... 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. Figure 3 Using ChIP–chip to measure the binding of RNA polymerase in cells...

... affect detection of gene expression by Affymetrix GeneChip® arrays Appl. Bioinformatics 2006 5 249 253 Affymetrix GeneChip alternative polyadenylation alternative splicing microarray post-transcriptional processing RNA Microarrays are pervasive technology, widely used...

...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...

[email protected] ). 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...

... of chromatin structure. 1 email [email protected] 8 7 2004 © 2004 The Biochemical Society 2004 chromatin glycine transporter HMGN microarray repair transcription HMGN (formerly HMG-14/-17) proteins alter chromatin architecture by decompacting the nucleosomal...

... simplex virus type 1 (HSV-1) microarray nuclear factor-κB RNA turnover HSV-1 (herpes simplex virus 1) has evolved an elaborate strategy to block host responses to infection. Of the numerous functions expressed by viral gene products designed to shut off the host, two are particularly important...

... 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...

...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...

... at University of Sheffield, 21 July 2003 19 September 2003 © 2003 Biochemical Society 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...

... and flexiblemodels for representing conditional dependence relations betweenmultiple interacting quantities, and their probabilistic nature is capable of handling noise inherent in both the biological processes and the microarray experiments. However, the inference problem is particularly hard in that interactions...

... of these algorithms and ask how well they correspond to current microarray data. 1 To whom correspondence should be addressed, at the Department of Mathematics, Imperial College London (e-mail [email protected] ). 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...

... 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...