... a stratified squamous epithelium remains an unanswered question. We have sought to determine whether oesophageal keratinocytes can be trans-differentiated into Barrett's oesophagus cells. Using an Affymetrix microarray, we found unexpectedly that gene-expression patterns in the Barrett's oesophagus were only...

...Soumyaroop Bhattacharya; Thomas J. Mariani High-throughput, genome-wide analytical technologies are now commonly used in all fields of medical research. The most commonly applied of these technologies, gene expression microarrays, have been shown to be both accurate and precise when properly...

... are carried out. Below, we provide a snapshot of these exciting new approaches to understanding the properties and functions of genomes. Given that sequencing-based assays may increasingly supersede microarray-based assays, we also compare and contrast data obtained from these distinct approaches. Next...

...), combined with DNA microarray analysis, is a powerful tool that permits global patterns of DNA binding to be measured. Here, we discuss the benefits of this approach and the application of this technique to bacterial systems. chromatin immunoprecipitation (ChIP) DNA binding Escherichia coli...

... The Authors Journal compilation © 2008 Biochemical Society 2008 Microarrays are pervasive technology, widely used in the life sciences to measure genome-wide transcriptional output in many organisms, phenotypes and tissues. A high-density oligonucleotide microarray, such as an Affymetrix GeneChip...

...S. Spiro Exposure of Escherichia coli to nitric oxide (NO) or nitrosating agents causes significant changes in patterns of gene expression. Three recent studies have used microarrays to analyse the response of the E. coli transcriptome to NO and nitrosative stress. Drawing on the array data, I...

... of nitrate or nitrite, in non-repressing media in which both strain MG1655 and an fnr deletion mutant grew at similar rates. Glycerol was used as the non-repressing carbon source and both trimethylamine- N -oxide and fumarate were added as terminal electron acceptors. Microarray data supplemented...

...@vt.edu ). 27 7 2005 © 2005 The Biochemical Society 2005 In order to study several aspects of microarray statistical analysis and gene network inference algorithms, a set of artificial gene network models was created representing a wide range of topological characteristics [ 24...

... first employed microarray analysis to assess global changes in butyrate-responsive genes using HT29 human colon carcinoma cells treated with butyrate. There was consistency in the butyrate response of selected genes in two other human colonic cell lines (HCT116 and AA/C1) using quantitative real-time...

... glycine transporter HMGN microarray repair transcription The DNA in eukaryotic cells is organized by histones and other proteins into chromatin which is comprised of arrays of nucleosomes. Significant advances have been made in recent years in understanding how the modification and remodelling...

... of ARE-containing RNAs, are induced and activated in infected cells and tristetraprolin interacts physically with the U L 41 protein. © 2004 The Biochemical Society 2004 AU-rich element herpes simplex virus type 1 (HSV-1) microarray nuclear factor-κB RNA turnover 1 To whom correspondence...

... apoptosis differentiation programme human polymorphonuclear leucocyte inflammation microarray neutrophil transcription Abbreviations used: CXCR2, CXC chemokine receptor 2; IL, interleukin; MIP, macrophage inflammatory protein; PMN, polymorphonuclear leucocyte; TNFα, tumour necrosis factor α...

... and abiotic characteristics in high-temperature habitats. Described here are functional genomics-based approaches, using cDNA microarrays, to gain insight into how ecological features such as biofilm formation, species interaction, and possibly even gene transfer may occur in native environments, as well...

... July 2003 © 2003 Biochemical Society 2003 Bayesian network Markov chain Monte Carlo (MCMC) microarray posterior probability receiver operator characteristic curve (ROC curve) reverse engineering Abbreviations used: MCMC, Markov chain Monte Carlo; ROC, receiver operator...

... of these algorithms and ask how well they correspond to current microarray data. © 2003 Biochemical Society 2003 dynamics gene chip gene network mathematical model microarray signalling network 4 August 2003 Unravelling Nature's Networks a Biochemical Society Focused Meeting held...

...R.K. Curtis; M.D. Brand Gene expression is complex: many mRNAs change in abundance in response to a new condition. But while some of these expression changes may be direct, many may be downstream, indirect effects. One of the major problems of microarray data analysis is distinguishing between...

...L.A. Soinov One of the central problems of functional genomics is revealing gene expression networks – the relationships between genes that reflect observations of how the expression level of each gene affects those of others. Microarray data are currently a major source of information about...

... Networks a Biochemical Society Focused Meeting held at University of Sheffield, 21 July 2003 genomics mathematical modelling microarray modularity networks proteomics U nravelling N ature s N etw orks Biochem icalSociety Focused M eeting Unravelling Nature s Networks: From Microarray...

... into a software file that is used as the design scheme for potentially any genomic assay in a microarray format. Microarray fabrication takes place in three-dimensional microchannel reaction carriers by in situ synthesis based on spatial light modulation. This set-up allows for maximum flexibility in design...

... microarray oxidative phosphorylation regulation analysis signalling Metabolite Channelling and Metabolic Complexity I5 Atkinson, D. E. ( I 990) in Control of Metabolic Processes (Comish-Bowden, A. and Cardenas, M. L., eds), pp. 4 13-427, Plenum Press, New York Cornish-Bowden, A. ( I 995) fundamentals...

... mitochondria1 isoforms, which is opposite to their relationship in the non-seed EST databases. The DNA microarray technology applied to oilseeds in our laboratories involves the appli- cation and fixing of DNA from the above- described E S T project to glass slides in high- density arrays. This technique...

...(dT) columns. cDNA filter arrays were pre- pared on nylon membranes (Zeta) using a dot-blot apparatus (Bio-Rad). Plasmid preparations of each Key words: gene expression, microarray. Abbreviations used: ACP, acyl carrier protein: BKR. 3-ketoacyl- ACP reductase; DAF, days after flowering; G3P, glycerol...