Comprehensive Identification of Cell Cycle–regulated Genes of the Yeast Saccharomyces cerevisiae by Microarray Hybridization
Paul T. Spellman,Gavin Sherlock,Gavin Sherlock,Michael Q. Zhang,Vishwanath R. Iyer,Kirk R. Anders,Michael B. Eisen,Patrick O. Brown,Patrick O. Brown,David Botstein,Bruce Futcher +10 more
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TLDR
A comprehensive catalog of yeast genes whose transcript levels vary periodically within the cell cycle is created, and it is found that the mRNA levels of more than half of these 800 genes respond to one or both of these cyclins.Abstract:
We sought to create a comprehensive catalog of yeast genes whose transcript levels vary periodically within the cell cycle. To this end, we used DNA microarrays and samples from yeast cultures sync...read more
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A stochastic differential equation model for quantifying transcriptional regulatory network in Saccharomyces cerevisiae
TL;DR: This study evaluated if the stochastic differential equation (SDE), which is prominent for modeling dynamic diffusion process originating from the irregular Brownian motion, can be applied in modeling the transcriptional regulatory network in Saccharomyces cerevisiae and results imply that advanced SDE model might be perfectly suited to portray transcriptional Regulatory networks.
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Statistical tests for identifying differentially expressed genes in time-course microarray experiments
Taesung Park,Sung-Gon Yi,Seungmook Lee,Seung Yeoun Lee,Dong-Hyun Yoo,Jun-Ik Ahn,Yong-Sung Lee +6 more
TL;DR: A statistical test procedure based on the ANOVA model is proposed to identify genes that have different gene expression profiles among experimental groups in time-course experiments and a permutation test which does not require the normality assumption is proposed.
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Sources of variability and effect of experimental approach on expression profiling data interpretation
TL;DR: It is found that experimental error was not a significant source of unwanted variability in expression profiling experiments, and pre-profile mixing of patient cRNA samples effectively normalized both intra- and inter-patient sources of variation.
Journal ArticleDOI
Defining the cell cycle for the tachyzoite stage of Toxoplasma gondii.
Jay R. Radke,Boris Striepen,Michael N. Guerini,Maria E. Jerome,David S. Roos,Michael W. White +5 more
TL;DR: In lieu of a short or missing G2, where checkpoints are thought to operate in other eukaryotes, the bimodal replication of tachyzoite chromosomes may represent a distinct premitotic checkpoint associated with endodyogeny.
Journal ArticleDOI
Genome-wide transcriptional analysis of the human cell cycle identifies genes differentially regulated in normal and cancer cells
Ziv Bar-Joseph,Zahava Siegfried,Michael Brandeis,Benedikt Brors,Yong Lu,Roland Eils,Brian David Dynlacht,Itamar Simon +7 more
TL;DR: Using a combined experimental and computational approach to deconvolve measured expression values into “single-cell” expression profiles, this work was able to overcome the limitations inherent in synchronizing nontransformed mammalian cells and identify 480 periodically expressed genes in primary human foreskin fibroblasts.
References
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TL;DR: A system of cluster analysis for genome-wide expression data from DNA microarray hybridization is described that uses standard statistical algorithms to arrange genes according to similarity in pattern of gene expression, finding in the budding yeast Saccharomyces cerevisiae that clustering gene expression data groups together efficiently genes of known similar function.
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TL;DR: The yeast Saccharomyces cerevisiae is now recognized as a model system representing a simple eukaryote whose genome can be easily manipulated and made particularly accessible to gene cloning and genetic engineering techniques.
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Raymond J. Cho,Michael J. Campbell,Elizabeth A. Winzeler,Lars M. Steinmetz,Andrew R. Conway,Lisa Wodicka,Tyra G. Wolfsberg,Andrei Gabrielian,David Landsman,David J. Lockhart,Ronald W. Davis +10 more
TL;DR: The genome-wide characterization of mRNA transcript levels during the cell cycle of the budding yeast S. cerevisiae indicates a mechanism for local chromosomal organization in global mRNA regulation and links a range of human genes to cell cycle period-specific biological functions.