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
Coordination of Growth Rate, Cell Cycle, Stress Response, and Metabolic Activity in Yeast
Matthew J. Brauer,Curtis Huttenhower,Edoardo M. Airoldi,Rachel Rosenstein,Rachel Rosenstein,John C. Matese,David Gresham,Viktor Marius Boer,Olga G. Troyanskaya,David Botstein +9 more
TL;DR: Using an aggregate of gene expression values, an "instantaneous growth rate" is predicted, useful in interpreting the system-level connections among growth rate, metabolism, stress, and the cell cycle.
Journal ArticleDOI
Analysis of gene expression data using self‐organizing maps
TL;DR: The SOM algorithm is applied to analyze published data of yeast gene expression and it is shown that SOM is an excellent tool for the analysis and visualization of gene expression profiles.
Journal ArticleDOI
Uncovering transcriptional regulation of metabolism by using metabolic network topology.
TL;DR: An algorithm that is based on hypothesis-driven data analysis to uncover the transcriptional regulatory architecture of metabolic networks is developed and finds that cells respond to perturbations by changing the expression pattern of several genes involved in the specific part of the metabolism in which a perturbation is introduced.
Journal ArticleDOI
Shifts in growth strategies reflect tradeoffs in cellular economics
TL;DR: It is shown how the shift in metabolic efficiency originates from a tradeoff between investments in enzyme synthesis and metabolic yields for alternative catabolic pathways, and elucidate how the optimization of growth by natural selection shapes growth strategies.
Journal ArticleDOI
GeoChip: a comprehensive microarray for investigating biogeochemical, ecological and environmental processes
Zhili He,Terry J. Gentry,Terry J. Gentry,Christopher W. Schadt,Liyou Wu,Liyou Wu,Jost Liebich,Jost Liebich,Song C. Chong,Zhijian Huang,Zhijian Huang,Wei-Min Wu,Baohua Gu,Phil Jardine,Craig S. Criddle,Jizhong Zhou,Jizhong Zhou +16 more
TL;DR: This is the first comprehensive microarray currently available for studying biogeochemical processes and functional activities of microbial communities important to human health, agriculture, energy, global climate change, ecosystem management, and environmental cleanup and restoration.
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.