allelic expression profiling to dissect genome wide association study signals
A genome wide association study of pulmonary tuberculosis susceptibility in Indonesians doc
... However, to account for multiple testing a stringent Bonferroni corrected alpha of P = 5.25 × 10-7 (0.05/95,207) is required to declare genome wide significance in this study Stage 3: testing TB association ... performed to stratify the association analysis by cohort A stringent Bonferroni corrected alpha of P = 5.25 × 10-7 (0.05/95,207) is required to declare genome wide significance in this study However, ... contributing factors, and the mechanism that triggers active disease is unlikely to be simplistic Aiming to expand TB disease knowledge, this study took a comprehensive search across the genome, and...
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Báo cáo y học: "Identification of novel genetic susceptibility loci for Behçet''''s disease using a genome-wide association study" pps
... (interferon regulatory factor 1) [6], TNF (tumor necrosis factor) [7,8], and PTPN22 (protein tyrosine phosphatase, non-receptor type 22) [9] Despite efforts to discover the genetic contribution to the disease ... be identified using an unbiased genome- wide association approach Herein, we used a DNA pooling technology to perform the first genome- wide association study in Behçet's disease We identify five ... involvement 44 (29%) A total of 152 patients were included in this study We have identified 10 possible candidate genes based on the unbiased genome- wide pooling association study Individual case-control...
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báo cáo khoa học: " The public health utility of genome-wide association study results for smoking behavior" docx
... The limitations of risk factors as prognostic tools N Engl J Med 2006, 355:2615-2617 Drgon T, Montoya I, Johnson C, Liu QR, Walther D, Hamer D, Uhl GR: Genomewide association for nicotine dependence ... regardless of genotype Abbreviations CHRNA, nicotinic cholinergic receptor; CPD, cigarettes smoked per day; GWAS, genome- wide association study; NRT, nicotine replacement therapy; SNP, single nucleotide ... value to serve as clinical markers of heightened risk of nicotine dependence and persistent smoking in the general population [9] To translate into a clinically valid marker, a risk factor has to...
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Efficient computational techniques for tag SNP selection, epistasis analysis, and genome wide association study
... is restricted to 50MB (max size = 3, r2=0.95) 135 xvii Chapter Introduction 1.1 1.1.1 Motivation Genome- wide association studies (GWAS) A genome- wide association study (GWAS) searches ... Foremost, I thank my mentor, Professor Wong Limsoon He has given me the academic freedom to explore a variety of topics in bioinformatics, which brings me to the field of genome- wide association studies ... preliminary 2.3.1 Study design The study design of GWAS can be categorized into two types: retrospective study and prospective study The most common retrospective study is the case-control study, in...
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TDT for human QTL mapping and genome wide association study
... TDT by a penalized logistic model to extend the TDT to genome- wide association study By virtue of this model, we convert the linkage study for gene mapping to variable selection problem A two-step ... has not been applied to genome- wide association study yet In this thesis, we provide an efficient logistic model and an algorithm to search the causal genes in the genome- wide scope This algorithm ... application of TDT to genomewide association study has not been tackled so far Since the rapid improvement in SNP genotyping technology makes it possible to find the genetic contributions to common disease,...
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Genome wide association study for reproduction traits in maternal pig breeds
... plot of Genome- Wide Association Study for NBA in LW_2 196 SI 2: Manhattan plot of Genome- Wide Association Study for NBA in LW_2a 196 SI 3: Manhattan plot of Genome- Wide Association Study for ... plot of Genome- Wide Association Study for NBA in LW_3 197 SI 5: Manhattan plot of Genome- Wide Association Study for NBA in LR_1 197 SI 6: Manhattan plot of Genome- Wide Association Study for ... plot of Genome- Wide Association Study for NBA in LR_3 198 SI 8: Manhattan plot of Genome- Wide Association Study for NBA in LR_3a 198 SI 9: Manhattan plot of Genome- Wide Association Study...
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báo cáo khoa học: " Moderate- to low-risk variant alleles of cutaneous malignancies and nevi: lessons from genome-wide association studies" pdf
... association to CM KRT5, G138E substitution [12] No association BCC, no association to CM 7q32 adjacent to KLF14 [12] No association BCC, no association to CM MTAP rs4636294 ref [37] Not known CM PLA2G6 ... Montgomery GW, Spector TD: Genome- wide association study identifies variants at 9p21 and 22q13 associated with development of cutaneous nevi Nat Genet 2009, 41:915-919 Published: 27 October 2009 doi:10.1186/gm95 ... melanocortin-stimulating hormone (α-MSH) to its transmembrane receptor, Melanocortin-1-receptor (MC1R), results in stimulation of adenylate cyclase (AC) to produce cAMP An antagonist to α-MSH, called Agouti protein...
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Báo cáo y học: "Genome-wide association studies in systemic lupus erythematosus: a perspective" docx
... corrects for stratification in genome- wide association studies Nat Genet 2006, 38: 904-909 10 Li M, Li C, Guan W: Evaluation of coverage variation of SNP chips for genome- wide association studies Eur ... KL, Gaffney PM: A genome- wide association scan identifies tumour necrosis factor alpha inducible protein (TNFAIP3/A20) as a susceptibility locus for systemic lupus erythematosus Nat Genet 2008, ... erythematosus Nat Genet 2008, 40:211216 Ioannidis JPA: Non-replication and inconsistency in the genome- wide association setting Hum Hered 2007, 64:203213 Neale BM, Purcell S: The positives, protocols...
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báo cáo khoa học: "Modeling the cumulative genetic risk for multiple sclerosis from genome-wide association data" ppt
... sclerosis identified by a genomewide study N Engl J Med 2007, 357:851-862 12 Australian and New Zealand Multiple Sclerosis Genetics Consortium: Genome- wide association study identifies new multiple ... receptor activity (GO:0004888) 0.0000274 Transmembrane receptor protein phosphatase activity 0.003811c Amine receptor activity Hematopoietin/interferon-class (D200-domain) cytokine receptor activity ... that failed to achieve genome- wide significance We then tested whether a significant fraction of the variance was related to contributions from additional common alleles with lower association...
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Báo cáo y học: " DNA microarray analysis of rheumatoid arthritis susceptibility genes identified by genome-wide association studies" docx
... between 112 rheumatoid arthritis patients and 45 healthy individuals Abbreviations GWAS, genome- wide association studies; RA, rheumatoid arthritis Competing interests This study was financially ... http://arthritis-research.com/content/12/2/401 Page of Table Candidate genes identified from rheumatoid arthritis genome- wide association studies Gene GeneID PMID Gene expression (up or down) Microarray P valuesa CD244 605554 18794858 ... with rheumatoid arthritis Nat Genet 2003, 34:395-402 Chang X, Zhao Y, Sun S, Zhang Y, Zhu Y: The expression of PADI4 in synovium of rheumatoid arthritis Rheumatol Int 2009, 12:1411-1416 Tokuhiro...
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Báo cáo y học: "Common gene expression strategies revealed by genome-wide analysis in yeast" ppt
... identifying sets of genes with similar expression patterns The two main approaches correspond to grouping or classifying genes according to their expression patterns and to represent them in a reduced ... MB, Storz G, Botstein D, Brown PO: Genomic expression programs in the response of yeast cells to environmental changes Mol Biol Cell 2000, 11:4241-4257 Genome Biology 2007, 8:R222 http://genomebiology.com/2007/8/10/R222 ... S, Pootoolal J, Robinson MD, Hughes TR: Genome- wide analysis of mRNA stability using transcription inhibitors and microarrays reveals posttranscriptional control of ribosome biogenesis factors...
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GENOME WIDE ASSOCIATION STUDIES OF CORONARY ARTERY DISEASE IN SINGAPOREAN CHINESE POPULATIONS
... and significances Study I: Genome wide scan of single nucleotide polymorphisms associated with myocardial infarction –Chapter Genome wide association analysis is a powerful tool to identify genetic ... adhere to the guidelines However, much less is known about the genetic basis of CAD Genome wide association analysis, which is a powerful tool to identify genetic variants, is commonly employed to ... we aimed to i) Discover genetic variants associated with CAD by genome wide association analysis ii) Replicate the susceptibility loci reported in the two Chinese GWAS Study II: Genome wide scan...
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Model selection methods and their application in genome wide association studies
... of the Generalized Tournament Approach in Genomewide Association Studies 72 5.1 Introduction to the multiple testing for genome- wide association studies 73 5.2 The generalized tournament screening ... it is hard to select truly causal features when the dimension P is large Such a problem has become especially prevalent in genome- wide association studies A genome- wide association study (GWAS) ... 1.3.1 Feature selection methods in genome- wide association studies In genome- wide association studies, a large number of statistical studies have been developed to detect genetic variants associated...
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Báo cáo y học: "Genome-wide expression profiling and bioinformatics analysis of diurnally regulated genes in the mouse prefrontal cortex" pps
... that these clusters tend to contain factors that regulate temporal expression of genes in other clusters Discussion In this study we performed a genome- wide expression profiling analysis on the ... gene expression - the gene expression levels change daily according to the time of a day Genome- wide microarray analysis has been used to identify genes with cyclic expression patterns at different ... identified in our experiment and genome- wide surveys of cycling genes in the mouse, rat and Drosophila The Ensembl-Compara multi-species database stores the results of genome- wide species comparisons,...
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Báo cáo y học: "Novel insights into the relationships between dendritic cell subsets in human and mouse revealed by genome-wide expression profiling" ppt
... This study comparing whole genome expression profiling of human and mouse leukocytes has identified for the first time conserved genetic programs common to all LN-DCs or specific to the plasmacytoid ... or cytoskeleton/actin binding, consistent with the particular morphology of DCs linked to the development of a high mem- Genome Biology 2008, 9:R17 http://genomebiology.com/2008/9/1/R17 Genome ... the transcription factor Mafb Reciprocally, some of the genes identified in this study as specific to LN- Genome Biology 2008, 9:R17 http://genomebiology.com/2008/9/1/R17 Genome Biology 2008,...
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Báo cáo y học: "Genome-wide gene expression in response to" pps
... parasitoids are likely to be very different, and their study, like that of responses to microbial pathogens, may reveal conserved Genome Biology 2005, 6:R94 http://genomebiology.com/2005/6/11/R94 Genome ... study of the transcriptional response of Drosophila to parasitoid attack It is the first global expression analysis of the immunologic defense of a host insect against parasitoids, and aims to ... putative transcription factor binding site motif that has not hitherto been linked to any known transcription factor The transcription factor binding sites of three known regulators of immunity were...
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Báo cáo khoa học: "Gene expression profiling of human dermal fibroblasts exposed to bleomycin sulphate does not differentiate between radiation sensitive and control patients" pptx
... gene ontology terms for genes down-regulated in bleomycin sulphate treated fibroblasts compared to controls Gene ontology term a Cell cycle 82 6.00E-16 Mitotic cell cycle 40 4.27E-15 Mitosis 33 ... of genes related to the expression of the differentiated phenotype, considered to be relevant to late normal tissue radiation injury, may be seen However the fibroblast response to bleomycin sulphate ... required to produce cell cycle arrest but not cell cytotoxicity Bleomycin sulphate is known to cause both G1/S and G2/M arrest [21] At high doses, extensive double strand DNA breaks and apoptosis...
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Báo cáo y học: "Gene expression profiling in the synovium identifies a predictive signature of absence of response to adalimumab therapy in rheumatoid arthritis" doc
... gene expression, relative to the mean gene expression in a standard sample normalized to *P < 0.05 CCL5, chemokine ligand 5; CTLA4, cytotoxic T-lymphocyte-associated antigen 4; LTB, lymphotoxin ... resistance to TNF blockade could be related to the effects of these cytokines on proinflammatory processes in poor responders However, the study of gene expression signatures does not allow us to make ... ANT, IT, A-LM helped to acquire the data BJVdE, PD, and FAH helped to design the study and contributed to the writing of the manuscript BRL helped to design the study and to acquire, analyze,...
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Cross-species comparison of genome-wide expression patterns pptx
... framework dissects expression patterns into those common to both species, as well as those that are exclusive to one dataset or the other Another study by Rifkin et al [14] investigated genome- wide expression ... differences in genome- wide expression data of six organisms PLoS Biol 2004, 2:E9 11 Quackenbush J: Microarrays - guilt by association Science 2003, 302:240-241 Genome Biology 2004, 5:232 http://genomebiology.com/2004/5/7/232 ... multiple organisms, leading to a metagene co -expression network A set of metagenes that are densely connected to each other in the co -expression network are considered to share the same function...
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Báo cáo y học: "Genome-wide assessment of imprinted expression in human cells." potx
... provide a less powerful cell system to study imprinting compared to primary fibroblasts, they offer the possibility to look for determinants of nonheritable allelic expression since the cells have ... the odorant receptor genes as well as genes encoding immunoglobulins, T-cell receptors, interleukins, and natural killer cell receptors [26-30] Historically, RME was linked to a subset of genes ... possible mechanism for the observed AE [33] In this study, we utilize a genome- wide method [32] to determine strongly biased AE in the transcriptome using family-based cell panels from two cell...
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