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Microarray Experiments (microarray + experiment)
Kinds of Microarray Experiments Selected AbstractsDNA Microarray Experiments: Biological and Technological AspectsBIOMETRICS, Issue 4 2002Danh V. Nguyen Summary. DNA microarray technologies, such as cDNA and oligonucleotide microarrays, promise to revolutionize biological research and further our understanding of biological processes. Due to the complex nature and sheer amount of data produced from microarray experiments, biologists have sought the collaboration of experts in the analytical sciences, including statisticians, among others. However, the biological and technical intricacies of microarray experiments are not easily accessible to analytical experts. One aim for this review is to provide a bridge to some of the relevant biological and technical aspects involved in microarray experiments. While there is already a large literature on the broad applications of the technology, basic research on the technology itself and studies to understand process variation remain in their infancy. We emphasize the importance of basic research in DNA array technologies to improve the reliability of future experiments. [source] Phototropin involvement in the expression of genes encoding chlorophyll and carotenoid biosynthesis enzymes and LHC apoproteins in Chlamydomonas reinhardtiiTHE PLANT JOURNAL, Issue 1 2006Chung-Soon Im Summary Phototropin (PHOT) is a photoreceptor involved in a variety of blue-light-elicited physiological processes including phototropism, chloroplast movement and stomatal opening in plants. The work presented here tests whether PHOT is involved in expression of light-regulated genes in Chlamydomonas reinhardtii. When C. reinhardtii was transferred from the dark to very low-fluence rate white light, there was a substantial increase in the level of transcripts encoding glutamate-1-semialdehyde aminotransferase (GSAT), phytoene desaturase (PDS) and light-harvesting polypeptides (e.g. LHCBM6). Increased levels of these transcripts were also elicited by low-intensity blue light, and this blue-light stimulation was suppressed in three different RNAi strains that synthesize low levels of PHOT. The levels of GSAT and LHCBM6 transcripts also increased following exposure of algal cells to low-intensity red light (RL). The red-light-dependent increase in transcript abundance was not affected by the electron transport inhibitor 3-(3,4-dichlorophenyl)-1,1-dimethylurea, implying that the influence of RL on transcript accumulation was not controlled by cytoplasmic redox conditions, and that a red-light photoreceptor(s) may be involved in regulating the levels of transcripts from specific photosynthesis-related genes in C. reinhardtii. Interestingly, elevated GSAT and LHCBM6 transcript levels in RL were significantly reduced in the PHOT RNAi strains, which raises the possibility of co-action between blue and RL signaling pathways. Microarray experiments indicated that the levels of several transcripts for photosystem (PS) I and II polypeptides were also modulated by PHOT. These data suggest that, in C. reinhardtii, (i) PHOT is involved in blue-light-mediated changes in transcript accumulation, (ii) synchronization of the synthesis of chlorophylls (Chl), carotenoids, Chl-binding proteins and other components of the photosynthetic apparatus is achieved, at least in part, through PHOT-mediated signaling, and (iii) a red-light photoreceptor can also influence levels of certain transcripts associated with photosynthetic function, although its action requires normal levels of PHOT. [source] Chemical strategies for immobilization of oligonucleotidesBIOTECHNOLOGY JOURNAL, Issue 11 2009Dalip Sethi Abstract The development of oligonucleotide-based microarrays (biochips) is a major thrust area in the rapidly growing biotechnology industry, which encompasses a diverse range of research areas including genomics, proteomics, computational biology, and pharmaceuticals, among other activities. Microarray experiments have proved to be unique in offering cost-effective and efficient analysis at the genomic level. In the last few years, biochips have gained increasing acceptance in the study of genetic and cellular processes. As the increase in experimental throughput has posed many challenges to the research community, considerable progress has been made in the advancement of microarray technology. In this review, chemical strategies for immobilization of oligonucleotides have been highlighted with special emphasis on post-synthetic immobilization of oligonucleotides on glass surface. The major objective of this article is to make the researchers acquainted with some most recent advances in this area. [source] Gene expression analysis in absence epilepsy using a monozygotic twin designEPILEPSIA, Issue 9 2008Ingo Helbig Summary Purpose: To identify genes involved in idiopathic absence epilepsies by analyzing gene expression using a monozygotic (MZ) twin design. Methods: Genome-wide gene expression in lymphoblastoid cell lines (LCLs) was determined using microarrays derived from five discordant and four concordant MZ twin pairs with idiopathic absence epilepsies and five unaffected MZ twin pairs. Gene expression was analyzed using three strategies: discordant MZ twins were compared as matched pairs, MZ twins concordant for epilepsy were compared to control MZ twins, and a singleton design of affected versus unaffected MZ twin individuals was used irrespective of twin pairing. An overlapping gene list was generated from these analyses. Dysregulation of genes recognized from the microarray experiment was validated using quantitative real time PCR (qRT-PCR) in the twin sample and in an independent sample of 18 sporadic absence cases and 24 healthy controls. Results: Sixty-five probe sets were identified from the three combined microarray analysis strategies. Sixteen genes were chosen for validation and nine of these genes confirmed by qRT-PCR in the twin sample. Differential expression for EGR1 (an immediate early gene) and RCN2 (coding for the calcium-binding protein Reticulocalbin 2) were reconfirmed by qRT-PCR in the independent sample. Discussion: Using a unique sample of discordant MZ twins, our study identified genes with altered expression, which suggests novel mechanisms in idiopathic absence epilepsy. Dysregulation of EGR1 and RCN2 is implicated in idiopathic absence epilepsy. [source] Microarray expression profiling: capturing a genome-wide portrait of the transcriptomeMOLECULAR MICROBIOLOGY, Issue 4 2003Tyrrell Conway Summary The bacterial transcriptome is a dynamic entity that reflects the organism's immediate, ongoing and genome-wide response to its environment. Microarray expression profiling provides a comprehensive portrait of the transcriptional world enabling us to view the organism as a ,system' that is more than the sum of its parts. The vigilance of microorganisms to environmental change, the alacrity of the transcriptional response, the short half-life of bacterial mRNA and the genome-scale nature of the investigation collectively explain the power of this method. These same features pose the most significant experimental design and execution issues which, unless surmounted, predictably generate a distorted image of the transcriptome. Conversely, the expression profile of a properly conceived and conducted microarray experiment can be used for hypothesis testing: disclosure of the metabolic and biosynthetic pathways that underlie adaptation of the organism to chang-ing conditions of growth; the identification of co-ordinately regulated genes; the regulatory circuits and signal transduction systems that mediate the adaptive response; and temporal features of developmental programmes. The study of bacterial pathogenesis by microarray expression profiling poses special challenges and opportunities. Although the technical hurdles are many, obtaining expression profiles of an organism growing in tissue will probably reveal strategies for growth and survival in the host's microenvironment. Identifying these colonization strategies and their cognate expression patterns involves a ,deconstruction' process that combines bioinformatics analysis and in vitro DNA array experimentation. [source] Linear Mixed Model Selection for False Discovery Rate Control in Microarray Data AnalysisBIOMETRICS, Issue 2 2010Cumhur Yusuf Demirkale Summary In a microarray experiment, one experimental design is used to obtain expression measures for all genes. One popular analysis method involves fitting the same linear mixed model for each gene, obtaining gene-specific,p -values for tests of interest involving fixed effects, and then choosing a threshold for significance that is intended to control false discovery rate (FDR) at a desired level. When one or more random factors have zero variance components for some genes, the standard practice of fitting the same full linear mixed model for all genes can result in failure to control FDR. We propose a new method that combines results from the fit of full and selected linear mixed models to identify differentially expressed genes and provide FDR control at target levels when the true underlying random effects structure varies across genes. [source] Developing transgenic arabidopsis plants to be metal-specific bioindicatorsENVIRONMENTAL TOXICOLOGY & CHEMISTRY, Issue 1 2003Beth A. Krizek Abstract Deoxyribonucleic acid (DNA) microarrays provide a means to assess genome-wide expression patterns after exposure of an organism to different xenobiotics. Potential uses for this technology include identification of unknown toxicants, assessment of toxicity of new compounds, and characterization of the cellular mechanisms of toxicant action. Here we describe another use of DNA microarrays in toxicant-specific gene discovery. Combining results from two DNA microarray experiments, we have identified genes from the model plant Arabidopsis thaliana that are induced in response to one but not other heavy metals. The promoters of these genes should be useful in developing metal-specific transgenic biomonitors. To test this idea, we have fused the promoter of one of the newly identified Ni-inducible genes (AHB1) to the ,-glucuronidase (GUS) reporter gene. Arabidopsis plants containing the AHB1::GUS transgene show reporter gene activity when they are grown on media containing Ni but not when grown on media containing Cd, Cu, Zn, or without added metals. Thus, this approach has resulted in the creation of a transgenic strain of Arabidopsis that can report on the presence and concentration of Ni in plant growth media. Such transgenic models can serve as cheap and efficient biomonitors of bioavailable heavy metal contamination in soils and sediments. [source] Genome-wide association analyses of expression phenotypesGENETIC EPIDEMIOLOGY, Issue S1 2007Gary K. Chen Abstract A number of issues arise when analyzing the large amount of data from high-throughput genotype and expression microarray experiments, including design and interpretation of genome-wide association studies of expression phenotypes. These issues were considered by contributions submitted to Group 1 of the Genetic Analysis Workshop 15 (GAW15), which focused on the association of quantitative expression data. These contributions evaluated diverse hypotheses, including those relevant to cancer and obesity research, and used various analytic techniques, many of which were derived from information theory. Several observations from these reports stand out. First, one needs to consider the genetic model of the trait of interest and carefully select which single nucleotide polymorphisms and individuals are included early in the design stage of a study. Second, by targeting specific pathways when analyzing genome-wide data, one can generate more interpretable results than agnostic approaches. Finally, for datasets with small sample sizes but a large number of features like the Genetic Analysis Workshop 15 dataset, machine learning approaches may be more practical than traditional parametric approaches. Genet Epidemiol 31 (Suppl. 1): S7,S11, 2007. © 2007 Wiley-Liss, Inc. [source] Expression profiling of Wilms tumors reveals new candidate genes for different clinical parametersINTERNATIONAL JOURNAL OF CANCER, Issue 8 2006B. Zirn Abstract Wilms tumor is the most frequent renal neoplasm in children, but our understanding of its genetic basis is still limited. We performed cDNA microarray experiments using 63 primary Wilms tumors with the aim of detecting new candidate genes associated with malignancy grade and tumor progression. All tumors had received preoperative chemotherapy as mandated by the SIOP protocol, which sets this study apart from related approaches in the Unites States that are based on untreated samples. The stratification of expression data according to clinical criteria allowed a rather clear distinction between different subsets of Wilms tumors. Clear-cut differences in expression patterns were discovered between relapse-free as opposed to relapsed tumors and tumors with intermediate risk as opposed to high risk histology. Several differentially expressed genes, e.g.TRIM22, CENPF, MYCN, CTGF, RARRES3 and EZH2, were associated with Wilms tumor progression. For a subset of differentially expressed genes, microarray data were confirmed by real-time RT-PCR on the original set of tumors. Interestingly, we found the retinoic acid pathway to be deregulated at different levels in advanced tumors suggesting that treatment of these tumors with retinoic acid may represent a promising novel therapeutic approach. © 2005 Wiley-Liss, Inc. [source] The function of the Egr1 transcription factor in cartilage formation and adaptation to microgravity in zebrafish, Danio rerioJOURNAL OF APPLIED ICHTHYOLOGY, Issue 2 2010M. Muller Summary Osteoporosis is one of the major concerns for an ageing human population and for passengers on long-term space flights. Teleosts represent a potentially interesting alternative for studying bone physiology. In zebrafish (Danio rerio), the cartilaginous elements that form the pharyngeal arches derive from cranial neural crest cells, whose proper patterning and morphogenesis require reciprocal interactions with other tissue types such as pharyngeal endoderm, ectoderm and mesoderm. We show how the zebrafish can be used to study the function of signal transduction pathways, such as the Fgf pathway, or that of particular genes, such as the zinc finger transcription factor Egr1, in pharyngeal skeleton formation and maintenance. We investigate the changes caused by microgravity and chemical treatments on zebrafish. We analyze early gene expression modification using whole genome microarray experiments and the long-term consequences by staining bone structures. [source] Functional and structural properties of stannin: Roles in cellular growth, selective toxicity, and mitochondrial responses to injuryJOURNAL OF CELLULAR BIOCHEMISTRY, Issue 2 2006M.L. Billingsley Abstract Stannin (Snn) was discovered using subtractive hybridization methodology designed to find gene products related to selective organotin toxicity and apoptosis. The cDNAs for Snn were first isolated from brain tissues sensitive to trimethyltin, and were subsequently used to localize, characterize, and identify genomic DNA, and other gene products of Snn. Snn is a highly conserved, 88 amino acid protein found primarily in vertebrates. There is a minor divergence in the C-terminal sequence between amphibians and primates, but a nearly complete conservation of the first 60 residues in all vertebrates sequenced to date. Snn is a membrane-bound protein and is localized, in part, to the mitochondria and other vesicular organelles, suggesting that both localization and conservation are significant for the overall function of the protein. The structure of Snn in a micellar environment and its architecture in lipid bilayers have been determined using a combination of solution and solid-state NMR, respectively. Snn structure comprised a single transmembrane domain (residues 10,33), a 28-residue linker region from residues 34,60 that contains a conserved CXC metal binding motif and a putative 14-3-3, binding region, and a cytoplasmic helix (residues 61,79), which is partially embedded into the membrane. Of primary interest is understanding how this highly-conserved peptide with an interesting structure and cellular localization transmits both normal and potentially toxic signals within the cell. Evidence to date suggests that organotins such as trimethyltin interact with the CXC region of Snn, which is vicinal to the putative 14-3-3 binding site. In vitro transfection analyses and microarray experiments have inferred a possible role of Snn in several key signaling systems, including activation of the p38-ERK cascade, p53-dependent pathways, and 14-3-3, protein-mediated processes. TNF, can induce Snn mRNA expression in endothelial cells in a PKC-, dependent manner. Studies with Snn siRNA suggest that this protein may be involved in growth regulation, since inhibition of Snn expression alone leads to reduced endothelial cells growth and induction of COP-1, a negative regulator of p53 function. A key piece of the puzzle, however, is how and why such a highly-conserved protein, localized to mitochondria, interacts with other regulatory proteins to alter growth and apoptosis. By knowing the structure, location, and possible signaling pathways involved, we propose that Snn constitutes an important sensor of mitochondrial damage, and plays a key role in the mediation of cross-talk between mitochondrial and nuclear compartments in specific cell types. J. Cell. Biochem. 98: 243,250, 2006. © 2006 Wiley-Liss, Inc. [source] Transcriptional changes in insulin- and lipid metabolism-related genes in the hippocampus of olfactory bulbectomized miceJOURNAL OF NEUROSCIENCE RESEARCH, Issue 14 2008Peter Gass Abstract Affymetrix chips were used to perform a hypothesis-free large-scale screening of transcripts in the hippocampus of olfactory bulbectomized mice, an established animal model of depression. Because only 11 transcripts were significantly changed, the statistically subsequent 25 transcripts below the significance level were additionally included in a first round of qRT-PCR evaluations. Furthermore, all 36 genes were then tested for mutual interactions or interactions with other molecules in a physiological context using PathwayArchitect software. Thirty of them were displayed in a network interacting with at least one partner molecule from the list or with other partner molecules known from the literature. All partner molecules from the most prominent 10 molecules of this network were then identified and put together into a new list. On those grounds, the hypothesis was made that metabolic network components of the insulin signaling pathway are perturbed in the disease. This pathway was subsequently tested by a second round of qRT-PCR, adding also a few additional candidate molecules belonging to this pathway. It turned out that the key target,FABP7,fell into the group of transcripts not significantly regulated within the chip data, and another key target,IRS1,did not show up in the chip experiments at all. In conclusion, our data reveal a problem with adhering to statistical significances in microarray experiments, insofar as molecules important for the disease may fall into the range of statistical noise. This approach may also be useful to find new targets for pharmacotherapy in affective disorders. © 2008 Wiley-Liss, Inc. [source] Microarray Analysis of Ethanol-Treated Cortical Neurons Reveals Disruption of Genes Related to the Ubiquitin-Proteasome Pathway and Protein SynthesisALCOHOLISM, Issue 12 2004Ramana Gutala Background: Chronic ethanol abuse results in deleterious behavioral responses such as tolerance, dependence, reinforcement, sensitization, and craving. The objective of this research was to identify transcripts that are differentially regulated in ethanol-treated cortical neurons compared with controls by using a pathway-focused complementary DNA microarray. Methods: Cortical neurons were isolated from postconception day 14 C57BL/6 mouse fetuses and cultured according to a standard protocol. The cortical neuronal cells were treated with 100 mM ethanol for five consecutive days with a change of media every day. A homeostatic pathway-focused microarray consisting of 638 sequence-verified genes was used to measure transcripts differentially regulated in four ethanol-treated cortical neuron samples and four control samples. Quantitative real-time reverse transcriptase-polymerase chain reaction analysis was used to verify the mRNA expression levels of genes of interest detected from the microarray experiments. Results: We identified 56 down-regulated and 10 up-regulated genes in ethanol-treated cortical neurons relative to untreated controls at a 5% false-discovery rate. The expression of many genes involved in ubiquitin-proteasome and protein synthesis was decreased by ethanol, including ubiquitin B, ubiquitin-like 3, ubiquitin-conjugating enzyme E3A, 20S proteasome ,- and ,-subunits, and members of the ribosomal proteins. Furthermore, the mRNA expression of heat shock proteins, myristoylated alanine-rich protein kinase C substrate, phosphatase and tensin homolog deleted on chromosome 10, and FK506 binding protein rapamycin-associated protein (FKBP) (mTOR) was also decreased in ethanol-treated cortical neurons. Quantitative real-time reverse transcriptase-polymerase chain reaction analysis of genes involved in the ubiquitin-proteasome cascade revealed a down-regulation of these genes, thereby corroborating our microarray results. Conclusions: Our results indicate that chronic ethanol treatment of cortical neurons resulted in decreased mRNA expression of genes involving the ubiquitin-proteasome pathway and ribosomal proteins together with mTOR expression leading to disruption of protein degradation mechanism and impairment of protein synthesis machinery. [source] Designs for two-colour microarray experimentsJOURNAL OF THE ROYAL STATISTICAL SOCIETY: SERIES C (APPLIED STATISTICS), Issue 4 2007R. A. Bailey Summary., Designs for two-colour microarray experiments can be viewed as block designs with two treatments per block. Explicit formulae for the A- and D-criteria are given for the case that the number of blocks is equal to the number of treatments. These show that the A- and D-optimality criteria conflict badly if there are 10 or more treatments. A similar analysis shows that designs with one or two extra blocks perform very much better, but again there is a conflict between the two optimality criteria for moderately large numbers of treatments. It is shown that this problem can be avoided by slightly increasing the number of blocks. The two colours that are used in each block effectively turn the block design into a row,column design. There is no need to use a design in which every treatment has each colour equally often: rather, an efficient row,column design should be used. For odd replication, it is recommended that the row,column design should be based on a bipartite graph, and it is proved that the optimal such design corresponds to an optimal block design for half the number of treatments. Efficient row,column designs are given for replications 3,6. It is shown how to adapt them for experiments in which some treatments have replication only 2. [source] An adaptive empirical Bayesian thresholding procedure for analysing microarray experiments with replicationJOURNAL OF THE ROYAL STATISTICAL SOCIETY: SERIES C (APPLIED STATISTICS), Issue 3 2007Rebecca E. Walls Summary., A typical microarray experiment attempts to ascertain which genes display differential expression in different samples. We model the data by using a two-component mixture model and develop an empirical Bayesian thresholding procedure, which was originally introduced for thresholding wavelet coefficients, as an alternative to the existing methods for determining differential expression across thousands of genes. The method is built on sound theoretical properties and has easy computer implementation in the R statistical package. Furthermore, we consider improvements to the standard empirical Bayesian procedure when replication is present, to increase the robustness and reliability of the method. We provide an introduction to microarrays for those who are unfamilar with the field and the proposed procedure is demonstrated with applications to two-channel complementary DNA microarray experiments. [source] Near-optimal designs for dual channel microarray studiesJOURNAL OF THE ROYAL STATISTICAL SOCIETY: SERIES C (APPLIED STATISTICS), Issue 5 2005Ernst Wit Summary., Much biological and medical research employs microarray studies to monitor gene expression levels across a wide range of organisms and under many experimental conditions. Dual channel microarrays are a common platform and allow two samples to be measured simultaneously. A frequently used design uses a common reference sample to make conditions across different arrays comparable. Our aim is to formulate microarray experiments in the experimental design context and to use simulated annealing to search for near-optimal designs. We identify a subclass of designs, the so-called interwoven loop designs, that seems to have good optimality properties compared with the near-optimal designs that are found by simulated annealing. Commonly used reference designs and dye swap designs are shown to be highly inefficient. [source] Differential analysis of DNA microarray gene expression dataMOLECULAR MICROBIOLOGY, Issue 4 2003G. Wesley Hatfield Summary Here, we review briefly the sources of experimental and biological variance that affect the interpretation of high-dimensional DNA microarray experiments. We discuss methods using a regularized t -test based on a Bayesian statistical framework that allow the identification of differentially regulated genes with a higher level of confidence than a simple t -test when only a few experimental replicates are available. We also describe a computational method for calculating the global false-positive and false-negative levels inherent in a DNA microarray data set. This method provides a probability of differential expression for each gene based on experiment-wide false-positive and -negative levels driven by experimental error and biological variance. [source] Comparative proteomic and transcriptional profiling of a bread wheat cultivar and its derived transgenic line overexpressing a low molecular weight glutenin subunit gene in the endospermPROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS, Issue 14 2008Federico Scossa Abstract We carried out a parallel transcriptional and proteomic comparison of seeds from a transformed bread wheat line that overexpresses a transgenic low molecular weight glutenin subunit gene relative to the corresponding nontransformed genotype. Proteomic analyses showed that, during seed development, several classes of endosperm proteins were differentially accumulated in the transformed endosperm. As a result of the strong increase in the amount of the transgenic protein, the endogenous glutenin subunit, all subclasses of gliadins, and metabolic as well as chloroform/methanol soluble proteins were diminished in the transgenic genotype. The differential accumulation detected by proteomic analyses, both in mature and developing seeds, was paralleled by the corresponding changes in transcript levels detected by microarray experiments. Our results suggest that the most evident effect of the strong overexpression of the transgenic glutenin gene consists in a global compensatory response involving a significant decrease in the amounts of polypeptides belonging to the prolamin superfamily. It is likely that such compensation is a consequence of the diversion of amino acid reserves and translation machinery to the synthesis of the transgenic glutenin subunit. [source] Anatomic site-specific proteomic signatures of gastrointestinal stromal tumorsPROTEOMICS - CLINICAL APPLICATIONS, Issue 5 2009Yoshiyuki Suehara Abstract The gastrointestinal stromal tumor (GIST) is the most common mesenchymal malignancy of the gastrointestinal tract. Its clinical course ranges widely from a curable disorder to a highly malignant disease. Although its clinical and molecular characteristics depend on the anatomic site of origin, the molecular background of GIST arising in different anatomical site has not been studied yet. To investigate the proteomic background of GIST, we examined the proteomic features corresponding to the anatomic site of tumor origin. Comparison of the proteomic profile of gastric (23 cases) and small intestinal (9 cases) GIST by 2-DE revealed 105 protein spots with significantly different intensity (p <0.01) between the two groups. Mass spectrometric study identified 68 distinct proteins for these 105 protein spots, including cancer-associated ones such as prohibitin, pigment epithelium-derived factor, and alpha-actinin 4. The intensity of 37/105 (35.2%) protein spots was significantly concordant with the corresponding mRNA levels (p <0.01). Although both 2-D DIGE and microarray experiments showed significant up-regulation of vimentin expression in small intestinal GIST, Western blotting did not show a significant difference between the two groups. In conclusion, our study demonstrates the proteins specially expressed in GIST depending on their site of origin, as well as the unique advantage offered by use of proteomics to acquire such data. The identified proteins may provide clues to understanding the different characteristics of GIST depending on their site of origin. [source] Experimental designs for 2-colour cDNA microarray experimentsAPPLIED STOCHASTIC MODELS IN BUSINESS AND INDUSTRY, Issue 5-6 2006Nam-Ky Nguyen Abstract Kerr and Churchill (Biostatistics 2001; 2:183,201) showed how varieties (e.g. type of tissues, drug treatments, etc.) are paired onto arrays by a catalogue of A-optimal incomplete block designs (IBDs) for 6,10 varieties (v), and number of blocks of size 2 between v and . These A-optimal IBDs were obtained by (i) generating all non-isomorphic connected graphs on v vertices using Brendan McKay's, MAKEG program (http://cs.anu.edu.au/people/bdm/nauty/) and (ii) comparing all designs of the same size on the basis of A-optimality to obtain the best ones. In this paper we will give a quick overview on IBDs and describe an algorithmic approach to extend the mentioned catalogue. We aim at IBDs with up to 100 varieties with equal as well as unequal replications. A catalogue of 2007 IBDs is given. We will also extend the concept of even designs in Kerr and Churchill (Biostatistics 2001; 2:183,201) to row-orthogonal designs. Copyright © 2006 John Wiley & Sons, Ltd. [source] Improved Detection of Differentially Expressed Genes Through Incorporation of Gene LocationsBIOMETRICS, Issue 3 2009Guanghua Xiao Summary In determining differential expression in cDNA microarray experiments, the expression level of an individual gene is usually assumed to be independent of the expression levels of other genes, but many recent studies have shown that a gene's expression level tends to be similar to that of its neighbors on a chromosome, and differentially expressed (DE) genes are likely to form clusters of similar transcriptional activity along the chromosome. When modeled as a one-dimensional spatial series, the expression level of genes on the same chromosome frequently exhibit significant spatial correlation, reflecting spatial patterns in transcription. By modeling these spatial correlations, we can obtain improved estimates of transcript levels. Here, we demonstrate the existence of spatial correlations in transcriptional activity in the,Escherichia coli,(E. coli) chromosome across more than 50 experimental conditions. Based on this finding, we propose a hierarchical Bayesian model that borrows information from neighboring genes to improve the estimation of the expression level of a given gene and hence the detection of DE genes. Furthermore, we extend the model to account for the circular structure of,E. coli,chromosome and the intergenetic distance between gene neighbors. The simulation studies and analysis of real data examples in,E. coli,and yeast,Saccharomyces cerevisiae,show that the proposed method outperforms the commonly used significant analysis of microarray (SAM),t -statistic in detecting DE genes. [source] A Copula Approach for Detecting Prognostic Genes Associated With Survival Outcome in Microarray StudiesBIOMETRICS, Issue 4 2007Kouros Owzar Summary A challenging and crucial issue in clinical studies in cancer involving gene microarray experiments is the discovery, among a large number of genes, of a relatively small panel of genes whose elements are associated with a relevant clinical outcome variable such as time-to-death or time-to-recurrence of disease. A semiparametric approach, using dependence functions known as copulas, is considered to quantify and estimate the pairwise association between the outcome and each gene expression. These time-to-event type endpoints are typically subject to censoring as not all events are realized at the time of the analysis. Furthermore, given that the total number of genes is typically large, it is imperative to control a relevant error rate in any gene discovery procedure. The proposed method addresses the two aforementioned issues by direct incorporation of the censoring mechanism and by appropriate statistical adjustment for multiplicity. The performance of the proposed method is studied through simulation and illustrated with an application using a case study in lung cancer. [source] Nonparametric Inference for Local Extrema with Application to Oligonucleotide Microarray Data in Yeast GenomeBIOMETRICS, Issue 2 2006Peter X.-K. Summary Identifying local extrema of expression profiles is one primary objective in some cDNA microarray experiments. To study the replication dynamics of the yeast genome, for example, local peaks of hybridization intensity profiles correspond to putative replication origins. We propose a nonparametric kernel smoothing (NKS) technique to detect local hybridization intensity extrema across chromosomes. The novelty of our approach is that we base our inference procedures on equilibrium points, namely those locations at which the first derivative of the intensity curve is zero. The proposed smoothing technique provides both point and interval estimation for the location of local extrema. Also, this technique can be used to test for the hypothesis of either one or multiple suspected locations being the true equilibrium points. We illustrate the proposed method on a microarray data set from an experiment designed to study the replication origins in the yeast genome, in that the locations of autonomous replication sequence (ARS) elements are identified through the equilibrium points of the smoothed intensity profile curve. Our method found a few ARS elements that were not detected by the current smoothing methods such as the Fourier convolution smoothing. [source] DNA Microarray Experiments: Biological and Technological AspectsBIOMETRICS, Issue 4 2002Danh V. Nguyen Summary. DNA microarray technologies, such as cDNA and oligonucleotide microarrays, promise to revolutionize biological research and further our understanding of biological processes. Due to the complex nature and sheer amount of data produced from microarray experiments, biologists have sought the collaboration of experts in the analytical sciences, including statisticians, among others. However, the biological and technical intricacies of microarray experiments are not easily accessible to analytical experts. One aim for this review is to provide a bridge to some of the relevant biological and technical aspects involved in microarray experiments. While there is already a large literature on the broad applications of the technology, basic research on the technology itself and studies to understand process variation remain in their infancy. We emphasize the importance of basic research in DNA array technologies to improve the reliability of future experiments. [source] Hepatic transcription response to high-fat treatment in mice: Microarray comparison of individual vs. pooled RNA samplesBIOTECHNOLOGY JOURNAL, Issue 9 2010Gyeong-Min Do Abstract Microarray analysis is an important tool in studying gene expression profiles in genomic research. Despite many concerns raised, mRNA samples are often pooled in microarray experiments to reduce the cost and complexity of analysis of transcript profiling. This study reports the results of microarray experiments designed to compare effects of pooling RNA samples and its impact on identifying profiles of mRNA transcripts and differentially expressed genes (DEGs) in the liver of C57BL/6J mice fed normal and high-fat diet. Pearson's correlation coefficient of transcripts between pooled and non-pooled RNA samples was 0.98 to 1.0. The impact of pooled vs. non-pooled RNA samples was also compared by number of transcripts or DEGs. Agreement of significant genes between pooled and non-pooled sets was fairly desirable based on t -test <0.05 and/or signal intensity ,2-fold. Biological process profile and the correlation coefficiency of fold change in the hepatic gene transcripts between pooled and non-pooled samples were also higher than 0.97. This suggests that pooling hepatic RNA samples can reflect the expression pattern of individual samples, and that properly constructed pools can provide nearly identical measures of transcription response to individual RNA sample. [source] DNA Microarrays: Experimental Issues, Data Analysis, and Application to Bacterial SystemsBIOTECHNOLOGY PROGRESS, Issue 5 2004Yandi Dharmadi DNA microarrays are currently used to study the transcriptional response of many organisms to genetic and environmental perturbations. Although there is much room for improvement of this technology, its potential has been clearly demonstrated in the past 5 years. The general consensus is that the bottleneck is now located in the processing and analysis of transcriptome data and its use for purposes other than the quantification of changes in gene expression levels. In this article we discuss technological aspects of DNA microarrays, statistical and biological issues pertinent to the design of microarray experiments, and statistical tools for microarray data analysis. A review on applications of DNA microarrays in the study of bacterial systems is presented. Special attention is given to studies in the following areas: (1) bacterial response to environmental changes; (2) gene identification, genome organization, and transcriptional regulation; and (3) genetic and metabolic engineering. Soon, the use of DNA microarray technologies in conjunction with other genome/system-wide analyses (e.g., proteomics, metabolomics, fluxomics, phenomics, etc.) will provide a better assessment of genotype-phenotype relationships in bacteria, which serve as a basis for understanding similar processes in more complex organisms. [source] Potent inhibition of in vivo angiogenesis and tumor growth by a novel cyclooxygenase-2 inhibitor, enoic acanthoic acidCANCER SCIENCE, Issue 12 2007Hye Jin Jung Recent studies have shown that cyclooxygenase-2 is crucially involved in angiogenesis. In fact, several specific cyclooxygenase-2 inhibitors suppress angiogenesis in vivo, suggesting that cyclooxygenase-2 is a promising target for the treatment of angiogenesis-related diseases. In the present study we investigate the activity of a new cyclooxygenase-2 inhibitor, enoic acanthoic acid (EAA), which was synthesized from the known natural cyclooxygenase-2 inhibitor, acanthoic acid (AA). The demonstration of a high correlation between EAA- and celecoxib-induced gene expression signatures in microarray experiments validated the specificity of EAA on cyclooxygenase-2. In angiogenesis assays, EAA potently inhibited basic fibroblast growth factor-induced invasion and tube formation of bovine aortic endothelial cells in vitro. Moreover, this inhibitor prevented both neovascularization of the chorioallantoic membrane of growing chick embryo and basic fibroblast growth factor-induced mouse corneal angiogenesis in vivo. EAA also significantly suppressed the growth of bladder tumors in a mouse model, showing better antitumor activity than celecoxib. Furthermore, gelatin zymogram analysis revealed that EAA potently inhibited the activities of matrix metalloproteinase 2 and 9. These results clearly demonstrate that EAA is a promising agent for the prevention and treatment of angiogenesis-related diseases including cancer. 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