Journal ArticleDOI
Exploring the Metabolic and Genetic Control of Gene Expression on a Genomic Scale
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TLDR
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.Abstract:
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. The expression profiles observed for genes with known metabolic functions pointed to features of the metabolic reprogramming that occur during the diauxic shift, and the expression patterns of many previously uncharacterized genes provided clues to their possible functions. The same DNA microarrays were also used to identify genes whose expression was affected by deletion of the transcriptional co-repressor TUP1 or overexpression of the transcriptional activator YAP1. These results demonstrate the feasibility and utility of this approach to genomewide exploration of gene expression patterns.read more
Citations
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Journal ArticleDOI
Global Gene Expression Profiles of Bacillus subtilis Grown under Anaerobic Conditions
TL;DR: Bacillus subtilis can grow under anaerobic conditions, either with nitrate or nitrite as the electron acceptor or by fermentation, and several hundred genes were observed to be induced or repressed under an aerobic conditions.
Journal ArticleDOI
Integrative Analysis of the Mitochondrial Proteome in Yeast
Holger Prokisch,Curt Scharfe,David G. Camp,Wenzhong Xiao,Lior David,Christophe Andreoli,Matthew E. Monroe,Ronald J. Moore,Marina A. Gritsenko,Christian Kozany,Kim K. Hixson,Heather M. Mottaz,Hans Zischka,Marius Ueffing,Zelek S. Herman,Ronald W. Davis,Thomas Meitinger,Peter J. Oefner,Richard D. Smith,Lars M. Steinmetz +19 more
TL;DR: It is shown that a combination of complementary approaches like deletion phenotype screening and mass spectrometry can identify over 75% of the known mitochondrial proteome, which has implications for choosing optimal genome-wide approaches for the study of other cellular systems, including organelles and pathways in various species.
Journal ArticleDOI
Applications of DNA microarrays in microbial systems.
TL;DR: DNA microarray technology allows a parallel analysis of RNA abundance and DNA homology for thousands of genes in a single experiment, greatly facilitating understanding of microbial metabolism.
Journal ArticleDOI
Genome-wide expression patterns in Saccharomyces cerevisiae : Comparison of drug treatments and genetic alterations affecting biosynthesis of ergosterol
TL;DR: In this paper, genome-wide transcript profiles following exposure to a number of antifungal agents targeting ergosterol biosynthesis (clotrimazole, fluconazole and itraconazole) were obtained.
Journal ArticleDOI
High-throughput screening of small molecules in miniaturized mammalian cell-based assays involving post-translational modifications
Brent R. Stockwell,Brent R. Stockwell,Stephen J. Haggarty,Stephen J. Haggarty,Stuart L. Schreiber,Stuart L. Schreiber +5 more
TL;DR: A miniaturized cell-based assay format that enables a genetic-like approach to understanding cellular pathways in mammalian systems using small molecules, rather than mutations, as the source of gene-product alterations, and is applicable to understanding a wide variety of cellular processes, especially those involving post-transitional modifications.
References
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Journal ArticleDOI
Quantitative monitoring of gene expression patterns with a complementary DNA microarray.
TL;DR: A high-capacity system was developed to monitor the expression of many genes in parallel by means of simultaneous, two-color fluorescence hybridization, which enabled detection of rare transcripts in probe mixtures derived from 2 micrograms of total cellular messenger RNA.
PatentDOI
Expression monitoring by hybridization to high density oligonucleotide arrays
TL;DR: In this article, the authors proposed a method for monitoring the expression levels of a multiplicity of genes by hybridizing a nucleic acid sample to a high density array of oligonucleotide probes and quantifying the hybridized nucleic acids in the array.
Journal ArticleDOI
Use of a cDNA microarray to analyse gene expression patterns in human cancer.
Joseph L. DeRisi,Lolita Penland,Patrick O. Brown,M. L. Bittner,P. S. Meltzer,M. Ray,Yi Chen,Y. A. Su,J. M. Trent +8 more
TL;DR: Previously unrecognized alterations in the expression of specific genes provide leads for further investigation of the genetic basis of the tumorigenic phenotype of these cells.
Journal ArticleDOI
Accessing Genetic Information with High-Density DNA Arrays
Mark S. Chee,Robert Yang,Earl Hubbell,Anthony Berno,Xiaohua C. Huang,David Stern,Jim Winkler,David J. Lockhart,Macdonald S. Morris,Stephen P. A. Fodor +9 more
TL;DR: The simultaneous analysis of the entire human mitochondrial genome is described here and can be used to address a variety of questions in molecular genetics including gene expression, genetic linkage, and genetic variability.
Journal ArticleDOI
A DNA microarray system for analyzing complex DNA samples using two-color fluorescent probe hybridization.
TL;DR: This work describes a general experimental approach, using microscopic arrays of DNA fragments on glass substrates for differential hybridization analysis of fluorescently labeled DNA samples, and demonstrates the utility of DNA microarrays in the analysis of complex DNA samples.