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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Modelling Gene Expression Data using Dynamic Bayesian Networks
TL;DR: This paper shows that most of the proposed discrete time models — including the boolean network model [Kau93, SS96], the linear model of D’haeseleer et al.
Journal ArticleDOI
Gene expression informatics--it's all in your mine.
TL;DR: Improved access to large electronic data sets, reliable and consistent annotation and effective tools for 'data mining' are critical to realize the full potential of whole–genome RNA expression studies.
Journal ArticleDOI
Genome-wide expression profiling of mid-gestation placenta and embryo using a 15,000 mouse developmental cDNA microarray
Tetsuya S. Tanaka,Saied A. Jaradat,Meng K. Lim,George J. Kargul,Xiaohong Wang,Marija J. Grahovac,Serafino Pantano,Yuri Sano,Yulan Piao,Ramaiah Nagaraja,Hirofumi Doi,William H. Wood,Kevin G. Becker,Minoru S.H. Ko +13 more
TL;DR: The number of genes highly expressed (and frequently specific) for placenta has been increased 5-fold over the total previously reported, illustrating the potential of the microarrays for tissue-specific gene discovery and analysis of mammalian developmental programs.
Journal ArticleDOI
A higher-order background model improves the detection of promoter regulatory elements by Gibbs sampling.
Gert Thijs,Magali Lescot,Kathleen Marchal,Stephane Rombauts,Bart De Moor,Pierre Rouzé,Yves Moreau +6 more
TL;DR: It is shown that the use of a higher-order model considerably enhances the performance of the motif finding algorithm in the presence of noisy data.
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Finding consistent patterns: A nonparametric approach for identifying differential expression in RNA-Seq data
Jun Li,Robert Tibshirani +1 more
TL;DR: A simple, non-parametric method with resampling to account for the different sequencing depths is introduced, and it is found that the method discovers more consistent patterns than competing methods.
References
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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.
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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.