PMID: 11931391Apr 5, 2002Paper

Genome wide oscillations in expression. Wavelet analysis of time series data from yeast expression arrays uncovers the dynamic architecture of phenotype

Molecular Biology Reports
Robert R Klevecz, Douglas B Murray

Abstract

A reanalysis of expression arrays in yeast cells synchronized by alpha factor blockade or through the use of temperature sensitive mutants uncovered a genome wide pattern of oscillations in mRNA concentrations. Using wavelet decomposition as a signal processing technique and enhancement strategies borrowed from image processing, noise and trends in the Stanford yeast cell cycle data were partitioned away from time series profiles to uncover genome-wide oscillations in expression. These oscillations which were typically of cell cycle or half cell cycle duration, 40 and 80 minutes in the Stanford data set suggest that there are large-scale temporal structures and high frequency oscillations in mRNA levels through the cell cycle. Wavelet decomposition, which acts like a band pass filter bank, was used to determine where most of the power appeared in the decomposition. The approximately 40-min oscillation is mirrored in continuous chemostat cultures. In these cultures, metabolic synchrony involving an unknown proportion of the transcriptome can be monitored by measurement of oxygen consumption and can be sustained for weeks. These 40-min oscillations are stable and precise with coefficients of variation less than 1% for both period...Continue Reading

Citations

Mar 28, 2008·Theory in Biosciences = Theorie in Den Biowissenschaften·Joseph P Zbilut, Alessandro Giuliani
Oct 20, 2010·International Journal of Molecular Sciences·Ildefonso Martínez de la Fuente
Jun 22, 2010·Journal of Biological Dynamics·Erik M BoczkoTodd R Young
Oct 11, 2014·PloS One·Ildefonso M De la FuenteLuis Martínez
Jul 12, 2002·Yeast
Nov 6, 2009·PloS One·Ildefonso M De la FuenteJuan Veguillas
Oct 14, 2011·BMC Systems Biology·Aliz R Rao, Matteo Pellegrini
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Nov 5, 2014·Frontiers in Cell and Developmental Biology·Cornelia AmarieiDouglas B Murray
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May 13, 2014·Journal of Mathematical Biology·Nathan BreitschTodd Young
Jan 22, 2004·Proceedings of the National Academy of Sciences of the United States of America·Robert R KleveczDouglas B Murray
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Nov 3, 2020·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Ovidiu PopaOliver Ebenhöh
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