdottir & Magali Mouy & Valgerdur Ste, 2008. "Genetics of gene expression and its effect on disease," Nature, Nature, vol. 452(7186), pages 423-428, March.
    3. Stephen B. Montgomery & Micha Sammeth & Maria Gutierrez-Arcelus & Radoslaw P. Lach & Catherine Ingle & James Nisbett & Roderic Guigo & Emmanouil T. Dermitzakis, 2010. "Transcriptome genetics using second generation sequencing in a Caucasian population," Nature, Nature, vol. 464(7289), pages 773-777, April.
    4. Michael Morley & Cliona M. Molony & Teresa M. Weber & James L. Devlin & Kathryn G. Ewens & Richard S. Spielman & Vivian G. Cheung, 2004. "Genetic analysis of genome-wide variation in human gene expression," Nature, Nature, vol. 430(7001), pages 743-747, August.
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