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Gene expression array analyses predict increased proto-oncogene expression in MMTV induced mammary tumors

VIRUS RESEARCH 2006年第2期119卷 177-186页

作者： Popken-Harris, Pamela Kirchhof, Nicole Harrison, Ben Harris, Lester F. Abbott NW Hosp David F Hickok Mem Canc Res Lab Minneapolis MN 55407 USA Univ Minnesota Ctr Canc Minneapolis MN 55455 USA Univ Minnesota Vet Diagnost Lab St Paul MN 55108 USA

Exogenous infection by milk-borne mouse mammary tumor viruses (MMTV) typically induce mouse mammary tumors in genetically susceptible mice at a rate of 90-95% by 1 year of age. In contrast to other transforming retroviruses, MMTV acts as an insertional mutagen and under the influence of steroid hormones induces oncogenic transformation after insertion into the host genome. As these events correspond with increases in adjacent *** transcription, we used expression array profiling to determine which commonly associated MMTV insertion site protooncogenes were transcriptionally active in MMTV induced mouse mammary tumors. To verify our gene expression array results we developed real-time quantitative RT-PCR assays for the common MMTV insertion site genes found in RIII/Sa mice (int-1/wnt-1, int-21fgf-3, int-3/Notch 4, and fg/8/AIGF) as well as two genes that were consistently up regulated (CCND1, and MAT-8) and two genes that were consistently down regulated (FN1 and MAT-8) in the MMTV induced tumors as compared to normal mammary gland. Finally, each tumor was also examined hi stopathologically. Our expression array findings support a model whereby just one or a few common MMTV insertions into the host genome sets up a dominant cascade of events that leave a characteristic molecular signature. (c) 2006 Elsevier B.V. All rights reserved.

关键词： MMTV expression array proto-oncogene RT-PCR

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Identification of age-dependent changes in expression of senescence-accelerated mouse (SAMP8) hippocampal proteins by expression array analysis

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BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS 2000年第3期272卷 657-661页

作者： Kumar, VB Franko, MP Farr, SA Armbrecht, HJ Morley, JE Vet Adm Med Ctr Ctr Geriatr Res Educ & Clin St Louis MO 63125 USA St Louis Univ Hlth Sci Ctr Div Geriatr St Louis MO 63104 USA

Aging is associated with extensive cognitive impairments, although the biochemical and physiological basis of these deficits are unknown. As the hippocampus plays a vital role in cognitive functions, we have selected this tissue to analyze changes in gene expression at two different ages. array technology is utilized to explore how gene expression in hippocampus is affected by accelerated cognitive impairment in Senescence-Accelerated Mouse (SAM P8) strain. We show that the expression of genes associated with stress response and xenobiotic metabolism are strongly affected at a time when cognitive impairment occurs. Affected genes include those involved both in signaling and chaperone function. The effector and regulator family of chaperones, which play an important role in protein folding, and also the xenobiotic metabolizing enzymes that play crucial role in antioxidant systems, show significant changes in gene expression between 4 and 12 months. (C) 2000 Academic Press.

关键词： expression array microarray hybridization protein folding aging mice

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New clustering method for expression array data

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Genome Biology 2000年第6期1卷 1-4页

作者： Rachel Brem

An algorithm has been described that clusters expression data from microarray experiments with respect to subsets of genes and other variables, rather than to all data at once.

关键词： array Data expression array Bone Marrow Mononuclear Cell Global Cluster Methodological Innovation

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RNA-Seq and expression arrays: Selection Guidelines for Genome-Wide expression Profiling

RNA-Seq and Expression Arrays: Selection Guidelines for Geno...

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作者： Jessica Minnier Nathan D. Pennock Qiuchen Guo Pepper Schedin Christina A. Harrington

The development of genome-wide gene expression profiling technologies over the past two decades has produced great opportunity for researchers to explore the transcriptome and to better understand biological systems and their perturbation. In this chapter we provide an overview of microarray and massively parallel sequencing technologies and their application to gene expression analysis. We discuss factors that impact expression data generation and analysis that which should be considered in the application of these technology platforms. We further present the results of a simple illustration study to highlight performance similarities and differences in expression profiling of protein-coding mRNAs with each platform. Based on technical and analytical differences between the two platforms, reports in the literature comparing arrays and RNA-Seq for gene expression, and our own example study and experience, we provide recommendations for platform selection for gene expression studies. less

关键词： Massively Parallel Signature Sequencing Microarray RNA-seq Gene expression Profiling Gene expression Analysis Differential expression expression array

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Probe Design for expression arrays Using OligoWiz

Probe Design for Expression Arrays Using OligoWiz

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作者： Rasmus Wernersson

Since all measurements from a DNA microarray is dependant on the probes used, a good choice of probes is of vital importance when designing custom microarrays. This chapter describes how to design expression arrays using the OligoWiz software suite. The desired general features of good probes and the issues which probe design must address are introduced and a conceptual (rather than mathematical) description of how OligoWiz scores the quality of the potential probes is presented. This is followed by a detailed step-by-step guide to designing expression arrays with OligoWiz. The scope of this chapter is exclusively on expression arrays. For an in-depth review of the entire field of probe design (including a comparison of different probe design packages) as well as instructions on how to produce special purpose arrays (e.g., splice detection arrays), please refer to (1). less

关键词： Nucleic Acid Microarray Microarray software bioinformatics oligonucleotide array Probe design expression array probe selection transcripts

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5′-Azacytidine expression arrays

5′-Azacytidine Expression Arrays

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作者： Paul Cairns

Epigenetic silencing of a gene can be reversed, resulting in reactivation of expression, by drugs such as the DNA methylation inhibitor 5-Aza-2′-deoxycytidine (5Aza-dC, azacytidine). This drug is added to cell culture media and is incorporated into the new strand during DNA replication in the cell. 5Aza-dC forms a covalent complex with the active sites of the DNA methyltransferase, depleting methyltransferase activity, which results in generalized demethylation. Until recently, global analyses of gene methylation in cancer cells were largely restricted to array or gel-based comparisons of the methylation status of CpG islands between normal and tumor cell DNA. An expression microarray-based screen has the advantage of a more genome-wide analysis with a better gene annotation and, coupled with a reactivation strategy, has the further advantage that it should preferentially identify reexpression of epigenetically silenced genes over methylated CpG islands that do not influence transcription. However, the direct reactivation of methylated genes, as well as secondary effects of azacytidine treatment, can lead to a cascade of deregulation in downstream unmethylated gene expression. A validation strategy is therefore the key for efficient identification of genes methylated in the wild-type cultured tumor cells. An azacytidine-based reactivation approach can only be used on cell lines so validation should include analysis of primary tumors. The potential of this approach for the identification of new hypermethylated genes and pathways has been demonstrated in bladder, colorectal, esophageal, and most other cancer types. less

关键词： Cell And Tissue Culture DNA Extraction Microarray Cell Proliferation Assay Cytotoxicity Assay Quantitative Reverse Transcription PCR Bisulfite Sequencing PCR Homo sapiens tumor cell lines tumor suppressor gene CpG island Azacytidine expression array epigenetic reactivation demethylation

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Induction of ZCCHC6 expression in peripheral blood mononuclear cells by HNSCC secretions

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GENE 2020年 754卷 144880-144880页

作者： Arayataweegool, Areeya Srisuttee, Ratakorn Bin-Alee, Fardeela Mahattanasakul, Patnarin Tangjaturonrasme, Napadon Kerekhanjanarong, Virachai Mutirangura, Apiwat Kitkumthorn, Nakarin Chulalongkorn Univ Fac Med Ctr Excellence Mol Genet Canc & Human Dis Dept Anat Bangkok 10330 Thailand King Mongkuts Inst Technol Ladkrabang Fac Med Bangkok 10520 Thailand Chulalongkorn Univ Fac Med Program Med Sci Bangkok 10330 Thailand Chulalongkorn Univ Fac Med Dept Otolaryngol Head & Neck Surg Bangkok 10330 Thailand Thai Red Cross Soc King Chulalongkorn Mem Hosp Dept Otolaryngol Head & Neck Surg Bangkok 10330 Thailand Mahidol Univ Fac Dent Dept Oral Biol Payathai Rd Bangkok 10400 Thailand

Cancer secretion can change the properties of adjacent cells, including peripheral blood mononuclear cells (PBMCs). We investigated whether such secretion influences messenger RNA expression in PBMCs of patients with head and neck squamous cell carcinoma (HNSCC). In the present study, co-culture model of normal PBMCs and HNSCC cell lines were established. The PBMCs were subsequently subjected to RNA sequencing for transcriptome analysis. Furthermore, expression data from the Gene expression Omnibus repository, platform GPL4133, series GSE39400, were gathered to analyze, afterward identify zinc finger CysCysHisCys (CCHC)-type domain-containing protein 6 (ZCCHC6) as the main gene involved in HNSCC. This gene was then validated by a quantitative real-time polymerase chain reaction. The results showed that ZCCHC6 was expressed at significantly higher levels in the patients with HNSCC than in the healthy controls, and the sensitivity and specificity of these findings for diagnostic purposes were 100.00% and 70.83%, respectively. In summary, our findings demonstrated that the secretion of HNSCC cells could cause the alterations in messenger RNA expression by PBMCs. The ZCCHC6 expression level may apply in HNSCC screening.

关键词： Head and neck squamous cell carcinoma (HNSCC) Peripheral blood mononuclear cells (PBMCs) RNA sequencing expression array ZCCHC6 expression

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Altered gene expression in murine placentas in an infection-induced intrauterine growth restriction model: a microarray analysis

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JOURNAL OF REPRODUCTIVE IMMUNOLOGY 2010年第2期85卷 140-148页

作者： Bobetsis, Y. A. Barros, S. P. Lin, D. M. Arce, R. M. Offenbacher, S. Univ Athens Athens 11527 Greece Univ N Carolina Sch Dent N Carolina Oral Hlth Inst Durham NC 27709 USA Gen Dent Katy TX 77450 USA

The biological mechanisms leading to incomplete intrauterine growth are not completely elucidated and few studies have investigated infection-mediated growth restriction. In this investigation we report the alterations induced by maternal infectious challenge in placental gene expression patterns using a murine model. Pregnant dams were challenged at day E7.5 with the oral human pathogen Campylobacter rectus to elicit fetal growth restriction. At embryonic day E16.5 placentas were collected to compare placental gene expression patterns from normal fetuses of unchallenged dams and growth restricted fetuses from infected dams. Differential gene expression patterns were determined using Agilent Oligo array (G4121A) with a false discovery rate of P < 0.05 and pathway analyses were performed. Seventy-four genes were differentially expressed during infection-mediated growth restriction with 9 genes significantly up-regulated, indicating that the effects of maternal infection on gene expression were predominantly suppressive. Pathway analyses indicated that 46 of the 65 genes that were significantly down-regulated were associated with placental/fetal development, and 26 of those were imprinted genes. Among the 9 genes that were up-regulated, 4 are involved in oxygen supply to the fetus and the development of the vascular system. Microarray analysis demonstrated that in the pregnant mouse model, maternal infection that induced growth restriction was associated with down-regulated placental expression of critical growth and developmental related genes, including many imprinted genes. These findings may have significant implications for our understanding of the mechanisms underlying infection-associated human fetal growth restriction and the role of differential placental expression of imprinted genes in fetal growth. (C) 2010 Elsevier Ireland Ltd. All rights reserved.

关键词： Fetal growth expression array Placenta Infection Development

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Analysis of methylation-sensitive transcriptome identifies GADD45a as a frequently methylated gene in breast cancer

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ONCOGENE 2005年第16期24卷 2705-2714页

作者： Wang, W Huper, G Guo, YQ Murphy, SK Olson, JA Marks, JR Dept Surg Med Ctr Dept Surg Durham NC 27710 USA Duke Univ Med Ctr Dept Obstet & Gynecol Durham NC 27710 USA

Treatment of the breast cancer cell line, MDAMB468 with the DNA methylation inhibitor, 5-azacytidine (5-AzaC) results in growth arrest, whereas the growth of the normal breast epithelial line DU99 ( telomerase immortalized) is relatively unaffected. Comparing gene expression profiles of these two lines after 5-AzaC treatment, we identified 36 genes that had relatively low basal levels in MDAMB468 cells compared to the DU99 line and were induced in the cancer cell line but not in the normal breast epithelial line. Of these genes, 33 have associated CpG islands greater than 300 bp in length but only three have been previously described as targets for aberrant methylation in human cancer. Northern blotting for five of these genes (alpha-Catenin, DTR, FYN, GADD45a, and Zyxin) verified the array results. Further analysis of one of these genes, GADD45a, showed that 5-AzaC induced expression in five additional breast cancer cell lines with little or no induction in three additional lines derived from normal breast epithelial cells. The CpG island associated with GADD45a was analysed by bisulfite sequencing, sampling over 100 CpG dinucleotides. We found that four CpG's, located approximately 700 bp upstream of the transcriptional start site are methylated in the majority of breast cancer cell lines and primary tumors but not in DNA from normal breast epithelia or matched lymphocytes from cancer patients. Therefore, this simple method of dynamic transcriptional pro. ling yielded a series of novel methylation-sensitive genes in breast cancer including the BRCA1 and p53 responsive gene, GADD45a.

关键词： GADD45a methylation breast cancer expression array

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expression of angiogenic and neurotrophic factors in the human amnion and choriodecidua

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AMERICAN JOURNAL OF OBSTETRICS AND GYNECOLOGY 2002年第3期187卷 728-734页

作者： Marvin, KW Keelan, JA Eykholt, RL Sato, TA Mitchell, MD Univ Auckland Fac Med & Hlth Sci Liggins Inst Auckland 1 New Zealand Univ Auckland Fac Med & Hlth Sci Div Pharmacol & Clin Pharmacol Auckland 1 New Zealand

OBJECTIVE: Our objective was to identify the novel or differential expression of growth or development associated genes in the human gestational membranes that might play roles in pregnancy or in term or preterm parturition. STUDY DESIGN: Complementary DNA arrays were probed with [alpha(33)P]dCTP-labeled-complementary DNA that was prepared from the RNA of reflected amnion and choriodecidua that represent term not-in-labor, term spontaneous labor, and preterm labor with and without chorioamnionitis (n = 4 per group). Differential expression (term not-in-labor vs term spontaneous labor or preterm labor with chorioamnionitis vs preterm labor without chorioamnionitis) was evaluated by Wilcoxon tests. RESULTS: All 16 amnion samples expressed angiogenic factors (endothelin-2 and -3, vascular endothelial growth factor, and vascular endothelial growth factor-B) and neurotrophic factors (ephrin-A2, ephrin receptors-A2, -B1, -B3, -B4, and -B5, neuropilin-2, p75/nerve growth factor receptor and semaphorin-F). In both amnion and choriodecidua, the expression of vascular endothelial growth factor and the angiopoietin receptor, Tie-2, were greater with term spontaneous labor than with term not-in-labor (P <.05);increased VEGF receptor-2 (flk-1) expression was observed in term spontaneous labor choriodecidua (P <.05) but not amnion. Ephrin-A1 expression increased with term spontaneous labor in both tissues (P <.05). Semaphorin-F expression decreased with preterm labor with chorioamnionitis in choriodecidua (P <.05), although the trend was not significant in amnion (P =. 1). CONCLUSION: Neurotrophic and angiogenic factor genes are expressed in amnion and choriodecidual membranes. Several of the genes exhibit differential expression with labor at term or in association with infection preterm, which suggests roles in or associated with these processes.

关键词： amnion choriodecidua cytokine expression array gestational tissue

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