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Problems of Fuzzy Clustering of Microarray Data

References Bezdek, J. C. Pattern Recognition with Fuzzy Objective Function Algorithms. New York: Plenum Press, 1981. Dembèlè, D., Kastner, P. "Fuzzy c-means method for clustering microarray data," Bioinformatics, Vol. 19, No.8, pp.973-980, May 2003. Futschik, M. E., Kasabov, K. "Fuzzy Clustering of Gene Expression data," Available: http://itb.biologie.huberlin.de/~futschik/publis/futschik_ieee.pdf Tarca, A. L., Romero, R., Draghici, S. "Analysis of

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Metadata Management and Semantics in Microarray Repositories

References Brazma A, Hingamp P, Quackenbush J, Sherlock G, Spellman P, Stoeckert C, Aach J, Ansorge W, Ball CA, Causton HC, Gaasterland T, Glenisson P, Holstege FC, Kim IF, Markowitz V, Matese JC, Parkinson H, Robinson A, Sarkans U, Schulze-Kremer S, Stewart J, Taylor R, Vilo J, Vingron M. Minimum information about a microarray experiment (MIAME)-toward standards for microarray data. Nat Genet. 2001; 29(4):365-371. MGED (Microarray Gene Expression Data) Society [Internet]. [cited 2011 May 3] ( http

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Antibody Microarray Expression Profiling Of Maize Roots Treated With Cadmium And Nickel

.J. – BROWN, P.O. 2001. Protein microarrays for highly parallel detection and quantitation of specific proteins and antibodies in complex solution. In Genome Biology , vol. 2 , pp. 1–13. HALL, J.L. 2002. Cellular mechanisms for heavy metal detoxification and tolerance. In Journal of Experimental Botany , vol. 53 , pp.1–11. HEDENFALK, I. – DUGGAN, D. – CHEN, Y. – RADMACHER, M. – BITTNER, M. SIMON, R. – MELTZER, P. – GUSTERSON, B. – ESTELLER, M. – KALLIONIEMI, P. – WILFORD, B. – BORG, A. – TRENT, J. 2001. Gene expression profiles in hereditary breast cancer

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Identification of upregulated genes in laminarin-treated poplar (Populus alba × P. tremula var. glandulosa) suspension cells by suppression subtractive hybridization and cDNA microarray

tent caterpillar (Malacosoma disstria): normalized and full-length cDNA libraries, expressed sequence tags, and a cDNA microarray for the study of insectinduced defences in poplar. Mol. Ecol. 15: 1275-1297. ROBB, J., B. LEE and R. N. NAZAR (2007): Gene suppression in a tolerant tomato-vascular pathogen interaction. Planta 226: 299-309. SCHMIDT, K., B. HEBERLE, J. KURRASCH, R. NEHLS and D. J. STAHL (2004): Suppression of phenylalanine ammonia lyase expression in sugar beet by the fungal pathogen Cercospora beticola is mediated at the

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Connection up- and down-regulation expression analysis of microarrays (CU-DREAM): a physiogenomic discovery tool

References 1. Smalheiser NR. Informatics and hypothesis-driven research. EMBO Rep. 2002; 3:702. 2. Barrett T, Troup DB, Wilhite SE, Ledoux P, Rudnev D, Evangelista C, et al. NCBI GEO: archive for highthroughput functional genomic data. Nucleic Acids Res. 2009; 37(Database issue):D885-90. 3. Edgar R, Barrett T. NCBI GEO standards and services for microarray data. Nat Biotechnol. 2006; 24:1471-2. 4. Barrett T, Troup DB, Wilhite SE, Ledoux P, Rudnev D, Evangelista C, et al. NCBI GEO: mining tens of

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Microarray Analysis of Gene Expression in Triploid Black Poplar

Abstract

Triploidy is a widespread phenomenon in cultivated and natural breeding plants and it can confer some growth advantages. Here, we analyzed genome-wide gene expression in triploid Populus euramericana (black poplar) using the Affymetrix poplar microarray to detect any possible correlation between triploid vigor and a unique gene expression profile. Among the 38,400 transcripts that were detected in triploid poplar, 1,564 and 2,015 genes were up- or downregulated, respectively, compared with the diploid. The majority of the upregulated genes in the triploid were associated with carbon and nitrogen metabolism, especially lignin and secondary metabolism. Other genes upregulated in the triploid included genes involved in sugar transport, and brassinosteroid (BR) and auxin metabolism. Downregulated genes were mostly related to the assembly and biosynthesis of ribosomes and the nucleosome macromolecular complex. The results suggested that BR and auxin levels were crucial in controlling sugar transport, photosynthesis and cell wall biosynthesis. Downregulated genes were associated with chromatin regulation in the triploid. The information from this analysis could provide an insight into the vigor of triploid poplar.

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Microarray technology reveals potentially novel genes and pathways involved in non-functioning pituitary adenomas

aggressiveness of NFPAs [ 11 ]. Recently, CCNB1 was found to mediate the proliferation-inhibiting role of miR-410, a small non-coding RNA, in GnPA [ 12 ]. Additionally, Chesnokova et al . [ 13 ] have identified that human pituitary tumors originated from gonadotroph cells express abundant FOXL2 , and both FOXL2 and PTTG promote cluster- ing expression and secretion from gonadotroph cells, thus restraining the proliferation of pituitary cells. Along with the development of microarray, transcriptome analysis has been widely utilized in understanding tumor mechanism

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The Use of SNP Microarrays for Biodiversity Studies of Sheep – A Review

Abstract

The conservation of farm animal genetic resources and their protection against genetic erosion requires knowledge of biodiversity status. Genetic variation in populations can be estimated using both traditional pedigree-based methods and molecular techniques. SNP microarrays are a new generation of molecular genetic tools, which have found application in analysis of biodiversity in populations of domestic and wild sheep, in studies of resistance to intestinal parasites and foot rot, and in searching for markers associated with meat and milk yield, or colour inheritance traits. The aim of the study is the review of recent literature on the biodiversity and the use of molecular markers for population genetics in different breeds and populations of sheep.

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Epithelium morphogenesis and oviduct development are regulated by significant increase of expression of genes after long-term in vitro primary culture – a microarray assays

Abstract

The correct oviductal development and morphogenesis of its epithelium are crucial factors influencing female fertility. Oviduct is involved in maintaining an optimal environment for gametes and preimplantation embryo development; secretory oviductal epithelial cells (OECs) synthesize components of oviductal fluid. Oviductal epithelium also participates in sperm binding and its hyperactivation. For better understanding of the genetic bases that underlay porcine oviductal development, OECs were isolated from porcine oviducts and established long-term primary culture. A microarray approach was utilized to determine the differentially expressed genes during specific time periods. Cells were harvested on day 7, 15 and 30 of in vitro primary culture and their RNA was isolated. Gene expression was analyzed and statistical analysis was performed. 48 differentially expressed genes belonging to “tube morphogenesis”, “tube development”, “morphogenesis of an epithelium”, “morphogenesis of branching structure” and “morphogenesis of branching epithelium” GO BP terms were selected, of which 10 most upregulated include BMP4, ARG1, SLIT2, FGFR1, DAB2, TNC, EPAS1, HHEX, ITGB3 and LOX. The results help to shed light on the porcine oviductal development and its epithelial morphogenesis, and show that after long-term culture the OECs still proliferate and maintain their tube forming properties.

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The Stability of Gene Selection in Microarray Experiments

References Aerts, S., Lambrechts, D., Maity, S., Van Loo, P., Coessens, B., De Smet, F., Tranchevent, L. C., De Moor, B., Marynen, P., Hassan, B., Carmeliet, P., & Moreau, Y. (2006). Gene prioritization through genomic data fusion. Nat Biotechnol, 24, 537-544. Boulesteix, A. L., & Slawski, M. (2009). Stability and aggregation of ranked gene lists. Brief Bioinformatics, 10, 556-568. Boulesteix, A. L., Strobl, C., Augustin, T., & Daumer, M. (2008). Evaluating Microarray-based Classifiers: An Overview

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