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
Dynamics of the yeast transcriptome during wine fermentation reveals a novel fermentation stress response
Virginia D. Marks,Shannan J. Ho Sui,Daniel J. Erasmus,George van der Merwe,Jochen Brumm,Wyeth W. Wasserman,Jennifer Bryan,Hennie J.J. van Vuuren +7 more
TL;DR: Genes involved in respiratory metabolism and gluconeogenesis were expressed during fermentation despite the presence of high concentrations of glucose, and Ethanol, rather than nutrient depletion, seems to be responsible for entry of yeast cells into the stationary phase.
Journal ArticleDOI
Empirical Establishment of Oligonucleotide Probe Design Criteria
TL;DR: A set of criteria are suggested for the design of gene-specific and group-specific oligonucleotide probes, and the experimentally established criteria should provide valuable information for new software and algorithms for microarray-based studies.
Journal ArticleDOI
Comparative analysis of plastid transcription profiles of entire plastid chromosomes from tobacco attributed to wild-type and PEP-deficient transcription machineries
Julia Legen,Sabine Kemp,Kirsten Krause,Birgit Profanter,Reinhold G. Herrmann,Rainer M. Maier +5 more
TL;DR: The findings show that the absence of photosynthesis-related, plastome-encoded polypeptides in PEP-deficient plants is not directly caused by a lack of transcription by PEP, and demonstrate that the functional integration of PEP and NEP into the genetic system of the plant cell during evolution is substantially more complex than presently supposed.
Journal ArticleDOI
GeneNote: whole genome expression profiles in normal human tissues
Orit Shmueli,Shirley Horn-Saban,Vered Chalifa-Caspi,Michael Shmoish,Ron Ophir,Hila Benjamin-Rodrig,Marilyn Safran,Eytan Domany,Doron Lancet +8 more
TL;DR: A novel data set, GeneNote (Gene Normal Tissue Expression), was produced to portray complete gene expression profiles in healthy human tissues using the Affymetrix GeneChip HG-U95 set, which includes 62 839 probe-sets.
Journal ArticleDOI
Global transcriptional program of p53 target genes during the process of apoptosis and cell cycle progression
Asra Mirza,Qun Wu,Luquan Wang,Terri McClanahan,W. Robert Bishop,Ferdous Gheyas,Wei Ding,Beth Hutchins,Tish Hockenberry,Paul Kirschmeier,Jonathan R. Greene,Suxing Liu +11 more
TL;DR: A small-scale quantitative chromatin immunoprecipitation analysis indicated that in vivo p53–DNA interaction was detected in eight out of 10 genes, suggesting that a portion of p53 target genes in the human genome could be negatively regulated by p53 via sequence-specific DNA binding.
References
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PatentDOI
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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
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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
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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.