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
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A Gene Signature Predictive for Outcome in Advanced Ovarian Cancer Identifies a Survival Factor: Microfibril-Associated Glycoprotein 2
Samuel C. Mok,Tomas Bonome,Vinod Vathipadiekal,Aaron Bell,Michael E. Johnson,Kwong Kwok Wong,Dong Choon Park,Dong Choon Park,Ke Hao,Daniel K.P. Yip,Howard Donninger,Laurent Ozbun,Goli Samimi,John N. Brady,Mike Randonovich,Cindy Pise-Masison,J. Carl Barrett,Wing Hung Wong,William R. Welch,Ross S. Berkowitz,Ross S. Berkowitz,Michael J. Birrer +21 more
TL;DR: Independent evaluation confirmed the association of a prognostic gene microfibril-associated glycoprotein 2 (MAGP2) with poor prognosis, whereas in vitro mechanistic analyses demonstrated its ability to prolong tumor cell survival and stimulate endothelial cell motility and survival via the alpha(V)beta(3) integrin receptor.
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Widespread collaboration of Isw2 and Sin3-Rpd3 chromatin remodeling complexes in transcriptional repression.
Thomas G. Fazzio,Charles Kooperberg,Jesse P. Goldmark,Cassandra L. Neal,Ryan Basom,Jeffrey J. Delrow,Toshio Tsukiyama +6 more
TL;DR: These data suggest that the Isw2 complex functions at Ume6-dependent and -independent loci to create DNase I-inaccessible chromatin structure by regulating the positioning or placement of nucleosomes.
Journal ArticleDOI
Adaptive quality-based clustering of gene expression profiles
TL;DR: A novel adaptive quality-based clustering algorithm that tackles some of the drawbacks of classical clustering algorithms and derives an optimal radius of the cluster so that only the significantly coexpressed genes are included in the cluster.
Journal ArticleDOI
Charting latency transcripts in Kaposi's sarcoma-associated herpesvirus by whole-genome real-time quantitative PCR.
TL;DR: It is demonstrated that the mRNA levels for KSHV LANA, v-cyclin, and v-FLIP do not increase at any time after viral reactivation, and the mRNA for LANA-2/vIRF-3 is similarly resistant to viral reactivating.
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Mechanism of metabolic control. Target of rapamycin signaling links nitrogen quality to the activity of the Rtg1 and Rtg3 transcription factors.
TL;DR: The results demonstrate that target of rapamycin signaling regulates specific anaplerotic reactions by coupling nitrogen quality to the activity and subcellular localization of distinct transcription factors.
References
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Journal ArticleDOI
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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.