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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Journal ArticleDOI
Multigenerational cortical inheritance of the Rax2 protein in orienting polarity and division in yeast.
Tracy Chen,Takatoshi Hiroko,Amitabha Chaudhuri,Fumika Inose,Matthew Lord,Shigeko Tanaka,John Chant,Atsushi Fujita +7 more
TL;DR: Diploid yeast cells repeatedly polarize and bud from their poles, probably because of highly stable marks of unknown composition, and Rax2, a membrane protein, was shown to behave as such a mark.
Book ChapterDOI
DNA Microarrays in Drug Discovery and Development
TL;DR: DNA microarrays are widely used to address a plethora of scientific questions in the pharmaceutical industry, particularly in drug discovery and development and promises to play a key role in furthering research in a number of fields, as discussed in this chapter.
Journal ArticleDOI
Increased tRNA modification and gene-specific codon usage regulate cell cycle progression during the DNA damage response
Ashish Patil,Madhu Dyavaiah,Fraulin Joseph,John P. Rooney,Clement T Y Chan,Peter C. Dedon,Thomas J. Begley +6 more
TL;DR: The data supports a model in which codon usage and tRNA modification are regulatory components of the DNA damage response, with both playing vital roles in cell cycle progression.
Journal ArticleDOI
Microarray-Based Analysis of Early Development in Xenopus laevis
Curtis R. Altmann,Esther Bell,Alexander Sczyrba,Alexander Sczyrba,Jason Pun,Stefan Bekiranov,Terry Gaasterland,Ali H. Brivanlou +7 more
TL;DR: The power of these global approaches to examine transcriptional regulation globally, during early vertebrate embryonic development, is demonstrated and optimized protocols for their application to molecular embryology are provided.
Journal ArticleDOI
Reduction strategies for hierarchical multi-label classification in protein function prediction.
TL;DR: This work presents a new hierarchical multi-label classification method based on multiple neural networks for the task of protein function prediction that was able to learn the relationships between the protein functions during training, and was useful for classification.
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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Real time quantitative PCR.
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.