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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Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks
Paul Shannon,Andrew Markiel,Owen Ozier,Nitin S. Baliga,Jonathan T. Wang,Daniel Ramage,Nada Amin,Benno Schwikowski,Trey Ideker +8 more
TL;DR: Several case studies of Cytoscape plug-ins are surveyed, including a search for interaction pathways correlating with changes in gene expression, a study of protein complexes involved in cellular recovery to DNA damage, inference of a combined physical/functional interaction network for Halobacterium, and an interface to detailed stochastic/kinetic gene regulatory models.
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.
Journal ArticleDOI
Molecular portraits of human breast tumours
Charles M. Perou,Therese Sørlie,Michael B. Eisen,Matt van de Rijn,Stefanie S. Jeffrey,Christian A. Rees,Jonathan R. Pollack,Douglas T. Ross,Hilde Johnsen,Lars A. Akslen,Øystein Fluge,Alexander Pergamenschikov,Cheryl A. Williams,Shirley Zhu,Per Eystein Lønning,Anne Lise Børresen-Dale,Patrick O. Brown,David Botstein +17 more
TL;DR: Variation in gene expression patterns in a set of 65 surgical specimens of human breast tumours from 42 different individuals were characterized using complementary DNA microarrays representing 8,102 human genes, providing a distinctive molecular portrait of each tumour.
Journal ArticleDOI
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
TL;DR: 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.
Journal ArticleDOI
Quantitative analysis of complex protein mixtures using isotope-coded affinity tags
TL;DR: An approach for the accurate quantification and concurrent sequence identification of the individual proteins within complex mixtures based on isotope-coded affinity tags and tandem mass spectrometry is described.
References
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Journal ArticleDOI
RAP1: a protean regulator in yeast
TL;DR: The yeast protein RAP1 is a sequence-specific DNA-binding protein that binds to many promoters, to two elements that silence mating-type genes, and to [(C)1-3A]n tracts at telomeres.
Journal ArticleDOI
The Two Acetyl-coenzyme A Synthetases of Saccharomyces cerevisiae Differ with Respect to Kinetic Properties and Transcriptional Regulation
Marco A. van den Berg,Marco A. van den Berg,Patricia de Jong-Gubbels,Christine J. Kortland,Christine J. Kortland,Johannes P. van Dijken,Jack T. Pronk,H. Yde Steensma,H. Yde Steensma +8 more
TL;DR: Characterization of enzyme activities in cell-free extracts from strains expressing either of the ACS1 and ACS2 genes revealed differences in the catalytic properties of the two enzymes, indicating that ACS2 (in)directly is involved in the transcriptional regulation of ACS1.
Journal ArticleDOI
Cadmium tolerance mediated by the yeast AP-1 protein requires the presence of an ATP-binding cassette transporter-encoding gene, YCF1.
TL;DR: It is shown here that the YCF1 gene, encoding a likely integral membrane protein, is required for yAP-1 to exert its normal effects on cadmium tolerance and that an important physiological target of y AP-1 transcriptional regulation is the Y CF1 structural gene.
Journal ArticleDOI
The CYC8 and TUP1 proteins involved in glucose repression in Saccharomyces cerevisiae are associated in a protein complex.
TL;DR: The absence of DNA-binding motifs and the presence of these repeated domains suggest that the CYC8 and TUP1 proteins function via protein-protein interaction with transcriptional regulatory proteins.
Journal ArticleDOI
The Saccharomyces cerevisiae HSP12 gene is activated by the high-osmolarity glycerol pathway and negatively regulated by protein kinase A.
TL;DR: In this paper, an extended 5'-flanking region of the HSP12 gene was cloned in order to identify cis-acting elements involved in regulation of this highly expressed stress gene, and it was shown that five repeats of the stress-responsive CCCCT motif (STRE) are essential to confer wild-type induced levels on a reporter gene upon osmostress, heat shock, and entry into stationary phase.