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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Coordinated Progression through Two Subtranscriptomes Underlies the Tachyzoite Cycle of Toxoplasma gondii
Michael S. Behnke,Michael S. Behnke,John C. Wootton,Margaret M. Lehmann,Joshua B. Radke,Joshua B. Radke,Olivier Lucas,Julie Nawas,L. David Sibley,Michael W. White,Michael W. White +10 more
TL;DR: The mechanisms responsible for cyclical gene expression timing are likely crucial to the efficiency of parasite replication and may provide new avenues for interfering with parasite growth.
Journal ArticleDOI
Building a dictionary for genomes: identification of presumptive regulatory sites by statistical analysis.
TL;DR: MobyDick as mentioned in this paper decomposes a set of DNA sequences into the most probable dictionary of motifs or words, which can be used to identify genes that are upregulated or downregulated.
Journal ArticleDOI
Phosphatidic Acid Is a pH Biosensor That Links Membrane Biogenesis to Metabolism
Barry P. Young,John J.H. Shin,Rick Orij,Jesse T. Chao,Shu Chen Li,Xue Li Guan,Xue Li Guan,Anthony Khong,Eric Jan,Markus R. Wenk,Markus R. Wenk,Markus R. Wenk,William A. Prinz,Gertien J. Smits,Christopher J. R. Loewen +14 more
TL;DR: In yeast, a rapid decrease in intracellular pH in response to glucose starvation regulated binding of PA to a transcription factor, Opi1, that coordinately repressed phospholipid metabolic genes, which enabled coupling of membrane biogenesis to nutrient availability.
Journal ArticleDOI
Multivariate regression analysis of distance matrices for testing associations between gene expression patterns and related variables
TL;DR: The proposed multivariate method avoids the need for reducing the dimensions of a similarity matrix, can be used to assess relationships between the genes used to construct the matrix and additional information collected on the samples under study, and can be use to analyze individual genes or groups of genes identified in different ways.
Journal ArticleDOI
Single-Molecule mRNA Decay Measurements Reveal Promoter- Regulated mRNA Stability in Yeast
TL;DR: This work found that two genes responsible for mitotic progression, SWI5 and CLB2, exhibit a mitosis-dependent mRNA stability switch, revealing the promoter-dependent control of mRNA stability, a regulatory mechanism that could be employed by a variety of mRNAs and organisms.
References
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Journal ArticleDOI
Cluster analysis and display of genome-wide expression patterns
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: Unlike other quantitative PCR methods, real-time PCR does not require post-PCR sample handling, preventing potential PCR product carry-over contamination and resulting in much faster and higher throughput assays.
Journal ArticleDOI
Exploring the Metabolic and Genetic Control of Gene Expression on a Genomic Scale
TL;DR: DNA microarrays containing virtually every gene of Saccharomyces cerevisiae were used to carry out a comprehensive investigation of the temporal program of gene expression accompanying the metabolic shift from fermentation to respiration, and the expression patterns of many previously uncharacterized genes provided clues to their possible functions.
Book ChapterDOI
Getting started with yeast.
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.
Journal ArticleDOI
A Genome-Wide Transcriptional Analysis of the Mitotic Cell Cycle
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.