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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Genomic analysis of gene expression relationships in transcriptional regulatory networks.
TL;DR: An extensive map of the transcriptional regulatory network in Saccharomyces cerevisiae is created, comprising 7419 interactions connecting 180 transcription factors with their target genes, and it is found that genes targeted by the same TF tend to be co-expressed, with the degree of co-expression increasing if genes share more than one TF.
Biclustering Algorithms: A Survey
TL;DR: Some of the algorithmic approaches to biclustering are reviewed and discussed and their properties are discussed.
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Learning Gene Functional Classifications from Multiple Data Types
TL;DR: This work considers the problem of inferring gene functional classifications from a heterogeneous data set consisting of DNA microarray expression measurements and phylogenetic profiles from whole-genome sequence comparisons and proposes an SVM kernel function that is explicitly heterogeneous.
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Selenoprotein R is a zinc-containing stereo-specific methionine sulfoxide reductase
TL;DR: A function of the conserved SelR enzyme family is identified, a pathway of methionine sulfoxide reduction is defined, a case of convergent evolution of similar function in structurally distinct enzymes is revealed, and a previously uncharacterized redox regulatory role of selenium in mammals is suggested.
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Cell cycle and checkpoint regulation of histone H3 K56 acetylation by Hst3 and Hst4
TL;DR: Evidence that Hst3 and Hst4, two paralogues of the histone deacetylase Sir2, target the cell cycle-regulated acetylation of H3 on K56 and are downregulated during DNA damage in a checkpoint-dependent manner is presented.
References
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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.
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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.