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Gilbert's syndrome: High frequency of the (TA)_7 TAA allele in India and its interaction with a novel CAT insertion in promoter of the gene for bilirubin UDP-glucuronosyltransferase 1 gene

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World Journal of Gastroenterology 2006年第14期12卷 2269-2275页

作者： Shabana Farheen Sanghamitra Sengupta Amal Santra Suparna Pal Gopal Krishna Dhali Meenakshi Chakravorty Partha P Majumder Abhijit Chowdhury Human Genetics unit Indian statistical Institute KolkataIndia Department of Gastroenterology Institute of Postgraduate Medical Education & Research KolkataIndia Human Genetics & genomics Division Indian Institute of Chemical Biology KolkataIndia

AIM： To identify the variants in U rase 1 （UGT1A1） gene in Gilbert＇s syndrome （GS） and to estimate the association between homozygosity for TA insertion and GS in India, as well as the frequency of TA insertion and its impact among normal controls in India. METHODS： Ninety-five GS cases and 95 normal controls were selected. Liver function and other tests were done. The promoter and all 5 exons of UGT1A1 gene were resequenced. Functional assessment of a novel trinucleotide insertion was done by in silico analysis and by estimating UGT1A1 promoter activity carried out by ludferase reporter assay of appropriate constructs in Hep G2 cell line. RESULTS： Among the GS patients, 80% were homozygous for the TA insertion, which was several-fold higher than reports from other ethnic groups. The mean UCB level was elevated among individuals with only one copy of this insertion, which was not significantly different from those with two copies. Many new DNA variants in UGT1A1 gene were discovered, including a trinucleotide （CAT） insertion in the promoter found in a subset （10%） of GS patients, but not among normal controls. In-silico analysis showed marked changes in the DNA-folding of the promoter and functional analysis showed a 20-fold reduction in transcription efficiency of UGT1A1 gene resulting from this insertion, thereby significantly elevating the UCB level. CONCLUSION： The genetic epidemiology of GS is variable across ethnic interactions among UGT1A1 groups and the epistatic promoter variants modulate bilirubin glucuronidation.

关键词： Unconjugated hyperbilirubinemia UGT1A1 gene DNA resequencing Luciferase reporter assay

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miRT:A Database of Validated Transcription Start Sites of Human MicroRNAs

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genomics, Proteomics & Bioinformatics 2012年第5期10卷 310-316页

作者： Malay Bhattacharyya Manali Das Sanghamitra Bandyopadhyay Machine Intelligence unit Indian Statistical Institute Department of Bioinformatics West Bengal University of Technology

MicroRNAs （miRNAs） are small endogenous non-coding RNAs of about 22 nt in length that take crucial roles in many biological pro cesses. These short RNAs regulate the expression of mRNAs by binding to their 3＇-UTRs or by translational repression. Many of the current studies focus on how mature miRNAs regulate mRNAs, however, very limited knowledge is available regarding their transcrip- tional loci. It is known that primary miRNAs （pri-miRs） are first transcribed from the DNA, followed by the formation of precursor miRNAs （pre-miRs） by endonuclease activity, which finally produces the mature miRNAs. Till date, many of the pre-miRs and mature miRNAs have been experimentally verified. But unfortunately, identification of the loci of pri-miRs, promoters and associated transcrip- tion start sites （TSSs） are still in progress. TSSs of only about 40% of the known mature miRNAs in human have been reported. This information, albeit limited, may be useful for further study of the regulation of miRNAs. In this paper, we provide a novel database of validated miRNA TSSs, miRT, by collecting data from several experimental studies that validate miRNA TSSs and are available for full download. We present miRT as a web server and it is also possible to convert the TSS loci between different genome built, miRT might be a valuable resource for advanced research on miRNA regulation, which is freely accessible at： http：//***/~bioinfo_miu/ miRT/***.

关键词： MicroRNA Transcription start site Primary transcript Transcriptional regulation Database

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Advances on methods for mapping QTL in plant

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Science Bulletin 2006年第23期51卷 2809-2818页

作者： ZHANG Yuan-Ming Section on statistical genomics, State Key Laboratory of Crop Genetics and Germplasm Enhancement/National Center for Soybean Improvement, College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China Section on statistical genomics State Key Laboratory of Crop Genetics and Germplasm Enhancement/National Center for Soybean Improvement College of Agriculture Nanjing Agricultural University Nanjing China

Advances on methods for mapping quantitative trait loci (QTL) are firstly summarized. Then, some new methods, including mapping multiple QTL, fine mapping of QTL, and mapping QTL for dynamic traits, are mainly described. Finally, some future prospects are proposed, including how to dig novel genes in the germplasm resource, map expression QTL (eQTL) by the use of all markers, phenotypes and micro-array data, identify QTL using genetic mating designs and detect viability loci. The purpose is to direct plant geneticists to choose a suitable method in the inheritance analysis of quantitative trait and in search of novel genes in germplasm resource so that more potential genetic information can be uncovered.

关键词： quantitative trait locus parameter estimation effect maximum likelihood method Bayesian method.

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AluScanCNV2:An R package for copy number variation calling and cancer risk prediction with next-generation sequencing data

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Genes & Diseases 2019年第1期6卷 43-46页

作者： Taobo Hu Si Chen Ata Ullah Hong Xue Division of Life Science Applied Genomics Centre and Centre for Statistical ScienceHong Kong University of Science and TechnologyClear Water BayHong Kong School of Basic Medicine and Clinical Pharmacy China Pharmaceutical UniversityNanjingChina

The usage of next-generation sequencing(NGS)to detect copy number variation(CNV)is widely accepted in cancer *** on an AluScanCNV software developed by us previously,an AluScanCNV2 software has been developed in the present study as an R package that performs CNV detection from NGS data obtained through AluScan,wholegenome sequencing or other targeted NGS *** applications would include the expedited usage of somatic CNVs for cancer subtyping,and usage of recurrent germline CNVs to perform machine learning-assisted prediction of a test subject’s susceptibility to cancer.

关键词： AluScan Bioinformatics Cancer subtyping Cancer predisposition Machine learning

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Elevation as a selective force on mitochondrial respiratory chain complexes of the Phrynocephalus lizards in the Tibetan plateau

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Current Zoology 2021年第2期67卷 191-199页

作者： Yuanting JIN Débora Y.C.BRANDT Jiasheng LI Yubin WO Haojie TONG Vladimir SHCHUR College of Life Science China Jiliang UniversityHangzhou310018China Department of Integrative Biology University of California at BerkeleyBerkeleyCA94720-3140USA International Laboratory of statistical and Computational genomics National Research University Higher School of EconomicsMoscowRussia

Animals living in extremely high elevations have to adapt to low temperatures and low oxygen availability(hypoxia),but the underlying genetic mechanisms associated with these adaptations are still *** mitochondrial respiratory chain can provide>95%of the ATP in animal cells,and its efficiency is influenced by temperature and oxygen ***,the respiratory chain complexes(RCCs)could be important molecular targets for positive selection associated with respiratory adaptation in high-altitude ***,we investigated positive selection in 5 RCCs and their assembly factors by analyzing sequences of 106 genes obtained through RNA-seq of all 15 Chinese Phrynocephalus lizard species,which are distributed from lowlands to the Tibetan plateau(average elevation>4,500 m).Our results indicate that evidence of positive selec-tion on RCC genes is not significantly different from assembly factors,and we found no difference in selective pressures among the 5 *** specifically looked for positive selection in line-ages where changes in habitat elevation *** group of lineages evolving from low to high altitude show stronger signals of positive selection than lineages evolving from high to low *** evolving from low to high elevation also have more shared codons under positive selection,though the changes are not equivalent at the amino acid *** study advan-ces our understanding of the genetic basis of animal respiratory metabolism evolution in extreme high environments and provides candidate genes for further confirmation with functional analyses.

关键词： elevation positive selection reptile plateau respiratory chain complexes

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Bicoid Signal Extraction with a Selection of Parametric and Nonparametric Signal Processing Techniques

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genomics, Proteomics & Bioinformatics 2015年第3期13卷 183-191页

作者： Zara Ghodsi Emmanuel Sirimal Silva Hossein Hassani The statistical Research Centre Bournemouth University Institute for International Energy Studies (ⅡES)

The maternal segmentation coordinate gene bicoid plays a significant role during Drosophila embryogenesis. The gradient of Bicoid, the protein encoded by this gene, determines most aspects of head and thorax development. This paper seeks to explore the applicability of a variety of signal processing techniques at extracting bicoid expression signal, and whether these methods can outperform the current model. We evaluate the use of six different powerful and widely-used models representing both parametric and nonparametric signal processing techniques to determine the most efficient method for signal extraetion in bicoid. The results are evaluated using both real and simulated data. Our findings show that the Singular Spectrum Analysis technique proposed in this paper outperforms the synthesis diffusion degradation model for filtering the noisy protein profile of bicoid whilst the exponential smoothing technique was found to be the next best alternative followed by the autoregressive integrated moving average.

关键词： Bicoid Drosophila melanogaster Signal extraction Signal processing

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Comparing the Time-Deformation Method with the Fractional Fourier Transform in Filtering Non-Stationary Processes

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Journal of Signal and Information Processing 2012年第4期3卷 491-501页

作者： Mengyuan Xu Wayne A. Woodward Henry L. Gray Department of statistical Science Southern Methodist University Dallas USA Statistics genomics unit NIH/NIMH (National Institutes of Health/National Institute of Mental Health) Bethesda USA

The classical linear filter is able to extract components from multi-component stochastic processes where the frequencies of components do not overlap over time, but fail for those processes where the frequencies overlap over time. In this paper, we discuss two filtering methods for non-stationary processes: the G-filtering method and the Fractional Fourier transform (FrFT) method. The FrFT method is mainly designed for linear chirp signals where the frequency is linearly changing with time. The G-filter can be used to filter signals with wide range of frequency behaviors such as linear chirps, quadratic chirps and other type of chirp signals with strong time-varying frequency behavior. If frequencies of the components can be approximated or separated by a straight line or a polynomial curve, the G-filter can successfully extract components from the original series. We show that the G-filter is applicable to a wider variety of filtering applications than methods such as the FrFT which require data of a specified frequency behavior.

关键词： Filtering Time-Frequency Time-Deformation Fractional Fourier Transform

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Genome-wide mapping of QTL associated with heterosis in the RIL-based NCIII design

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Chinese Science Bulletin 2012年第21期57卷 2655-2665页

作者： HE XiaoHong HU ZhongLi ZHANG Yuan-Ming Section on statistical genomics State Key Laboratory of Crop Genetics and Germplasm Enhancement&Chinese National Center for Soybean ImprovementCollege of AgricultnreNanjing Agricultural UniversityNanjing 210095China State Key Laboratory of Hybrid Rice College of Life SciencesWuhan UniversityWuhan 430072China

Heterosis represents one of the most revolutionary advancements in crop *** the genetic dissection of heterosis,NCIII design is one of the most powerful and widely used mating ***,the methodologies for quantitative trait loci (QTL) detection in the design were mostly based on composite interval ***,in this study,our purpose was to develop a statistical method for mapping epistatic QTL associated with heterosis in the RIL-based NCIII ***,we derivated the expectations of two classical linear transformations,Z 1 and Z 2,while a quantitative trait was controlled by two QTL with digenic epistasis and arbitrary linkage under the F ∞ and F 2 metric ***,we constructed an epistatic genetic model that includes all markers on the whole genome simultaneously,and estimated all the parameters in the model by the empirical Bayes ***,a series of Monte Carlo simulation experiments was carried out to confirm the proposed *** results show that:(1) all the augmented genetic parameters for main-effect QTL could be rightly identified with satisfactory statistical power and precision;(2) the statistical powers in the detection of augmented epistatic effects were substantively affected by the signs of pure epistatic effects;(3) it is more difficult to detect epistatic QTL than to detect main-effect QTL;(4) statistical power is higher in the RIL-based NCIII design than in the F 2-based NCIII design,especially in the detection of the augmented epistatic effect that consists of two pure epistatic effects in opposite directions.

关键词：数量性状位点全基因组杂种优势设计测绘上位性效应统计方法复合区间作图

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Methods for Population-Based eQTL Analysis in Human Genetics

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Tsinghua Science and Technology 2014年第6期19卷 624-634页

作者： Lu Tian Andrew Quitadamo Frederick Lin Xinghua Shi Department of Bioinformatics and genomics College of Computing and Informatics University of North Carolina at Charlotte NC 28223 USA

Gene expression is a critical process in biological system that is influenced and modulated by many factors including genetic variation. Expression Quantitative Trait Loci（e QTL） analysis provides a powerful way to understand how genetic variants affect gene expression. For genome wide e QTL analysis, the number of genetic variants and that of genes are large and thus the search space is tremendous. Therefore, e QTL analysis brings about computational and statistical challenges. In this paper, we provide a comprehensive review of recent advances in methods for e QTL analysis in population-based studies. We first present traditional pairwise association methods, which are widely used in human genetics. To account for expression heterogeneity, we investigate the methods for correcting confounding factors. Next, we discuss newly developed statistical learning methods including Lasso-based models. In the conclusion, we provide an overview of future method development in analyzing e QTL associations. Although we focus on human genetics in this review, the methods are applicable to many other organisms.

关键词： expression Quantitative Trait Loci(e QTL) analysis confounding factors sparse learning models Lasso

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DNA methylation in schizophrenia: progress and challenges

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Science Bulletin 2015年第2期60卷 149-155,I0001页

作者：宗小芬胡茂林李宗昌曹红宝陈晓岗唐劲松 Institute of Mental Health The Second Xiangya Hospital of Central South University unit on statistical genomics National Institute of Mental Health NIH Bethesda 20852 USA Key Laboratory of Psychiatry and Mental Health of Hunan Province Central South University National Technology of Institute of Psychiatry Central South University

Schizophrenia is a heterogeneous psychiatric disorder broadly accepted being caused by genetic and environmental factors. Although conventional genetic studies have identified some candidate genes for schizophrenia, low odds ratios and penetrance, and a lack of reproducibility have limited their explanatory power. Despite the major efforts made toward identifying environmental factors in schizophrenia, methodological limitations and inconsistent findings of epidemiological reports have obstructed attempts to identify exogenous causal factors. Epigenetic mechanisms, mediating between environment and genes, have recently been proposed to play an important role in the pathogenesis of schizophrenia. DNA methylation is the most stable and well-characterized epigenetic modification. In this paper, we briefly introduce DNA methylation mechanisms, genome-wide DNA methylation studies, and identify specific genomic methylation sites in individuals diagnosed with schizophrenia. The outline candidate genes such as Reelin and COMT, are also outlined before paying attention to the conundrum of recent researches.

关键词： Schizophrenia Epigenetics DNA methylation Reelin Catechol-O-methyltransferase

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