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Expressed Repeat Elements Improve RT-qPCR Normalization across a Wide Range of Zebrafish Gene Expression Studies

by Suzanne Vanhauwaert, Gert Van Peer, Ali Rihani, Els Janssens, Pieter Rondou, Steve Lefever, Anne De, Paul J. Coucke, Frank Speleman, Jo V, Andy Willaert , 2014
"... The selection and validation of stably expressed reference genes is a critical issue for proper RT-qPCR data normalization. In zebrafish expression studies, many commonly used reference genes are not generally applicable given their variability in expression levels under a variety of experimental co ..."
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conditions. Inappropriate use of these reference genes may lead to false interpretation of expression data and unreliable conclusions. In this study, we evaluated a novel normalization method in zebrafish using expressed repetitive elements (ERE) as reference targets, instead of specific protein coding m

Finding groups in gene expression data

by David J Hand , Nicholas A Heard - J Biomed Biotechnol
"... The vast potential of the genomic insight offered by microarray technologies has led to their widespread use since they were introduced a decade ago. Application areas include gene function discovery, disease diagnosis, and inferring regulatory networks. Microarray experiments enable large-scale, h ..."
Abstract - Cited by 10 (0 self) - Add to MetaCart
. This paper reviews these various tools for finding interesting subgroups. INTRODUCTION Microarray gene expression studies are now routinely used to measure the transcription levels of an organism's genes at a particular instant of time. These mRNA levels serve as a proxy for either the level

Gene expression study of the flavodiiron proteins from the cyanobacterium Synechocystis sp

by Vera L Gonçalves , Lígia M Saraiva , Miguel Teixeira - PCC 6803. Biochem. Soc. Trans. 2011
"... Abstract The flavodi-iron proteins, also named FDPs, are an extensive family of enzymes able to reduce dioxygen to water and/or nitric oxide to nitrous oxide. These proteins are formed by a metallo-β-lactamase-like module with a di-iron catalytic site fused to a flavodoxin-like module bearing an FM ..."
Abstract - Cited by 1 (0 self) - Add to MetaCart
. PCC6803 containing four genes coding for putative FDPs. However, the function of those proteins remains unclear. In the present study, we have analysed the expression profile of these genes under oxidative and nitrosative stress conditions. The results indicate that one of the flavodi-iron genes

Microarray analysis of orthologous genes: conservation of the translational machinery across species at the sequence and expression level

by Jose L Jiménez, Michael P Mitchell, John G Sgouros - GENOME BIOLOGY , 2002
"... Background: Genome projects have provided a vast amount of sequence information. Sequence refereed research deposited research comparison between species helps to establish functional catalogues within organisms and to study how they are maintained and modified across phylogenetic groups during evol ..."
Abstract - Cited by 2 (0 self) - Add to MetaCart
for the identification of upstream regulatory motifs of yeast genes involved in protein synthesis. Comparison of these yeast co-regulated genes against the archaeal and bacterial operons indicates that the components of the protein translation process are conserved across organisms at the expression level with minor

Detecting network motifs in gene co-expression networks

by Xinxia Peng, Michael A. Langston, Arnold M. Saxton, Nicole E. Baldwin, Jay R. Snoddy , 2004
"... Biological networks can be broken down into modules, groups of interacting molecules. To uncover these functional modules and study their evolution, our research groups are developing graphtheory based strategies for the analysis of gene expression data. We are looking for groups of completely conne ..."
Abstract - Cited by 5 (0 self) - Add to MetaCart
connected subgraphs (e.g. cliques) in which corresponding members have the same combination of protein domains in co-expression networks. The common pattern shown by a group of similar cliques is a “network motif ” that may be reused multiple times within organisms. We have developed algorithms

Cloning and expression of the phosphotriesterase gene hocA from

by Pseudomonas Monteilii C, Irene Horne, Tara D. Sutherl, John G. Oakeshott, Robyn J. Russell
"... The cloning of a gene encoding the novel phosphotriesterase from Pseudomonas monteilii C11, which enabled it to use the organophosphate (OP) coroxon as its sole phosphorus source, is described. The gene, called hocA (hydrolysis of coroxon) consists of 501 bp and encodes a protein of 19 kDa. This pro ..."
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expression of hocA was observed from an integrative hocA–lacZ fusion when cultures were grown in the absence of phosphate, suggesting that it might be part of the Pho regulon, but the phosphate-regulated promoter was not cloned in this study. This is believed to be the first study in which a gene required

An Interactive Database of Cocaine- ResponsiveGene Expression

by Willard M Freeman , Kathryn E Dougherty , Sally E Vacca , Kent E Vrana , 2002
"... The postgenomic era of large-scale gene expression studies is inundating drugabuse researchers and many other scientists with findings related to geneexpression. This information is distributed across many different journals, andrequires laborious literature searches. Here, we present an interactiv ..."
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The postgenomic era of large-scale gene expression studies is inundating drugabuse researchers and many other scientists with findings related to geneexpression. This information is distributed across many different journals, andrequires laborious literature searches. Here, we present

Duplicate gene enrichment and expression pattern diversification in multicellularity

by Timothy Padawer, Ralph E. Leighty, Degeng Wang , 2010
"... The enrichment of duplicate genes, and there-fore paralogs (proteins coded by duplicate genes), in multicellular versus unicellular organisms enhances genomic functional innovation. This study quantitatively examined relationships among paralog enrichment, expression pattern diversifica-tion and mul ..."
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The enrichment of duplicate genes, and there-fore paralogs (proteins coded by duplicate genes), in multicellular versus unicellular organisms enhances genomic functional innovation. This study quantitatively examined relationships among paralog enrichment, expression pattern diversifica-tion

Expression of a Drosophila GATA Transcription Factor in Multiple Tissues in the Developing Embryos

by unknown authors
"... GATA transcription factors are DNA-binding proteins that recognize the core consensus sequence, WGATAR. Previous studies indicated that GATA factors play an important role in the development of tissue-specific functions in vertebrates. Here we report the identification of a new Drosophila melanogast ..."
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that are homozygous lethal at the embryonic stage. Using a genetic scheme, it was demonstrated that the lack of dGATAc function can block normal embryonic development. Our results suggest that the dGATAc protein is a tissue-specific transcription factor that is vital to the development of multiple organ systems in D

Evidence for multiple levels of regulation of Oenococcus oeni clpPclpL locus expression in response to stress

by Charlotte Beltramo, Cosette Gr, Fabrice Pierre, Jean Guzzo - J. Bacteriol , 2004
"... A locus containing the clpP and clpL genes in the lactic acid bacterium Oenococcus oeni was studied. Real-time reverse transcription-PCR analysis revealed different induction factors involved in expression of these genes during stress. According to the conditions, clpP and clpL genes could be transc ..."
Abstract - Cited by 7 (2 self) - Add to MetaCart
A locus containing the clpP and clpL genes in the lactic acid bacterium Oenococcus oeni was studied. Real-time reverse transcription-PCR analysis revealed different induction factors involved in expression of these genes during stress. According to the conditions, clpP and clpL genes could
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