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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Global gene expression during short‐term ethanol stress in Saccharomyces cerevisiae
TL;DR: ‘management’ of the energy pool (especially ATP) seems to constitute an ethanol stress response and to involve different mechanisms.
Journal ArticleDOI
Applications of dna microarrays in biology
TL;DR: Directed at the genome sequence itself, microarrays have been used to identify novel genes, binding sites of transcription factors, changes in DNA copy number, and variations from a baseline sequence, such as in emerging strains of pathogens or complex mutations in disease-causing human genes.
Journal ArticleDOI
Transcriptome analysis of all two‐component regulatory system mutants of Escherichia coli K‐12
Taku Oshima,Hirofumi Aiba,Yasushi Masuda,Shigehiko Kanaya,Masahito Sugiura,Barry L. Wanner,Hirotada Mori,Takeshi Mizuno +7 more
TL;DR: Results support the view that a network of functional interactions, such as cross‐regulation, exists between different two‐component systems of Escherichia coli.
Journal ArticleDOI
Improved Statistical Inference from DNA Microarray Data Using Analysis of Variance and A Bayesian Statistical Framework ANALYSIS OF GLOBAL GENE EXPRESSION IN ESCHERICHIA COLIK12
Anthony D. Long,Harry J. Mangalam,Bob Y.P. Chan,Lorenzo Tolleri,G. Wesley Hatfield,Pierre Baldi +5 more
TL;DR: New statistical tests based on thet test that can be conveniently used on high density array data to test for statistically significant differences between treatments identify genes that are up- or down-regulated following an experimental manipulation more reliably than approaches based only on a t test or fold change.
Journal ArticleDOI
Mitochondrial Dysfunction Leads to Nuclear Genome Instability via an Iron-Sulfur Cluster Defect
Joshua R. Veatch,Michael A. McMurray,Michael A. McMurray,Michael A. McMurray,Zara W. Nelson,Daniel E. Gottschling +5 more
TL;DR: It was found that downregulation of nonmitochondrial ISC protein biogenesis was sufficient to cause increased genomic instability in cells with intact mitochondrial function, which suggests mitochondrial dysfunction stimulates nuclear genome instability by inhibiting the production of ISC-containing protein(s), which are required for maintenance of nuclear genome integrity.
References
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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
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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.
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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.
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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.