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MicroRNA profiling in pediatric acute lymphoblastic leukemia: novel prognostic tools

LEUKEMIA & LYMPHOMA 2012年第12期53卷 2517-2520页

作者： Mosakhani, Neda Sarhadi, Virinder Kaur Usvasalo, Anu Karjalainen-Lindsberg, Marja-Liisa Lahti, Leo Tuononen, Katja Saarinen-Pihkala, Ulla M. Knuutila, Sakari Univ Helsinki Dept Pathol Haartman Inst FI-00014 Helsinki Finland Univ Helsinki HUSLAB FI-00014 Helsinki Finland Univ Helsinki Cent Hosp FI-00014 Helsinki Finland Univ Helsinki Childrens Hosp FI-00014 Helsinki Finland Wageningen Univ Microbiol Lab Wageningen Netherlands

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关键词： MICRORNA RESEARCH DNA microarrays microarray technology GENE expression microarrays LEUKEMIA in children GENETIC aspects

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A commentary on Implication of gene copy number variation in health and diseases

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JOURNAL OF HUMAN GENETICS 2012年第2期57卷 79-80页

作者： Kaname, Tadashi Ryukoku Univ Grad Sch Med Dept Med Genet Nishihara Okinawa 9030215 Japan

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Don't give up on GWAS

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MOLECULAR PSYCHIATRY 2012年第1期17卷 2-+页

作者： Sullivan, P. Univ N Carolina iPSYCH Chapel Hill NC 27515 USA

A letter to the editor is presented on the genome-wide association studies (GWAS) through microarrays for testing psychiatric diseases' genetic variants.

关键词： LETTERS to the editor PATHOLOGICAL psychology microarray technology

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Claims and counterclaims of X-chromosome compensation

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NATURE STRUCTURAL & MOLECULAR BIOLOGY 2012年第1期19卷 3-5页

作者： Birchler, James A. Univ Missouri Div Biol Sci Columbia MO 65211 USA

Is there upregulation of the single active X chromosome in mammals or not? Recent studies take different points of view.

关键词： X chromosome CHROMOSOMES PHYSIOLOGY MAMMAL genetics microarray technology GENE expression EQUIPMENT & supplies

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Employment of gene expression profiling to identify transcriptional regulators of hepatic stellate cells

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FIBROGENESIS & TISSUE REPAIR 2012年第1-Sup期5卷 S12-S12页

作者： Shimada, Hideaki Rajagopalan, Lakshman E. Pfizer Inc Inflammat Res Unit Pfizer Global Res & Dev 700 Chesterfield Pkwy West Chesterfield MO 63017 USA

Activated hepatic stellate cells (HSC) play a central role in scar formation that leads to liver fibrosis. The molecular mechanisms underlying this process are not fully understood. microarray and bioinformatics analyses have proven to be useful in identifying transcription factors that regulate cellular processes such as cell differentiation. Using oligonucleotide microarrays, we performed transcriptional analyses of activated human HSC cultured on Matrigel-coated tissue culture dishes. Examination of microarray data following Matrigel-induced deactivation of HSC revealed a significant down-regulation of myocardin, an important transcriptional regulator in smooth and cardiac muscle development. Thus, gene expression profiling as well as functional assays of activated HSC have provided the first evidence of the involvement of myocardin in HSC activation.

关键词： GENE expression GENETIC regulation GENETIC transcription LIVER cells microarray technology BIOINFORMATICS TRANSCRIPTION factors MYOCARDIN

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Genomic sciences for developmentalists: The current state of affairs

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DEVELOPMENT AND PSYCHOPATHOLOGY 2012年第4期24卷 1157-1164页

作者： Grigorenko, Elena L. Cicchetti, Dante Yale Univ Ctr Child Study New Haven CT 06519 USA Columbia Univ New York NY 10027 USA Moscow MV Lomonosov State Univ Moscow Russia Univ Minnesota Inst Child Dev Minneapolis MN 55455 USA Univ Rochester Mt Hope Family Ctr Rochester NY 14627 USA

Our work on this Special Issue has been an extremely interesting experience. We had a chance to review and comment on the work of a number of leading scholars in the field of genetic and genomic sciences and had the opportunity to reflect on the status of the field, now approaching the 10th anniversary of the finalization of the first sequence of the human genome in 2003 (Human Genome Program, 2008). These 10 years have been fundamentally important, even revolutionary, for the field of genomics and genetics. They have been no less important for fields of science that use genomic and genetic knowledge to advance their cause: psychiatry and psychology in general, and developmental psychopathology in particular.

关键词： PATHOLOGICAL psychology SAMPLING (Statistics) DEVELOPMENTAL psychology EMPIRICAL research NUCLEOTIDE sequence microarray technology DEVELOPMENTAL biology

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Detecting bad SNPS from Illumina BeadChips using Jeffreys distance

Detecting bad SNPS from Illumina BeadChips using Jeffreys di...

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4th International Conference on Knowledge and Systems Engineering, KSE 2012

作者： Nguyen, Son Hoang Le, Sy Vinh Le, Si Quang University of Engineering and Technology VNU Viet Nam University of Engineering and Technology Insitute of Information Technology VNU Viet Nam Wellcome Trust Center for Human Genetics University of Oxford Roosevelt Drive Oxford OX3 7BN United Kingdom

ISBN: (纸本)9780769547602

Current microarray technologies are able to assay thousands of samples over million of SNPs simultaneously. Computational approaches have been developed to analyse a huge amount of data from microarray chips to understand sophisticated human genomes. The data from microarray chips might contain errors due to bad samples or bad SNPs. In this paper, we propose a method to detect bad SNPs from the probe intensities data of Illumina Beadchips. This approach measures the difference among results determined by three software Illuminus, GenoSNP and Gencall to detect the unstable SNPs. Experiment with SNP data in chromosome 20 of Kenyan people demonstrates the usefulness of our method. This approach reduces the number of SNPs that are needed to check manually. Furthermore, it has the ability in detecting bad SNPs that have not been recognized by other criteria. © 2012 IEEE.

关键词： microarray Chromosomes, Human, Pair 20 Human Genome microarray technology

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Autosomal Dominant Pseudohypoaldosteronism Type 1 in an Infant with Salt Wasting Crisis Associated with Urinary Tract Infection and Obstructive Uropathy

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CASE REPORTS IN ENDOCRINOLOGY 2013年第unknown期2013卷 524647页

作者： Bowden, Sasigarn A. Cozzi, Corin Hickey, Scott E. Thrush, Devon Lamb Astbury, Caroline Nuthakki, Sushma Ohio State Univ Coll Med Nationwide Childrens Hosp Div Endocrinol Columbus OH 43205 USA Ohio State Univ Coll Med Nationwide Childrens Hosp Div Neonatol Columbus OH 43205 USA Ohio State Univ Coll Med Nationwide Childrens Hosp Div Mol & Human GenetDept Pediat Columbus OH 43205 USA Ohio State Univ Coll Med Nationwide Childrens Hosp Dept Pathol & Lab Med Columbus OH 43205 USA

Type 1 pseudohypoaldosteronism (PHA1) is a salt wasting syndrome caused by renal resistance to aldosterone. Primary renal PHA1 or autosomal dominant PHA1 is caused by mutations in mineralocorticoids receptor gene (NR3C2), while secondary PHA1 is frequently associated with urinary tract infection (UTI) and/or urinary tract malformations (UTM). We report a 14-day-old male infant presenting with severe hyperkalemia, hyponatremic dehydration, metabolic acidosis, and markedly elevated serum aldosterone level, initially thought to have secondary PHA1 due to the associated UTI and posterior urethral valves. His serum aldosterone remained elevated at 5 months of age, despite resolution of salt wasting symptoms. Chromosomal microarray analysis revealed a deletion of exons 3-5 in NR3C2 in the patient and his asymptomatic mother who also had elevated serum aldosterone level, confirming that he had primary or autosomal dominant PHA1. Our case raises the possibility that some patients with secondary PHA1 attributed to UTI and/or UTM may instead have primary autosomal dominant PHA1, for which genetic testing should be considered to identify the cause, determine future recurrence risk, and possibly prevent the life-threatening salt wasting in a subsequent family member. Future clinical research is needed to investigate the potential overlapping between secondary PHA1 and primary autosomal dominant PHA1.

关键词： HYPOALDOSTERONISM URINARY tract infections WASTING syndrome ALDOSTERONE MINERALOCORTICOIDS microarray technology

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Analyzing Gene Expression Profile in K562 Cells Exposed to Sodium Valproate Using microarray Combined with the Connectivity Map Database

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JOURNAL OF BIOMEDICINE AND BIOtechnology 2012年第1期2012卷 654291-654291页

作者： Zhang, Xiang-Zhong Yin, Ai-Hua Lin, Dong-Jun Zhu, Xiao-Yu Ding, Qian Wang, Chun-Huai Chen, Yun-Xian Sun Yat Sen Univ Affiliated Hosp 1 Dept Hematol Guangzhou 510080 Guangdong Peoples R China Sun Yat Sen Univ Affiliated Hosp 3 Dept Hematol Guangzhou 510630 Guangdong Peoples R China Women & Children Hosp Guangdong Prov Prenatal Diag Ctr Guangzhou 510010 Guangdong Peoples R China Dept Hlth Guangdong Prov Maternal & Children Meta Key Lab Guangzhou 510010 Guangdong Peoples R China Anhui Med Univ Anhui Prov Hosp Dept Hematol Hefei 230001 Anhui Peoples R China Guizhou Prov Hosp Anhui Prov Hosp Guiyang 550002 Guizhou Peoples R China

To explore the mechanism underlying antileukaemia effect of sodium valproate, the growth and survival of the K562 cell line were investigated. Global profiles of gene expression in K562 cells exposed to sodium valproate were assessed and validated. The differentially expressed genes identified were further used to query the connectivity map database to retrieve a ranked list of compounds that act on the same intracellular targets as sodium valproate. A significant increase in cell apoptosis and a change in gene expression profile were observed in valproate-exposed K562 cells. The significant enrichment analysis of gene ontology terms for the differentially expressed genes showed that these genes were involved in many important biological processes. Eight differentially expressed genes involved in apoptosis were verified by quantitative real-time PCR. The connectivity map analysis showed gene expression profile in K562 cells exposed to sodium valproate was most similar to that of HDACi and PI3K inhibitors, suggesting that sodium valproate might exert antileukaemic action by inhibiting HDAC as well as inhibiting PI3K pathway. In conclusion, our data might provide clues to elucidate the molecular and therapeutic potential of VPA in leukaemia treatment, and the connectivity map is a useful tool for exploring the molecular mechanism of drug action.

关键词： ANTINEOPLASTIC agents APOPTOSIS CELL culture CELLULAR signal transduction POLYMERASE chain reaction FINANCING of research T-test (Statistics) VALPROIC acid DATA analysis software microarray technology GENE expression profiling DESCRIPTIVE statistics LEUKEMIA chemotherapy

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Inflammatory Pathways in Parkinson's Disease;A BNE microarray Study

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PARKINSONS DISEASE 2012年第2012期2012卷 214714-214714页

作者： Durrenberger, Pascal. F. Gruenblatt, Edna Fernando, Francesca S. Monoranu, Camelia Maria Evans, Jordan Riederer, Peter Reynolds, Richard Dexter, David T. Univ London Imperial Coll Sci Technol & Med Fac Med Ctr Neurosci Div Expt Med London W12 0NN England Univ Hosp Wurzburg Natl Parkinson Fdn Ctr Excellence Res Lab Dept Psychiat Psychosomat & Psychotherapy Neurochem Lab D-98070 Wurzburg Germany Univ Zurich Hosp Child & Adolescent Psychiat Neurochem Lab CH-8050 Zurich Switzerland Univ Wurzburg Inst Pathol Dept Neuropathol D-97080 Wurzburg Germany

The aetiology of Parkinson's disease (PD) is yet to be fully understood but it is becoming more and more evident that neuronal cell death may be multifactorial in essence. The main focus of PD research is to better understand substantia nigra homeostasis disruption, particularly in relation to the wide-spread deposition of the aberrant protein alpha-synuclein. microarray technology contributed towards PD research with several studies to date and one gene, ALDH1A1 (Aldehyde dehydrogenase 1 family, member A1), consistently reappeared across studies including the present study, highlighting dopamine (DA) metabolism dysfunction resulting in oxidative stress and most probably leading to neuronal cell death. Neuronal cell death leads to increased inflammation through the activation of astrocytes and microglia. Using our dataset, we aimed to isolate some of these pathways so to offer potential novel neuroprotective therapeutic avenues. To that effect our study has focused on the upregulation of P2X7 (purinergic receptor P2X, ligand-gated ion channel, 7) receptor pathway (microglial activation) and on the NOS3 (nitric oxide synthase 3) pathway (angiogenesis). In summary, although the exact initiator of striatal DA neuronal cell death remains to be determined, based on our analysis, this event does not remain without consequence. Extracellular ATP and reactive astrocytes appear to be responsible for the activation of microglia which in turn release proinflammatory cytokines contributing further to the parkinsonian condition. In addition to tackling oxidative stress pathways we also suggest to reduce microglial and endothelial activation to support neuronal outgrowth.

关键词： CORRELATION (Statistics) FISHER exact test PARKINSON'S disease POLYMERASE chain reaction FINANCING of research T-test (Statistics) GENOMICS EQUIPMENT & supplies DISEASE prevalence REVERSE transcriptase polymerase chain reaction DATA analysis software microarray technology DESCRIPTIVE statistics

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