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Microarray Data (microarray + data)

Distribution by Scientific Domains
Medical Sciences36%
Life Sciences28%
Mathematics and Statistics24%
Chemistry10%
Distribution within Medical Sciences
Oncology & Radiotherapy11%

Terms modified by Microarray Data

  • microarray data analysis
    		•
  • microarray data set
    		•

    Selected Abstracts

    Statistical Analysis of Microarray Data

    ADDICTION BIOLOGY, Issue 1 2005
    Mark Reimers
    Microarrays promise dynamic snapshots of cell activity, but microarray results are unfortunately not straightforward to interpret. This article aims to distill the most useful practical results from the vast body of literature availalable on microarray data analysis. Topics covered include: experimental design issues, normalization, quality control, exploratory analysis, and tests for differential expression. Special attention is paid to the peculiarities of low-level analysis of Affymetrix chips, and the multiple testing problem in determining differential expression. The aim of this article is to provide useful answers to the most common practical issues in microarray data analysis. The main topics are pre-processing (normalization), and detecting differential expression. Subsidiary topics include experimental design, and exploratory analysis. Further discussion is found at the author's web page (http://discover.nci.nih.gov, Notes on Microarray Data Analysis). [source]

    Pilot Study Examining the Utility of Microarray Data to Identify Genes Associated with Weight in Transplant Recipients

    NURSING & HEALTH SCIENCES, Issue 2 2006
    Ann Cashion
    Purpose/Methods:, Obesity, a complex, polygenic disorder and a growing epidemic in transplant recipients, is a risk factor for chronic diseases. This secondary data analysis identified if microarray technologies and bioinformatics could find differences in gene expression profiles between liver transplant recipients with low Body Mass Index (BMI < 29; n = 5) vs. high (BMI > 29; n = 7). Blood was hybridized on Human U133 Plus 2 GeneChip (Affymetrix) and analyzed using GeneSpring Software. Results:, Groups were similar in age and race, but not gender. Expression levels of 852 genes were different between the low and high BMI groups (P < 0.05). The majority (562) of the changes associated with high BMI were decreases in transcript levels. Among the 852 genes associated with BMI, 263 and 14 genes were affected greater than 2- or 5-fold, respectively. Following functionally classification using Gene Ontology (GO), we found that 19 genes (P < 0.00008) belonged to defense response and 15 genes (P < 0.00006) belonged to immune response. Conclusion:, These data could point the way toward therapeutic interventions and identify those at-risk. These results demonstrate that we can (1) extract high quality RNA from immunosuppressed patients; (2) manage large datasets and perform statistical and functional analysis. [source]

    Incorporating Predictor Network in Penalized Regression with Application to Microarray Data

    BIOMETRICS, Issue 2 2010
    Wei Pan
    Summary We consider penalized linear regression, especially for "large,p, small,n" problems, for which the relationships among predictors are described a priori by a network. A class of motivating examples includes modeling a phenotype through gene expression profiles while accounting for coordinated functioning of genes in the form of biological pathways or networks. To incorporate the prior knowledge of the similar effect sizes of neighboring predictors in a network, we propose a grouped penalty based on the,L, -norm that smoothes the regression coefficients of the predictors over the network. The main feature of the proposed method is its ability to automatically realize grouped variable selection and exploit grouping effects. We also discuss effects of the choices of the , and some weights inside the,L, -norm. Simulation studies demonstrate the superior finite-sample performance of the proposed method as compared to Lasso, elastic net, and a recently proposed network-based method. The new method performs best in variable selection across all simulation set-ups considered. For illustration, the method is applied to a microarray dataset to predict survival times for some glioblastoma patients using a gene expression dataset and a gene network compiled from some Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. [source]

    Variable Selection for Model-Based High-Dimensional Clustering and Its Application to Microarray Data

    BIOMETRICS, Issue 2 2008
    Sijian Wang
    Summary Variable selection in high-dimensional clustering analysis is an important yet challenging problem. In this article, we propose two methods that simultaneously separate data points into similar clusters and select informative variables that contribute to the clustering. Our methods are in the framework of penalized model-based clustering. Unlike the classical L1 -norm penalization, the penalty terms that we propose make use of the fact that parameters belonging to one variable should be treated as a natural "group." Numerical results indicate that the two new methods tend to remove noninformative variables more effectively and provide better clustering results than the L1 -norm approach. [source]

    Nonparametric Inference for Local Extrema with Application to Oligonucleotide Microarray Data in Yeast Genome

    BIOMETRICS, Issue 2 2006
    Peter 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]

    Protein chip-based microarray profiling of oxidized low density lipoprotein-treated cells

    PROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS, Issue 5 2005
    Sergiy Sukhanov
    Abstract Commercially available high-content Ab380 and extensively validated DLM26 homemade protein microarrays were used to profile the effects of the pro-atherogenic molecule, oxidized low density lipoprotein (OxLDL), on human aortic smooth muscle cells. Protein microarrays detected 298 proteins in cell lysates and 54 of these were differentially regulated. Microarray data were validated by immunoblotting for a selected set of up- and down-regulated proteins. The protein microarray data sets were compared with our recent cDNA microarray-based gene expression results in order to characterize the global effect of OxLDL on smooth muscle cell functions. A group of cell-cell interaction molecules was classified as up-regulated by OxLDL, whereas nucleic acid/protein biosynthesis, structural and humoral response proteins/genes were under-expressed in cells treated by OxLDL. These findings reveal the major pattern of OxLDL-induced effects on the human aortic smooth muscle cells functions and also demonstrate that protein chip-based microarrays could be a useful proteomic tool to profile disease-related states of muscle cells. [source]

    Nuclear factor TDP-43 can affect selected microRNA levels

    FEBS JOURNAL, Issue 10 2010
    Emanuele Buratti
    TDP-43 has recently been described as the major component of the inclusions found in the brain of patients with a variety of neurodegenerative diseases, such as frontotemporal lobar degeneration and amyotrophic lateral sclerosis. TDP-43 is a ubiquitous protein whose specific functions are probably crucial to establishing its pathogenic role. Apart from its involvement in transcription, splicing and mRNA stability, TDP-43 has also been described as a Drosha-associated protein. However, our knowledge of the role of TDP-43 in the microRNA (miRNA) synthesis pathway is limited to the association mentioned above. Here we report for the first time which changes occur in the total miRNA population following TDP-43 knockdown in culture cells. In particular, we have observed that let-7b and miR-663 expression levels are down- and upregulated, respectively. Interestingly, both miRNAs are capable of binding directly to TDP-43 in different positions: within the miRNA sequence itself (let-7b) or in the hairpin precursor (miR-663). Using microarray data and real-time PCR we have also identified several candidate transcripts whose expression levels are selectively affected by these TDP-43,miRNA interactions. [source]

    Identification of direct and indirect targets of the Gln3 and Gat1 activators by transcriptional profiling in response to nitrogen availability in the short and long term

    FEMS YEAST RESEARCH, Issue 5 2006
    Bart Scherens
    Abstract Nitrogen catabolite repression (NCR) consists in the specific inhibition of transcriptional activation of genes encoding the permeases and catabolic enzymes needed to degrade poor nitrogen sources. Under nitrogen limitation or rapamycin treatment, NCR genes are activated by Gln3 or Gat1, or by both factors. To compare the sets of genes responding to rapamycin or to nitrogen limitation, we used DNA microarrays to establishing the expression profiles of a wild type strain, and of a double gln3,,gat1, strain, grown on glutamine, after addition of rapamycin, on proline, or after a shift from glutamine to proline. Analysis of microarray data revealed 392 genes whose expression was dependent on the nitrogen source quality. 91 genes were activated in a GATA factor-dependent manner in all growth conditions, suggesting a direct role of Gln3 and Gat1 in their expression. Other genes were only transiently up-regulated (stress-responsive genes) or down-regulated (genes encoding ribosomal proteins and translational factors) upon nitrogen limitation, and this regulation was delayed in a gln3,,gat1, strain. Repression of amino acid and nucleotide biosynthetic genes after a nitrogen shift did not depend on Gcn4. Several transporter genes were repressed as a consequence of enhanced levels of NCR-responsive permeases present at the plasma membrane. [source]

    Identification of genes with abnormal expression changes in acute myeloid leukemia

    GENES, CHROMOSOMES AND CANCER, Issue 1 2008
    Derek L. Stirewalt
    Acute myeloid leukemia (AML) is one of the most common and deadly forms of hematopoietic malignancies. We hypothesized that microarray studies could identify previously unrecognized expression changes that occur only in AML blasts. We were particularly interested in those genes with increased expression in AML, believing that these genes may be potential therapeutic targets. To test this hypothesis, we compared gene expression profiles between normal hematopoietic cells from 38 healthy donors and leukemic blasts from 26 AML patients. Normal hematopoietic samples included CD34+ selected cells (N = 18), unselected bone marrows (N = 10), and unselected peripheral bloods (N = 10). Twenty genes displayed AML-specific expression changes that were not found in the normal hematopoietic cells. Subsequent analyses using microarray data from 285 additional AML patients confirmed expression changes for 13 of the 20 genes. Seven genes (BIK, CCNA1, FUT4, IL3RA, HOMER3, JAG1, WT1) displayed increased expression in AML, while 6 genes (ALDHA1A, PELO, PLXNC1, PRUNE, SERPINB9, TRIB2) displayed decreased expression. Quantitative RT/PCR studies for the 7 over-expressed genes were performed in an independent set of 9 normal and 21 pediatric AML samples. All 7 over-expressed genes displayed an increased expression in the AML samples compared to normals. Three of the 7 over-expressed genes (WT1, CCNA1, and IL3RA) have already been linked to leukemogenesis and/or AML prognosis, while little is known about the role of the other 4 over-expressed genes in AML. Future studies will determine their potential role in leukemogenesis and their clinical significance. This article contains Supplementary Material available at http://www.interscience.wiley.com/jpages/1045-2257/suppmat. © 2007 Wiley-Liss, Inc. [source]

    Onset of promiscuous gene expression in murine fetal thymus organ culture

    IMMUNOLOGY, Issue 3 2006
    Renato Sousa Cardoso
    Summary T-cell differentiation and induction of tolerance to self-antigens occurs mainly in the thymus. Thymic stromal cells, specifically medullary thymic epithelial cells, express a diverse set of genes encoding parenchymal organ-specific proteins. This phenomenon has been termed promiscuous gene expression (PGE) and has been implicated in preventing organ-specific autoimmunity by inducing T-cell tolerance to self antigens. Early thymopoiesis and the critical factors involved in T-cell differentiation can be reproduced in vitro by murine fetal thymus organ culture (FTOC), which mimics the natural thymic microenvironment. To evaluate the occurrence of PGE in FTOC, gene expression profiling during in vitro thymic development in BALB/c mice was performed using a set of nylon cDNA microarrays containing 9216 sequences. The statistical analysis of the microarray data (sam program) revealed the temporal repression and induction of 57 parenchymal and seven lymphoid organ-specific genes. Most of the genes analysed are repressed during early thymic development (15,17 days post-coitum). The expression of the autoimmune regulator (AIRE) gene at 16 days post-coitum marks the onset of PGE. This precedes the induction of parenchymal organ genes during the late developmental phase at 20 days post-coitum. The mechanism of T-cell tolerance induction begins during fetal development and continues into adulthood. Our findings are significant because they show a fine demarcation of PGE onset, which plays a central role in induction of T-cell tolerance. [source]

    Microarray analysis of acaricide-inducible gene expression in the southern cattle tick, Rhipicephalus (Boophilus) microplus

    INSECT MOLECULAR BIOLOGY, Issue 6 2008
    L. Saldivar
    Abstract Acaricide-inducible differential gene expression was studied in larvae of Rhipicephalus (Boophilus) microplus using a microarray-based approach. The acaricides used were: coumaphos, permethrin, ivermectin, and amitraz. The microarrays contained over 13 000 probes, having been derived from a previously described R. microplus gene index (BmiGI Version 2; Wang et al., 2007). Relative quantitative reverse transcriptase-PCR, real time PCR, and serial analysis of gene expression data was used to verify microarray data. Among the differentially expressed genes with informative annotation were legumain, glutathione S-transferase, and a putative salivary gland-associated protein. [source]

    Guidelines for reporting of DNA microarray data

    INTERNATIONAL ENDODONTIC JOURNAL, Issue 10 2010
    Paul M. H. Dummer Editor-in-Chief
    No abstract is available for this article. [source]

    Expression profiling of Wilms tumors reveals new candidate genes for different clinical parameters

    INTERNATIONAL JOURNAL OF CANCER, Issue 8 2006
    B. 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]

    Control of chondrocyte gene expression by actin dynamics: a novel role of cholesterol/Ror-, signalling in endochondral bone growth

    JOURNAL OF CELLULAR AND MOLECULAR MEDICINE, Issue 9b 2009
    Anita Woods
    Abstract Elucidating the signalling pathways that regulate chondrocyte differentiation, such as the actin cytoskeleton and Rho GTPases, during development is essential for understanding of pathological conditions of cartilage, such as chondrodysplasias and osteoarthritis. Manipulation of actin dynamics in tibia organ cultures isolated from E15.5 mice results in pronounced enhancement of endochondral bone growth and specific changes in growth plate architecture. Global changes in gene expression were examined of primary chondrocytes isolated from embryonic tibia, treated with the compounds cytochalasin D, jasplakinolide (actin modifiers) and the ROCK inhibitor Y27632. Cytochalasin D elicited the most pronounced response and induced many features of hypertrophic chondrocyte differentiation. Bioinformatics analyses of microarray data and expression validation by real-time PCR and immunohistochemistry resulted in the identification of the nuclear receptor retinoid related orphan receptor-, (Ror-,) as a novel putative regulator of chondrocyte hypertrophy. Expression of Ror-, target genes, (Lpl, fatty acid binding protein 4 [Fabp4], Cd36 and kruppel-like factor 5 [Klf15]) were induced during chondrocyte hypertrophy and by cytochalasin D and are cholesterol dependent. Stimulation of Ror-, by cholesterol results in increased bone growth and enlarged, rounded cells, a phenotype similar to chondrocyte hypertrophy and to the changes induced by cytochalasin D, while inhibition of cholesterol synthesis by lovastatin inhibits cytochalasin D induced bone growth. Additionally, we show that in a mouse model of cartilage specific (Col2-Cre) Rac1, inactivation results in increased Hif-1, (a regulator of Rora gene expression) and Ror-,+ cells within hypertrophic growth plates. We provide evidence that cholesterol signalling through increased Ror-, expression stimulates chondrocyte hypertrophy and partially mediates responses of cartilage to actin dynamics. [source]

    Endomyocardial biopsy derived adherent proliferating cells,A potential cell source for cardiac tissue engineering

    JOURNAL OF CELLULAR BIOCHEMISTRY, Issue 3 2010
    Marion Haag
    Abstract Heart diseases are a leading cause of morbidity and mortality. Cardiac stem cells (CSC) are considered as candidates for cardiac-directed cell therapies. However, clinical translation is hampered since their isolation and expansion is complex. We describe a population of human cardiac derived adherent proliferating (CAP) cells that can be reliably and efficiently isolated and expanded from endomyocardial biopsies (0.1,cm3). Growth kinetics revealed a mean cell doubling time of 49.9,h and a high number of 2.54,×,107 cells in passage 3. Microarray analysis directed at investigating the gene expression profile of human CAP cells demonstrated the absence of the hematopoietic cell markers CD34 and CD45, and of CD90, which is expressed on mesenchymal stem cells (MSC) and fibroblasts. These data were confirmed by flow cytometry analysis. CAP cells could not be differentiated into adipocytes, osteoblasts, chondrocytes, or myoblasts, demonstrating the absence of multilineage potential. Moreover, despite the expression of heart muscle markers like ,-sarcomeric actin and cardiac myosin, CAP cells cannot be differentiated into cardiomyocytes. Regarding functionality, CAP cells were especially positive for many genes involved in angiogenesis like angiopoietin-1, VEGF, KDR, and neuropilins. Globally, principal component and hierarchical clustering analysis and comparison with microarray data from many undifferentiated and differentiated reference cell types, revealed a unique identity of CAP cells. In conclusion, we have identified a unique cardiac tissue derived cell type that can be isolated and expanded from endomyocardial biopsies and which presents a potential cell source for cardiac repair. Results indicate that these cells rather support angiogenesis than cardiomyocyte differentiation. J. Cell. Biochem. 109: 564,575, 2010. © 2009 Wiley-Liss, Inc. [source]

    Selective induction of mucin-3 by hypoxia in intestinal epithelia

    JOURNAL OF CELLULAR BIOCHEMISTRY, Issue 6 2006
    Nancy A. Louis
    Abstract Epithelial cells line mucosal surfaces (e.g., lung, intestine) and critically function as a semipermeable barrier to the outside world. Mucosal organs are highly vascular with extensive metabolic demands, and for this reason, are particularly susceptible to diminished blood flow and resultant tissue hypoxia. Here, we pursue the hypothesis that intestinal barrier function is regulated in a protective manner by hypoxia responsive genes. We demonstrate by PCR confirmation of microarray data and by avidin blotting of immunoprecipitated human Mucin 3 (MUC3), that surface MUC3 expression is induced in T84 intestinal epithelial cells following exposure to hypoxia. MUC3 RNA is minimally detectable while surface protein expression is absent under baseline normoxic conditions. There is a robust induction in both the mRNA (first evident by 8 h) and protein expression, first observed and maximally expressed following 24 h hypoxia. This is followed by a subsequent decline in protein expression, which remains well above baseline at 48 h of hypoxia. Further, we demonstrate that this induction of MUC3 protein is associated with a transient increase in the barrier restorative peptide, intestinal trefoil factor (ITF). ITF not only colocalizes with MUC3, by confocal microscopy, to the apical surface of T84 cells following exposure to hypoxia, but is also found, by co-immunoprecipitation, to be physically associated with MUC3, following 24 h of hypoxia. In exploration of the mechanism of hypoxic regulation of mucin 3 expression, we demonstrated by luciferase assay that the full-length promoter for mouse Mucin 3 (Muc3) is hypoxia-responsive with a 5.08,±,1.76-fold induction following 24 h of hypoxia. Furthermore, analysis of both the human (MUC3A) and mouse (Muc3) promoters revealed potential HIF-1 binding sites which were shown by chromatin immunoprecipitation to bind the pivotal hypoxia-regulating transcription factor HIF-1,. Taken together, these studies implicate the HIF-1, mediated hypoxic induced expression of mucin 3 and associated ITF in the maintenance of intestinal barrier function under hypoxic conditions. J. Cell. Biochem. 99: 1616,1627, 2006. © 2006 Wiley-Liss, Inc. [source]

    Temporal expression changes during differentiation of neural stem cells derived from mouse embryonic stem cell

    JOURNAL OF CELLULAR BIOCHEMISTRY, Issue 3 2004
    Joon-Ik Ahn
    Abstract Temporal analysis in gene expression during differentiation of neural stem cells (NSCs) was performed by using in-house microarrays composed of 10,368 genes. The changes in mRNA level were measured during differentiation day 1, 2, 3, 6, 12, and 15. Out of 10,368 genes analyzed, 259 genes were up-regulated or down-regulated by 2-fold or more at least at one time-point during differentiation, and were classified into six clusters based on their expression patterns by K-means clustering. Clusters characterized by gradual increase have large numbers of genes involved in transport and cell adhesion; those which showed gradual decrease have much of genes in nucleic acid metabolism, cell cycle, transcription factor, and RNA processing. In situ hybridization (ISH) validated microarray data and it also showed that Fox M1, cyclin D2, and CDK4 were highly expressed in CNS germinal zones and ectonucleotide pyrophosphatase/phosphodiesterase 2 (Enpp2) was highly expressed in choroid plexus where stem/progenitor cells are possibly located. Together, this clustering analysis of expression patterns of functionally classified genes may give insight into understanding of CNS development and mechanisms of NSCs proliferation and differentiation. © 2004 Wiley-Liss, Inc. [source]

    Microarray data classification using inductive logic programming and gene ontology background information

    JOURNAL OF CHEMOMETRICS, Issue 5 2010
    Einar Ryeng
    Abstract There exists many databases containing information on genes that are useful for background information in machine learning analysis of microarray data. The gene ontology and gene ontology annotation projects are among the most comprehensive of these. We demonstrate how inductive logic programming (ILP) can be used to build classification rules for microarray data which naturally incorporates the gene ontology and annotations to it as background knowledge without removing the inherent graph structure of the ontology. The ILP rules generated are parsimonious and easy to interpret. Copyright © 2010 John Wiley & Sons, Ltd. [source]

    Reassessment of microarray expression data of porokeratosis by quantitative real-time polymerase chain reaction

    JOURNAL OF CUTANEOUS PATHOLOGY, Issue 3 2010
    Zheng-Hua Zhang
    Background: Porokeratosis (PK) is a heterogeneous group of keratinization disorders that exhibit similarities with psoriasis at both the clinical and molecular levels. Methods: The transcript levels of keratin (KRT) 6A, 16, 17, S100A7, A8, A9, p53 and three candidate genes (i.e. SART3, SSH1 and ARPC3) were reassessed in pairwise lesional and uninvolved skin from nine patients with PK by real-time quantitative polymerase chain reaction (RTQ,PCR). Results: The results of RTQ,PCR confirmed that KRT6A, 16, S100A7, A8 and A9 (p = 0.008) were mostly up-regulated in the lesional skin when compared with uninvolved skin. Different from the microarray data, there was no significant difference observed in KRT17 expression patterns between lesional and normal-appearing skin (p = 0.066). No statistical difference was observed in p53 and three candidate genes' expression patterns between lesional and uninvolved skin. Conclusions: In the present study, 9 of the 10 gene expression measured by RTQ,PCR in PK were statistically comparable to microarray data. KRT6A was identified as specific biomarker for porokeratotic keratinocytes, as it was the most significantly up-regulated gene in the nine patient samples. Zhang Z-H, Wang Z-M, Crosby ME, Kang KF, Luan J, Huang W, Xiang L-H, Zheng Z-Z. Reassessment of microarray expression data of porokeratosis by quantitative real-time polymerase chain reaction. [source]

    Yin yang 1 directly regulates the transcription of RE-1 silencing transcription factor

    JOURNAL OF NEUROSCIENCE RESEARCH, Issue 6 2008
    Lichun Jiang
    Abstract The RE-1 silencing transcription factor (REST) is a master transcription factor that plays a critical role in embryo development, especially during the process of neurogenesis and neural plasticity. However, the mechanism of REST gene transcription regulation is still an open question. Here, by combining bioinformatics analysis and experimental studies, we report that the transcription factor Yin Yang 1 (YY1) bound to a conserved YY1 binding site in the promoter of the mouse REST gene and positively regulated activity of this promoter in SH-SY5Y cells. Furthermore, analysis of microarray data revealed a significant correlation between the expression of YY1 and REST genes. Overall, this study suggests that YY1 directly regulates expression of the REST gene. © 2007 Wiley-Liss, Inc. [source]

    Identification of genes related to mechanical stress in human periodontal ligament cells using microarray analysis

    JOURNAL OF PERIODONTAL RESEARCH, Issue 1 2007
    R. M. S. De Araujo
    Background and Objective:, Differential expression of genes in human periodontal ligament (PDL) under mechanical stress, such as orthodontic force, is thought to be involved in the remodeling of PDL cells and periodontal tissues. However, little is known about the genes expressed in PDL cells under mechanical stress. Material and Methods:, We employed microarray analysis to assess, in a comprehensive manner, the gene expression profiles in PDL cells compressed by a static force using an in vitro three-dimensional culture system. Six genes were selected and validated by quantitative real-time polymerase chain reaction analysis, consistent with the microarray data. Results:, The microarray data revealed that 108 of 30,000 genes tested were differentially expressed by mechanical force loading. Among them, 85 genes were up-regulated by mechanical stress, while 23 genes were down-regulated, judging by the thresholds of a two-fold increase/decrease compared with the controls. Thirty-two of the up-regulated and eight of the down-regulated genes, well-characterized in protein function, were involved in numerous biological processes including cell communication, cell signaling, cell cycle, stress response, and calcium release. However, several genes differentially expressed in our microarray data have not been well defined as stress-response molecules. Conclusion:, Our microarray is the first to show the gene profile in PDL cells caused by mechanical stress; however, further studies to clarify the physiological function of these molecules in PDL cells are required. [source]

    A Bayesian discovery procedure

    JOURNAL OF THE ROYAL STATISTICAL SOCIETY: SERIES B (STATISTICAL METHODOLOGY), Issue 5 2009
    Michele Guindani
    Summary., We discuss a Bayesian discovery procedure for multiple-comparison problems. We show that, under a coherent decision theoretic framework, a loss function combining true positive and false positive counts leads to a decision rule that is based on a threshold of the posterior probability of the alternative. Under a semiparametric model for the data, we show that the Bayes rule can be approximated by the optimal discovery procedure, which was recently introduced by Storey. Improving the approximation leads us to a Bayesian discovery procedure, which exploits the multiple shrinkage in clusters that are implied by the assumed non-parametric model. We compare the Bayesian discovery procedure and the optimal discovery procedure estimates in a simple simulation study and in an assessment of differential gene expression based on microarray data from tumour samples. We extend the setting of the optimal discovery procedure by discussing modifications of the loss function that lead to different single-thresholding statistics. Finally, we provide an application of the previous arguments to dependent (spatial) data. [source]

    Bayesian classification of tumours by using gene expression data

    JOURNAL OF THE ROYAL STATISTICAL SOCIETY: SERIES B (STATISTICAL METHODOLOGY), Issue 2 2005
    Bani K. Mallick
    Summary., Precise classification of tumours is critical for the diagnosis and treatment of cancer. Diagnostic pathology has traditionally relied on macroscopic and microscopic histology and tumour morphology as the basis for the classification of tumours. Current classification frameworks, however, cannot discriminate between tumours with similar histopathologic features, which vary in clinical course and in response to treatment. In recent years, there has been a move towards the use of complementary deoxyribonucleic acid microarrays for the classi-fication of tumours. These high throughput assays provide relative messenger ribonucleic acid expression measurements simultaneously for thousands of genes. A key statistical task is to perform classification via different expression patterns. Gene expression profiles may offer more information than classical morphology and may provide an alternative to classical tumour diagnosis schemes. The paper considers several Bayesian classification methods based on reproducing kernel Hilbert spaces for the analysis of microarray data. We consider the logistic likelihood as well as likelihoods related to support vector machine models. It is shown through simulation and examples that support vector machine models with multiple shrinkage parameters produce fewer misclassification errors than several existing classical methods as well as Bayesian methods based on the logistic likelihood or those involving only one shrinkage parameter. [source]

    DNA Microarrays: Their Use and Misuse

    MICROCIRCULATION, Issue 1 2002
    Xinmin Li
    DNA microarray represents one of the major advances in functional genomics. Its ability to study expression of several thousands of genes or even all genes in the entire genome in a single experiment has changed the way in which we address basic biomedical questions. Numerous publications have shown its utility in drug discovery, disease diagnosis, novel gene identification, and understanding complex biological systems. However, there are substantive technical issues associated with the use of this technology that limit the interpretation of microarray data. In this review, we first give an overview of DNA microarray technology and then focus on uncertainty areas of microarray technology that include making microarrays, isolation of RNA and labeling, hybridization and scanning, and data analysis. The center theme of this review is to improve microarray reproducibility by addressing common technical problems. Finally, we briefly summarize microarray's applications in biomedical research. [source]

    Dynamics of global gene expression changes during brain metastasis formation

    NEUROPATHOLOGY, Issue 4 2009
    Norihiko Saito
    As methods of cancer diagnosis and treatment improve, interest in metastatic brain tumors continues to increase. In the present study, we attempted to characterize genetically the dynamic changes occurring during brain metastasis formation by DNA microarray, and attempted to compare these findings with histological observations. Lewis lung carcinoma cells were injected into C57BL/6Ncrj mice carotid arteries. The mice were sacrificed at days 1,9 after injection. We performed histological observation and genome-wide expression profiling using a DNA microarray. In histological observation, tumor cells were observed in capillary vessels at day 1 after injection. At day 3, the tumor cells had begun to proliferate. At day 6, the metastatic foci showed "perivascular proliferations". Next, we performed a pairwise comparison of gene expression microarray data from day 1 to day 9 after injection. The first major change occurred between Phase Two and Phase Three. When hierarchical clustering was performed between different samples using the 867 genes, they could be classified into identical clusters for days 1 and 2, identical clusters for day 3 to day 5, and identical clusters for day 6 to day 9. For time course analysis, we extracted 623 genes by the pairwise comparison. By using the quality threshold (QT) nonhierarchical clustering method, we identified 37 expression patterns. These patterns can be separated into eight clusters by using the k-means method. The microarray results reported here strongly suggest that a large number of genes exhibit a spike pattern, which is tantamount to phase-specific expression. [source]

    Identification of secreted proteins regulated by cAMP in glioblastoma cells using glycopeptide capture and label-free quantification

    PROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS, Issue 3 2009
    Jennifer J. Hill Dr.
    Abstract Exposure of glioblastoma U87MG cells to a cAMP analog leads to a decrease in proliferation, invasion, and angiogenic potential. Here, we apply a label-free MS-based approach to identify formerly N -linked glycopeptides that change in abundance upon cAMP treatment. Over 150 unique glycopeptides in three biological repetitions were quantified, leading to the identification of 14 upregulated proteins and 21 downregulated proteins due to cAMP treatment. Of these, eight have been validated, either through comparison with microarray data or by Western blot. We estimate our ability to identify differentially expressed peptides at greater than 85% in a single biological repetition, while the analysis of multiple biological repetitions lowers the false positive rate to ,2%. Many of the proteins identified in this study are involved in cell signaling and some, such as Tenascin C, Cathepsin L, Neuroblastoma suppressor of tumorigenicity, and AXL/UFO tyrosine,protein kinase receptor, have been previously shown to be involved in glioblastoma progression. We also identify several semitryptic peptides that increase in abundance upon cAMP treatment, suggesting that cAMP regulates protease activity in these cells. Overall, these results demonstrate the benefits of using a highly specific enrichment method for quantitative proteomic experiments. [source]

    Transcriptional Analysis of Buffalo (Bubalus bubalis) Oocytes During In Vitro Maturation Using Bovine cDNA Microarray

    REPRODUCTION IN DOMESTIC ANIMALS, Issue 1 2010
    OM Kandil
    Contents The need for improving in vitro production of buffalo embryos necessitates a better understanding of the molecular mechanisms regulating early development including oocyte maturation. Here, we used bovine cDNA microarray platform to investigate mRNA abundance of buffalo oocytes before and after in vitro maturation. For this, a total of six pools each contains 50 immature or in vitro matured buffalo oocytes were used for mRNA isolation and subsequent cDNA synthesis. The BlueChip bovine cDNA microarray (with approximately 2000 clones) was used to analyse gene expression profiles between immature and matured oocytes. Statistical analysis of microarray data revealed a total of 104 transcripts to be differentially expressed between the two oocyte groups. Among these, transcription factors (ZFP91), M-phase mitotic cell cycle (MPHOSPH9), growth factor (BMP15) and DNA binding (HMGN2) were found to be up-regulated in immature oocytes. Similarly, matured oocytes were found to be enriched with genes involved in cytoskeleton (ACTB), hydrogen ion transporting (ATP6V1C2) and structural constituent of ribosome (RPS27A). Quantitative real-time polymerase chain reaction validated the expression profile of some selected transcripts during array analysis. In conclusion, to our knowledge, this is the first large-scale expression study to identify candidate genes differentially abundant and with potential role during buffalo oocyte maturation. [source]

    Down-regulation of ATM protein in HRS cells of nodular sclerosis Hodgkin's lymphoma in children occurs in the absence of ATM gene inactivation,

    THE JOURNAL OF PATHOLOGY, Issue 3 2007
    S Bose
    Abstract The tumour component of classical Hodgkin's lymphoma (cHL), Hodgkin Reed,Sternberg (HRS) cells, are believed to be derived from germinal centre (GC) B cells but intriguingly display a characteristic loss of B cell receptor (BCR) expression. The precise mechanisms by which BCR-negative HRS cell progenitors survive negative selection during the GC reaction remain obscure. Individuals with ataxia telangiectasia, caused by biallelic inactivation of the DNA damage response gene, ataxia telangiectasia mutated (ATM), have a higher risk of cHL development. Here we show that, in contrast to normal GC B cells that expressed low but detectable ATM protein, ATM protein was not detected in HRS cells of 17/18 cases of paediatric cHL, all but one with nodular sclerosis (NS) subtype. A comprehensive analysis of the ATM gene in microdissected HRS cells of nine representative tumours showed no evidence of either loss of heterozygosity or consistent pathogenic mutations. Furthermore, bisulphite sequencing of the ATM promoter from HRS cells of five tumours also revealed the absence of hypermethylation. Since our microarray data suggested significantly reduced ATM transcription in HRS cells compared to GC B cells, we conclude that loss of ATM expression could be the result of alterations in upstream regulators of ATM transcription. Importantly, ATM loss in paediatric cHLs has clinical implications and could be potentially exploited to guide future, less toxic, tumour-specific treatments. Copyright © 2007 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd. [source]

    Current Applications of Microarrays in Head and Neck Cancer Research

    THE LARYNGOSCOPE, Issue 2 2004
    FRCS Eng, Giles C. Warner MSc
    Abstract Objectives/Hypothesis: The objective was to introduce microarray technology and its applications in cancer research to the head and neck clinician. Study Design: Literature review combined with methodology and examples from the authors' experiences with microarray analysis of tumors of the head and neck. Methods: Search of literature and the authors' experience was made for technical details, alternative methods of data analysis, available bioinformatics tools, and applications of microarrays in cancer research. Results: Microarrays allow the simultaneous analysis of the expression of thousands of genes. The use of a well-developed microarray study design leads to informative results. There are various bioinformatics resources widely available to aid in the analysis of microarray data. However, there is not yet a gold standard for analysis because this methodology is still evolving. Conclusion: Microarray studies may allow researchers to identify genetic changes relevant to diagnosis and prognosis in patients with head and neck cancer. Although still relatively new, this powerful methodology has immense potential to aid in understanding of the genetic changes that are important in head and neck cancer. [source]

    Interspecies comparison of prostate cancer gene-expression profiles reveals genes associated with aggressive tumors

    THE PROSTATE, Issue 10 2009
    Itai Kela
    Abstract Prostate cancer (PC) is a heterogeneous disease whose aggressive phenotype is the second leading cause of cancer-related death in men. The identification of key molecules and pathways that play a pivotal role in PC progression towards an aggressive form is crucial. A major effort towards this end has been taken by global analyses of gene expression profiles. However, the large body of data did not provide a definitive idea about the genes which are associated with the aggressive growth of PC. In order to identify such genes, we performed an interspecies comparison between several human data sets and high quality microarray data that we generated from the transgenic adenocarcinoma of mouse prostate (TRAMP) strain. The TRAMP PC mimics the histological and pathological appearance as well as the aggressive phenotype of human PC (huPC). Analysis of the microarray data, derived from microdissected TRAMP specimens removed at different stages of the disease yielded genetic signatures delineating the TRAMP PC development and progression. Comparison of the TRAMP data with a set of genes representing the core expression signature of huPC yielded a limited set genes. Some of these genes are known predictors of poor prognosis in huPC. Interestingly, the modulation of genes responsible for the invasive phenotype of huPC occurs in TRAMP already during the transition to prostate intraepithelial neoplasia (PIN) and onwards to localized tumors. We therefore suggest that critical oncogenic events leading to an aggressive phenotype of huPC can be studied in the PIN stage of TRAMP. Prostate 69:1034,1044, 2009. © 2009 Wiley-Liss, Inc. [source]