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
Dynamical analysis of gene networks requires both mRNA and protein expression information
TL;DR: A mechanistic model for circadian rhythmicity is considered which shows agreement with experimental observations when protein and mRNA information are included and a framework for acquiring and analyzing experimental and mathematically derived information about gene networks is proposed.
Dissertation
Principled computational methods for the validation and discovery of genetic regulatory networks
TL;DR: This work demonstrates how graphical models, and Bayesian networks in particular, can be used to model genetic regulatory networks and develops methods for extending Bayesian network semantics to include edge annotations that allow us to model statistical dependencies between biological factors with greater refinement.
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Identification and analysis of Arabidopsis expressed sequence tags characteristic of non-coding RNAs.
TL;DR: In this paper, the authors identified 19 clones with characteristics of ncRNAs, nine putative peptide-coding RNAs with open reading frames smaller than 100 amino acids, and 11 that could not be differentiated between the two categories.
Journal ArticleDOI
Filling gaps in a metabolic network using expression information
TL;DR: The MEP method is complementary to the sequence homology and genome context methods that are currently being used to identify missing metabolic genes and predicts over 20% of all known Saccharomyces cerevisiae metabolic enzyme-encoding genes within the top 50 out of 5594 candidates for their enzymatic function.
Journal ArticleDOI
Strong feature sets from small samples.
Seungchan Kim,Edward R. Dougherty,Junior Barrera,Yi Chen,Michael L. Bittner,Jeffrey M. Trent +5 more
TL;DR: This paper proposes mitigating the small-sample problem by designing classifiers from a probability distribution resulting from spreading the mass of the sample points to make classification more difficult, while maintaining sample geometry.
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.