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Artículos de revistas sobre el tema "Gene Array"

Autor: Grafiati

Publicado: 4 de junio de 2021

Última modificación: 20 de febrero de 2023

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1

Zhang, Xiaoling, Marc E. Lenburg, and Avrum Spira. "Comparison of Nasal Epithelial Smoking-Induced Gene Expression on Affymetrix Exon 1.0 and Gene 1.0 ST Arrays." Scientific World Journal 2013 (2013): 1–7. http://dx.doi.org/10.1155/2013/951416.

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We have previously defined the impact of tobacco smoking on nasal epithelium gene expression using Affymetrix Exon 1.0 ST arrays. In this paper, we compared the performance of the Affymetrix GeneChip Human Gene 1.0 ST array with the Human Exon 1.0 ST array for detecting nasal smoking-related gene expression changes. RNA collected from the nasal epithelium of five current smokers and five never smokers was hybridized to both arrays. While the intersample correlation within each array platform was relatively higher in the Gene array than that in the Exon array, the majority of the genes most cha

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2

Aschheim, Kathy. "Gene detection by array." Nature Biotechnology 18, no. 11 (November 2000): 1129. http://dx.doi.org/10.1038/81066.

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3

Thomas, E. V., K. H. Phillippy, B. Brahamsha, D. M. Haaland, J. A. Timlin, L. D. H. Elbourne, B. Palenik, and I. T. Paulsen. "Statistical Analysis of Microarray Data with Replicated Spots: A Case Study withSynechococcusWH8102." Comparative and Functional Genomics 2009 (2009): 1–11. http://dx.doi.org/10.1155/2009/950171.

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Until recently microarray experiments often involved relatively few arrays with only a single representation of each gene on each array. A complete genome microarray with multiple spots per gene (spread out spatially across the array) was developed in order to compare the gene expression of a marine cyanobacterium and a knockout mutant strain in a defined artificial seawater medium. Statistical methods were developed for analysis in the special situation of this case study where there is gene replication within an array and where relatively few arrays are used, which can be the case with curre

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4

Gellert, Pascal, Mizue Teranishi, Katharina Jenniches, Piera De Gaspari, David John, Karsten grosse Kreymborg, Thomas Braun, and Shizuka Uchida. "Gene Array Analyzer: alternative usage of gene arrays to study alternative splicing events." Nucleic Acids Research 40, no. 6 (November 28, 2011): 2414–25. http://dx.doi.org/10.1093/nar/gkr1110.

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5

Walsh, James Bruce. "Persistence of Tandem Arrays: Implications for Satellite and Simple-Sequence DNAs." Genetics 115, no. 3 (March 1, 1987): 553–67. http://dx.doi.org/10.1093/genetics/115.3.553.

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ABSTRACT Recombination processes acting on tandem arrays are suggested here to have probable intrinsic biases, producing an expected net decrease in array size following each event, in contrast to previous models which assume no net change in array size. We examine the implications of this by modeling copy number dynamics in a tandem array under the joint interactions of sister-strand unequal crossing over (rate γ per generation per copy) and intrastrand recombination resulting in deletion (rate ∊ per generation per copy). Assuming no gene amplification or selection, the expected mean persiste

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6

Alkahtani, Mohammed, Yihua Hu, Zuyu Wu, Colin Sokol Kuka, Muflih S. Alhammad, and Chen Zhang. "Gene Evaluation Algorithm for Reconfiguration of Medium and Large Size Photovoltaic Arrays Exhibiting Non-Uniform Aging." Energies 13, no. 8 (April 14, 2020): 1921. http://dx.doi.org/10.3390/en13081921.

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Aging is known to exert various non-uniform effects on photovoltaic (PV) modules within a PV array that consequently can result in non-uniform operational parameters affecting the individual PV modules, leading to a variable power output of the overall PV array. This study presents an algorithm for optimising the configuration of a PV array within which different PV modules are subject to non-uniform aging processes. The PV array reconfiguration approach suggests maximising power generation across non-uniformly aged PV arrays by merely repositioning, rather than replacing, the PV modules, ther

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7

Mocellin, Simone, Maurizio Provenzano, Carlo Riccardo Rossi, Pierluigi Pilati, Donato Nitti, and Mario Lise. "DNA Array-Based Gene Profiling." Annals of Surgery 241, no. 1 (January 2005): 16–26. http://dx.doi.org/10.1097/01.sla.0000150157.83537.53.

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8

O'Neill, Paul. "Gene array breakthrough for glioblastoma." Trends in Molecular Medicine 7, no. 9 (September 2001): 387. http://dx.doi.org/10.1016/s1471-4914(01)02145-1.

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9

AOKI, Hiroshi, Akiko KITAJIMA, and Hiroaki TAO. "Electrochemical Gene Sensor Arrays Prepared Using Non-contact Nanoliter Array Spotting of Gene Probes." Analytical Sciences 26, no. 3 (2010): 367–70. http://dx.doi.org/10.2116/analsci.26.367.

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10

Johnston, Mark. "Gene chips: Array of hope for understanding gene regulation." Current Biology 8, no. 5 (February 1998): R171—R174. http://dx.doi.org/10.1016/s0960-9822(98)70103-4.

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11

Müller, Stefanie, Robert Geffers, and Stephan Günther. "Analysis of gene expression in Lassa virus-infected HuH-7 cells." Journal of General Virology 88, no. 5 (May 1, 2007): 1568–75. http://dx.doi.org/10.1099/vir.0.82529-0.

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The pathogenesis of Lassa fever is poorly understood. As the liver is a major target organ of Lassa virus, gene expression in Lassa virus-infected HuH-7 cells, a differentiated human hepatoma cell line, was studied. Cellular mRNA levels were measured at the late phase of acute infection, when virtually all cells expressed large amounts of nucleoprotein, and virus RNA concentration had reached >108 copies (ml supernatant)−1. Two types of transcription array were used: cDNA-based macroarrays with a set of 3500 genes (Atlas Human 1.2 arrays; Clontech) and oligonucleotide-based microarrays cove

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12

Ghanekar, Ruchi, Vinodh Srinivasasainagendra, and Grier P. Page. "Cross-Chip Probe Matching Tool: A Web-Based Tool for Linking Microarray Probes within and across Plant Species." International Journal of Plant Genomics 2008 (October 21, 2008): 1–7. http://dx.doi.org/10.1155/2008/451327.

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The CCPMT is a free, web-based tool that allows plant investigators to rapidly determine if a given gene is present across various microarray platforms, which, of a list of genes, is present on array(s), and which gene a probe or probe set queries and vice versa, and to compare and contrast the gene contents of arrays. The CCPMT also maps a probe or probe sets to a gene or genes within and across species, and permits the mapping of the entire content from one array to another. By using the CCPMT, investigators will have a better understanding of the contents of arrays, a better ability to link

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13

Liu, E. T. "Gene Array Technologies in Biological Investigations." Proceedings of the IEEE 93, no. 4 (April 2005): 737–49. http://dx.doi.org/10.1109/jproc.2005.844617.

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14

Higgins, John P. T. "Gene Array Studies in Renal Neoplasia." Scientific World JOURNAL 6 (2006): 502–11. http://dx.doi.org/10.1100/tsw.2006.109.

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Renal cell carcinoma (RCC) is comprised of several distinct histologic subtypes many of which have characteristic cytogenetic abnormalities. The molecular pathogenesis of some of these neoplasms is beginning to be elucidated. Yet renal cell carcinoma is often discovered at an advanced clinical stage and effective pharmacologic therapies for this disease remain to be discovered. For these reasons, renal cell carcinoma is ideally suited to the genome scale investigation made possible by DNA microarrays. A number of DNA array studies of renal cell carcinoma have been published. Renal cell carcino

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15

Hu, Yuxin, Chang Han, Zhonglin Mou, and Jiayang Li. "Monitoring gene expression by cDNA array." Chinese Science Bulletin 44, no. 5 (March 1999): 441–44. http://dx.doi.org/10.1007/bf02977884.

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16

Shackel, Nicholas A., Mark D. Gorrell, and Geoffrey W. McCaughan. "Gene array analysis and the liver." Hepatology 36, no. 6 (December 2002): 1313–25. http://dx.doi.org/10.1002/hep.1840360603.

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17

Dorer, Douglas R., and Steven Henikoff. "Transgene Repeat Arrays Interact With Distant Heterochromatin and Cause Silencing in cis and trans." Genetics 147, no. 3 (November 1, 1997): 1181–90. http://dx.doi.org/10.1093/genetics/147.3.1181.

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Tandem repeats of Drosophila transgenes can cause heterochromatic variegation for transgene expression in a copy-number and orientation-dependent manner. Here, we demonstrate different ways in which these transgene repeat arrays interact with other sequences at a distance, displaying properties identical to those of a naturally occurring block of interstitial heterochromatin. Arrays consisting of tandemly repeated white transgenes are strongly affected by proximity to constitutive heterochromatin. Moving an array closer to heterochromatin enhanced variegation, and enhancement was reverted by r

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18

Santamaría-Gómez, Javier, Miguel Ángel Rubio, Rocío López-Igual, Ana B. Romero-Losada, Fernando M. Delgado-Chaves, Roque Bru-Martínez, Francisco J. Romero-Campero, et al. "Role of a cryptic tRNA gene operon in survival under translational stress." Nucleic Acids Research 49, no. 15 (August 11, 2021): 8757–76. http://dx.doi.org/10.1093/nar/gkab661.

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Abstract As compared to eukaryotes, bacteria have a reduced tRNA gene set encoding between 30 and 220 tRNAs. Although in most bacterial phyla tRNA genes are dispersed in the genome, many species from distinct phyla also show genes forming arrays. Here, we show that two types of arrays with distinct evolutionary origins exist. This work focuses on long tRNA gene arrays (L-arrays) that encompass up to 43 genes, which disseminate by horizontal gene transfer and contribute supernumerary tRNA genes to the host. Although in the few cases previously studied these arrays were reported to be poorly tra

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19

Gestal, Alicia M., H. W. Stokes, Sally R. Partridge, and Ruth M. Hall. "Recombination between the dfrA12-orfF-aadA2 Cassette Array and an aadA1 Gene Cassette Creates a Hybrid Cassette, aadA8b." Antimicrobial Agents and Chemotherapy 49, no. 11 (November 2005): 4771–74. http://dx.doi.org/10.1128/aac.49.11.4771-4774.2005.

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ABSTRACT Homologous recombination between closely related gene cassettes, such as aadA1 and aadA2, which are 89% identical, can create hybrid cassettes and hybrids of existing cassette arrays. A new cassette array, dfrA12-orfF-aadA8b, which was created by such a recombination event occurring within the aadA2 cassette in the dfrA12-orfF-aadA2 array, has been identified.

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20

Saito, I., R. Groves, E. Giulotto, M. Rolfe, and G. R. Stark. "Evolution and stability of chromosomal DNA coamplified with the CAD gene." Molecular and Cellular Biology 9, no. 6 (June 1989): 2445–52. http://dx.doi.org/10.1128/mcb.9.6.2445-2452.1989.

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We have compared clones of Syrian hamster cells selected for the first amplification of the CAD gene with clones selected for further amplification. The large domain amplified initially was not reamplified as an intact unit. Instead, subregions were reamplified preferentially, and parts of the initial array were often lost. These events reduced the average amount of coamplified DNA accompanying each copy of the selected gene. The degree of amplification was small in the first step (about three extra copies of CAD per cell), but second-step amplifications to a high copy number (up to 60 extra c

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21

Saito, I., R. Groves, E. Giulotto, M. Rolfe, and G. R. Stark. "Evolution and stability of chromosomal DNA coamplified with the CAD gene." Molecular and Cellular Biology 9, no. 6 (June 1989): 2445–52. http://dx.doi.org/10.1128/mcb.9.6.2445.

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We have compared clones of Syrian hamster cells selected for the first amplification of the CAD gene with clones selected for further amplification. The large domain amplified initially was not reamplified as an intact unit. Instead, subregions were reamplified preferentially, and parts of the initial array were often lost. These events reduced the average amount of coamplified DNA accompanying each copy of the selected gene. The degree of amplification was small in the first step (about three extra copies of CAD per cell), but second-step amplifications to a high copy number (up to 60 extra c

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22

Natarajan, Shobhana, Cindy Groff-Vindman, and Michael J. McEachern. "Factors Influencing the Recombinational Expansion and Spread of Telomeric Tandem Arrays in Kluyveromyces lactis." Eukaryotic Cell 2, no. 5 (October 2003): 1115–27. http://dx.doi.org/10.1128/ec.2.5.1115-1127.2003.

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ABSTRACT We have previously shown that DNA circles containing telomeric repeats and a marker gene can promote the recombinational elongation of telomeres in Kluyveromyces lactis by a mechanism proposed to involve rolling-circle DNA synthesis. Wild-type cells acquire a long tandem array at a single telomere, while telomerase deletion (ter1-Δ) cells, acquire an array and also spread it to multiple telomeres. In this study, we further examine the factors that affect the formation and spread of telomeric tandem arrays. We show that a telomerase+ strain with short telomeres and high levels of subte

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23

Kowtharapu, Bhavani S., Jyoti Damaraju, Nitesh Kumar Singh, Josefin Ziebart, Rainer Bader, Dirk Koczan, and Oliver Stachs. "Analysis of the Differential Gene and Protein Expression Profiles of Corneal Epithelial Cells Stimulated with Alternating Current Electric Fields." Genes 12, no. 2 (February 20, 2021): 299. http://dx.doi.org/10.3390/genes12020299.

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In cells, intrinsic endogenous direct current (DC) electric fields (EFs) serve as morphogenetic cues and are necessary for several important cellular responses including activation of multiple signaling pathways, cell migration, tissue regeneration and wound healing. Endogenous DC EFs, generated spontaneously following injury in physiological conditions, directly correlate with wound healing rate, and different cell types respond to these EFs via directional orientation and migration. Application of external DC EFs results in electrode polarity and is known to activate intracellular signaling

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24

Kim, Yeonjung, Neil McLaughlin, Kim Lindstrom, Toshio Tsukiyama, and David J. Clark. "Activation of Saccharomyces cerevisiae HIS3 Results in Gcn4p-Dependent, SWI/SNF-Dependent Mobilization of Nucleosomes over the EntireGene." Molecular and Cellular Biology 26, no. 22 (September 18, 2006): 8607–22. http://dx.doi.org/10.1128/mcb.00678-06.

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ABSTRACT The effects of transcriptional activation on the chromatin structure of the Saccharomyces cerevisiae HIS3 gene were addressed by mapping the precise positions of nucleosomes in uninduced and induced chromatin. In the absence of the Gcn4p activator, the HIS3 gene is organized into a predominant nucleosomal array. In wild-type chromatin, this array is disrupted, and several alternative overlapping nucleosomal arrays are formed. The disruption of the predominant array also requires the SWI/SNF remodeling machine, indicating that the SWI/SNF complex plays an important role in nucleosome m

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25

Lee, Jae K. "Analysis Issues for Gene Expression Array Data." Clinical Chemistry 47, no. 8 (August 1, 2001): 1350–52. http://dx.doi.org/10.1093/clinchem/47.8.1350.

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26

Leonard, P., T. Sharp, S. Henderson, D. Hewitt, J. Pringle, A. Sandison, A. Goodship, J. Whelan, and C. Boshoff. "Gene expression array profile of human osteosarcoma." British Journal of Cancer 89, no. 12 (December 2003): 2284–88. http://dx.doi.org/10.1038/sj.bjc.6601389.

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27

Nitta, Kouichi, and Jun Tanida. "Gene Network Inference Using Optical Array Logic." Optical Review 10, no. 2 (March 2003): 82–88. http://dx.doi.org/10.1007/s10043-003-0082-z.

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28

Maier, Elmar, Sebastian Meier-Ewert, David Bancroft, and Hans Lehrach. "Automated array technologies for gene expression profiling." Drug Discovery Today 2, no. 8 (August 1997): 315–24. http://dx.doi.org/10.1016/s1359-6446(97)01054-4.

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29

Pena, Maria, Xiaofang Wu, Mary Rose, Roberta Lima, and Jennifer Peters-Hall. "Glandular gene array profiling in pediatric rhinosinusitis." Otolaryngology - Head and Neck Surgery 141, no. 3 (September 2009): P98. http://dx.doi.org/10.1016/j.otohns.2009.06.304.

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30

Mehla, Rajeev, and Velpandi Ayyavoo. "Gene Array Studies in HIV-1 Infection." Current HIV/AIDS Reports 9, no. 1 (December 20, 2011): 34–43. http://dx.doi.org/10.1007/s11904-011-0100-x.

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31

Leone, Paola E., Brian A. Walker, David Gonzalez, Matthew Jenner, Fiona M. Ross, Cheng Li, Faith E. Davies, and Gareth J. Morgan. "Status of Chromosome 13 in Multiple Myeloma: Integrated Approach Using SNP Mapping Array and Gene Expression Array." Blood 106, no. 11 (November 16, 2005): 1563. http://dx.doi.org/10.1182/blood.v106.11.1563.1563.

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Abstract Deletions on chromosome 13 are thought to be one of the most important prognostic features in Multiple Myeloma (MM). The biology underlying this is, however, uncertain. Chromosome 13 abnormalities have been evaluated conventionally by FISH using probes for 13q14, covering the retinoblastoma gene (RB1) region. Typically, for recurrent regions of loss of heterozygosity (LOH) it is possible to map a minimally deleted region within which an important gene may be located. This should be the case with 13q−, or alternatively there may be linkage with another genetic lesion, which could be co

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32

Comelli, Elena M., Margarida Amado, Steven R. Head, and James C. Paulson. "Custom microarray for glycobiologists: considerations for glycosyltransferase gene expression profiling." Biochemical Society Symposia 69 (October 1, 2002): 135–42. http://dx.doi.org/10.1042/bss0690135.

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The development of microarray technology offers the unprecedented possibility of studying the expression of thousands of genes in one experiment. Its exploitation in the glycobiology field will eventually allow the parallel investigation of the expression of many glycosyltransferases, which will ultimately lead to an understanding of the regulation of glycoconjugate synthesis. While numerous gene arrays are available on the market, e.g. the Affymetrix GeneChip® arrays, glycosyltransferases are not adequately represented, which makes comprehensive surveys of their gene expression difficult. Thi

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33

Mackin, Robert D., Ruth A. Frey, Carmina Gutierrez, Ashley A. Farre, Shoji Kawamura, Diana M. Mitchell, and Deborah L. Stenkamp. "Endocrine regulation of multichromatic color vision." Proceedings of the National Academy of Sciences 116, no. 34 (August 5, 2019): 16882–91. http://dx.doi.org/10.1073/pnas.1904783116.

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Vertebrate color vision requires spectrally selective opsin-based pigments, expressed in distinct cone photoreceptor populations. In primates and in fish, spectrally divergent opsin genes may reside in head-to-tail tandem arrays. Mechanisms underlying differential expression from such arrays have not been fully elucidated. Regulation of human red (LWS) vs. green (MWS) opsins is considered a stochastic event, whereby upstream enhancers associate randomly with promoters of the proximal or distal gene, and one of these associations becomes permanent. We demonstrate that, distinct from this stocha

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34

Edgar, R. "Gene Expression Omnibus: NCBI gene expression and hybridization array data repository." Nucleic Acids Research 30, no. 1 (January 1, 2002): 207–10. http://dx.doi.org/10.1093/nar/30.1.207.

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35

Li, Jiexun, Hua Su, Hsinchun Chen, and Bernard W. Futscher. "Optimal Search-Based Gene Subset Selection for Gene Array Cancer Classification." IEEE Transactions on Information Technology in Biomedicine 11, no. 4 (July 2007): 398–405. http://dx.doi.org/10.1109/titb.2007.892693.

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36

Oshikawa, Maiko, Naoyuki Sugano, Ryo Ishigaki, and Koichi Ito. "Gene expression in the developing rat mandible: a gene array study." Archives of Oral Biology 49, no. 4 (April 2004): 325–29. http://dx.doi.org/10.1016/j.archoralbio.2003.09.008.

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37

Kellogg, E. A., and R. Appels. "Intraspecific and interspecific variation in 5S RNA genes are decoupled in diploid wheat relatives." Genetics 140, no. 1 (May 1, 1995): 325–43. http://dx.doi.org/10.1093/genetics/140.1.325.

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Abstract 5S RNAs form part of the ribosome in most organisms. In some, e.g., prokaryotes and some fungi, the genes are part of the ribosomal operon, but in most eukaryotes they are in tandem arrays of hundreds to thousands of copies separate from the main ribosomal array. 5S RNA genes can be aligned across kingdoms. We were therefore surprised to find that, for 28 diploid species of the wheat tribe (Triticeae), nucleotide diversity within an array is up to 6.2% in the genes, not significantly different from that of the nontranscribed spacers. Rates of concerted evolution must therefore be insu

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38

Rosolowski, M., H. Berger, C. Schwaenen, S. Wessendorf, M. Loeffler, D. Hasenclever, and M. Kreuz. "Development and Implementation of an Analysis Tool for Array-based Comparative Genomic Hybridization." Methods of Information in Medicine 46, no. 05 (2007): 608–13. http://dx.doi.org/10.1160/me9064.

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Summary Objectives: Array-comparative genomic hybridization (aCGH) is a high-throughput method to detect and map copy number aberrations in the genome. Multi-step analysis of high-dimensional data requires an integrated suite of bioinformatic tools. In this paperwe detail an analysis pipeline for array CGH data. Methods: We developed an analysis tool for array CGH data which supports single and multi-chip analyses as well as combined analyses with paired mRNA gene expression data. The functions supporting relevant steps of analysis were implemented using the open source software R and combined

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39

DEEB, SAMIR S. "Molecular genetics of color-vision deficiencies." Visual Neuroscience 21, no. 3 (May 2004): 191–96. http://dx.doi.org/10.1017/s0952523804213244.

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The normal X-chromosome-linked color-vision gene array is composed of a single long-wave-sensitive (L-) pigment gene followed by one or more middle-wave-sensitive (M-) pigment genes. The expression of these genes to form L- or M-cones is controlled by the proximal promoter and by the locus control region. The high degree of homology between the L- and M-pigment genes predisposed them to unequal recombination, leading to gene deletion or the formation of L/M hybrid genes that explain the majority of the common red–green color-vision deficiencies. Hybrid genes encode a variety of L-like or M-lik

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40

Sun, Fang-Lin, Matthew H. Cuaycong, and Sarah C. R. Elgin. "Long-Range Nucleosome Ordering Is Associated with Gene Silencing in Drosophila melanogaster Pericentric Heterochromatin." Molecular and Cellular Biology 21, no. 8 (April 15, 2001): 2867–79. http://dx.doi.org/10.1128/mcb.21.8.2867-2879.2001.

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ABSTRACT We have used line HS-2 of Drosophila melanogaster, carrying a silenced transgene in the pericentric heterochromatin, to investigate in detail the chromatin structure imposed by this environment. Digestion of the chromatin with micrococcal nuclease (MNase) shows a nucleosome array with extensive long-range order, indicating regular spacing, and with well-defined MNase cleavage fragments, indicating a smaller MNase target in the linker region. The repeating unit is ca. 10 bp larger than that observed for bulkDrosophila chromatin. The silenced transgene shows both a loss of DNase I-hyper

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41

Cronin, Maureen, Krishna Ghosh, Frank Sistare, John Quackenbush, Vincent Vilker, and Catherine O’Connell. "Universal RNA Reference Materials for Gene Expression." Clinical Chemistry 50, no. 8 (August 1, 2004): 1464–71. http://dx.doi.org/10.1373/clinchem.2004.035675.

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Abstract A workshop entitled “Metrology and Standards Needs for Gene Expression Technologies: Universal RNA Standards” was held in March 2003 to define the requirements for standardizing RNA-based molecular assays, specifically microarray and quantitative reverse-transcriptase-PCR technologies. NIST sponsored the workshop, and participants represented government, industry, academia, and clinic. Workshop participants concluded that as a first step, two RNA reference materials could be defined that would help in standardization of gene-expression technologies: an Assay Process Reference Material

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42

Hiratsuka, K., Y. Kamino, T. Nagata, Y. Takahashi, S. Asai, K. Ishikawa, and Y. Abiko. "Microarray Analysis of Gene Expression Changes in Aging in Mouse Submandibular Gland." Journal of Dental Research 81, no. 10 (October 2002): 679–82. http://dx.doi.org/10.1177/154405910208101005.

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Little is known about the effect of salivary gland function during aging based on gene expression. Recently emerged DNA array technology provides a sensitive, quantitative, rapid approach to the monitoring of the global pattern of gene expression. In this study, we used high-density oligonucleotide arrays to monitor the changes of gene expression levels in the submandibular gland (SMG) by comparing adult mice with elderly adult mice. Of the 1328 genes screened, 160 genes (12.0%) showed more than two-fold changes; 154 (96.3%) of these genes, associated with transcription regulation, transport,

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43

Wu, Zhong, Martin Schlumpberger, Sameen Raza, Jiaye Yu, John DiCarlo, Yexun Wang, and Vikram Devgan. "Pathway Signature PCR Array: a novel method for studying inflammatory responses (173.11)." Journal of Immunology 188, no. 1_Supplement (May 1, 2012): 173.11. http://dx.doi.org/10.4049/jimmunol.188.supp.173.11.

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Abstract Signaling pathways play central roles in cellular physiology, and assessing the state of pathways helps clarify molecular mechanisms of disease and inflammatory responses. Gene expression signatures of pathway activation status enable reliable measurement of pathway activity. Our group developed Pathway Signature PCR Arrays to analyze gene expression and determine pathway activity within a single real-time PCR experiment. This study identified a set of genes that provide a gene signature for evaluating IL6/STAT3 pathway activity. A set of 88 signature genes were derived from microarra

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Wong, Lee-Jun C., David Dimmock, Michael T. Geraghty, Richard Quan, Uta Lichter-Konecki, Jing Wang, Ellen K. Brundage, Fernando Scaglia, and A. Craig Chinault. "Utility of Oligonucleotide Array–Based Comparative Genomic Hybridization for Detection of Target Gene Deletions." Clinical Chemistry 54, no. 7 (July 1, 2008): 1141–48. http://dx.doi.org/10.1373/clinchem.2008.103721.

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Abstract Background: Direct DNA sequencing is the primary clinical technique for identifying mutations in human disease, but sequencing often does not detect intragenic or whole-gene deletions. Oligonucleotide array–based comparative genomic hybridization (CGH) is currently in clinical use to detect major changes in chromosomal copy number. Methods: A custom oligonucleotide-based microarray was constructed to provide high-density coverage of an initial set of 130 nuclear genes involved in the pathogenesis of metabolic and mitochondrial disorders. Standard array CGH procedures were used to test

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45

Liu, Hong, Asher Zilberstein, Pascal Pannier, Frederic Fleche, Christopher Arendt, Christoph Lengauer, and Chang S. Hahn. "Evaluating Translocation Gene Fusions by SNP Array Data." Cancer Informatics 11 (December 21, 2011): CIN.S8026. http://dx.doi.org/10.4137/cin.s8026.

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Somatic cell genetic alterations are a hallmark of tumor development and progression. Although various technologies have been developed and utilized to identify genetic aberrations, identifying genetic translocations at the chromosomal level is still a challenging task. High density SNP microarrays are useful to measure DNA copy number variation (CNV) across the genome. Utilizing SNP array data of cancer cell lines and patient samples, we evaluated the CNV and copy number breakpoints for several known fusion genes implicated in tumorigenesis. This analysis demonstrated the potential utility of

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46

Etchebarne, B., W. Nobis, M. Allen, and M. Van de Haar. "Design of a bovine metabolism oligonucleotide gene array." Journal of Animal and Feed Sciences 13, Suppl. 1 (August 30, 2004): 385–88. http://dx.doi.org/10.22358/jafs/73943/2004.

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47

Geschwind, Daniel H. "Sharing gene expression data: an array of options." Nature Reviews Neuroscience 2, no. 6 (June 2001): 435–38. http://dx.doi.org/10.1038/35077576.

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Mocellin, Simone, Ena Wang, Monica Panelli, Pierluigi Pilati, and Francesco M. Marincola. "DNA Array-Based Gene Profiling in Tumor Immunology." Clinical Cancer Research 10, no. 14 (July 15, 2004): 4597–606. http://dx.doi.org/10.1158/1078-0432.ccr-04-0327.

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Dozmorov, I., and M. Centola. "An associative analysis of gene expression array data." Bioinformatics 19, no. 2 (January 22, 2003): 204–11. http://dx.doi.org/10.1093/bioinformatics/19.2.204.

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50

Han, Eun-Soo, and Susan G. Hilsenbeck. "Array-based gene expression profiling to study aging." Mechanisms of Ageing and Development 122, no. 10 (July 2001): 999–1018. http://dx.doi.org/10.1016/s0047-6374(01)00215-9.

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