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
Citations
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Transcriptional Coregulation by the Cell Integrity Mitogen-Activated Protein Kinase Slt2 and the Cell Cycle Regulator Swi4
TL;DR: A new Slt2-dependent mode of Swi 4 regulation is established and roles for Swi4 beyond its prominent role in controlling cell cycle transcription are suggested.
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Improving missing value estimation in microarray data with gene ontology
TL;DR: It is concluded that even a small proportion of annotated genes can provide improvements in data quality significant for the eventual interpretation of the microarray experiments, and by considering GO information in the k-nearest neighbor algorithm the authors can enhance its performance considerably.
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Artificial neural networks distinguish among subtypes of neoplastic colorectal lesions
Florin M. Selaru,Yan Xu,Jing Yin,Tong Zou,Thomas C. Liu,Yuriko Mori,John M. Abraham,Fumiaki Sato,Suna Wang,Charlie Twigg,Andreea Olaru,Valentina Shustova,Anatoly Leytin,Prodromos Hytiroglou,David Shibata,Noam Harpaz,Stephen J. Meltzer +16 more
TL;DR: The results suggest that ANNs have the potential to discriminate among subtly different clinical entities, such as IBDNs and SACs, as well as to identify gene subsets having the power to make these diagnostic distinctions.
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Microarray-based analysis of gene expression in very large gene families: the cytochrome P450 gene superfamily of Arabidopsis thaliana.
TL;DR: Experiments to systematically evaluate the specificity of P450 microarrays showed that conditions could be optimized to provide a very high degree of hybridization specificity, and exhibited essentially no cross-hybridization between families and within subfamilies.
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A Bayesian regression approach to the inference of regulatory networks from gene expression data
Simon Rogers,Mark Girolami +1 more
TL;DR: This work proposes a new algorithmic method for inferring interactions between genes using data from gene knockout experiments using the Sparse Bayesian regression algorithm of Tipping and Faul, which outperforms a recently published correlation-based approach.
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: 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.
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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.
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.