检索结果-内蒙古大学图书馆

Visualization of the phylogenetic content of five genomes using dekapentagonal maps

GENOME BIOLOGY 2004年第3期5卷 1-11页

作者： Zhaxybayeva, O Hamel, L Raymond, J Gogarten, JP Univ Connecticut Dept Mol & Cell Biol Storrs CT 06269 USA Univ Rhode Isl Dept Comp Sci & Stat Kingston RI 02881 USA Arizona State Univ Dept Chem & Biochem Tempe AZ 85287 USA

The methods presented here summarize phylogenetic relationships of genomes in visually appealing and informative figures. Dekapentagonal maps depict phylogenetic information for orthologous genes present in five genomes, and provide a pre-screen for putatively horizontally transferred genes. If the majority of individual gene phylogenies are unresolved, bipartition histograms provide a means of uncovering and analyzing the plurality consensus. Analyses of genomes representing five photosynthetic bacterial phyla and of the prokaryotic contributions to the eukaryotic cell illustrate the utility of the methods.

关键词： additional data file Probability Vector Phylogenetic Information Ureaplasma Urealyticum Chlorobium Tepidum

来源：评论

学校读者我要写书评

暂无评论

Novel gene and gene model detection using a whole genome open reading frame analysis in proteomics

引用

GENOME BIOLOGY 2006年第4期7卷 R35-R35页

作者： Fermin, Damian Allen, Baxter B. Blackwell, Thomas W. Menon, Rajasree Adamski, Marcin Xu, Yin Ulintz, Peter Omenn, Gilbert S. States, David J. Univ Michigan Bioinformat Program Ann Arbor MI 48109 USA Univ Michigan Dept Internal Med Ann Arbor MI 48109 USA Univ Michigan Dept Human Genet Ann Arbor MI 48109 USA

Background: Defining the location of genes and the precise nature of gene products remains a fundamental challenge in genome annotation. Interrogating tandem mass spectrometry data using genomic sequence provides an unbiased method to identify novel translation products. A six-frame translation of the entire human genome was used as the query database to search for novel blood proteins in the data from the Human Proteome Organization Plasma Proteome Project. Because this target database is orders of magnitude larger than the databases traditionally employed in tandem mass spectra analysis, careful attention to significance testing is required. Confidence of identification is assessed using our previously described Poisson statistic, which estimates the significance of multi-peptide identifications incorporating the length of the matching sequence, number of spectra searched and size of the target sequence database. Results: Applying a false discovery rate threshold of 0.05, we identified 282 significant open reading frames, each containing two or more peptide matches. There were 627 novel peptides associated with these open reading frames that mapped to a unique genomic coordinate placed within the start/stop points of previously annotated genes. These peptides matched 1,110 distinct tandem MS spectra. Peptides fell into four categories based upon where their genomic coordinates placed them relative to annotated exons within the parent gene. Conclusion: This work provides evidence for novel alternative splice variants in many previously annotated genes. These findings suggest that annotation of the genome is not yet complete and that proteomics has the potential to further add to our understanding of gene structures.

关键词： additional data file Mass Spectrometry data Tandem Mass Spectrum Peptide Match International Protein Index

来源：评论

学校读者我要写书评

暂无评论

Multiple effects govern endogenous retrovirus survival patterns in human gene introns

引用

GENOME BIOLOGY 2006年第9期7卷 R86-R86页

作者： van de Lagemaat, Louie N. Medstrand, Patrik Mager, Dixie L. British Columbia Canc Res Ctr Terry Fox Lab Vancouver BC V5Z 1L3 Canada Univ British Columbia Dept Med Genet Vancouver BC V6T 1Z3 Canada Lund Univ Dept Expt Med Sci S-22184 Lund Sweden

Background: Endogenous retroviruses ( ERVs) and solitary long terminal repeats ( LTRs) have a significant antisense bias when located in gene introns, suggesting strong negative selective pressure on such elements oriented in the same transcriptional direction as the enclosing gene. It has been assumed that this bias reflects the presence of strong transcriptional regulatory signals within LTRs but little work has been done to investigate this phenomenon further. Results: In the analysis reported here, we found significant differences between individual human ERV families in their prevalence within genes and degree of antisense bias and show that, regardless of orientation, ERVs of most families are less likely to be found in introns than in intergenic regions. Examination of density profiles of ERVs across transcriptional units and the transcription signals present in the consensus ERVs suggests the importance of splice acceptor sites, in conjunction with splice donor and polyadenylation signals, as the major targets for selection against most families of ERVs/LTRs. Furthermore, analysis of annotated human mRNA splicing events involving ERV sequence revealed that the relatively young human ERVs ( HERVs), HERV9 and HERV-K ( HML-2), are involved in no human mRNA splicing events at all when oriented antisense to gene transcription, while elements in the sense direction in transcribed regions show considerable bias for use of strong splice sites. Conclusion: Our observations suggest suppression of splicing among young intronic ERVs oriented antisense to gene transcription, which may account for their reduced mutagenicity and higher fixation rate in gene introns.

关键词： Splice Site additional data file Polyadenylation Signal Splice Signal Orientation Bias

来源：评论

学校读者我要写书评

暂无评论

Early and long-standing rheumatoid arthritis: distinct molecular signatures identified by gene-expression profiling in synovia

引用

ARTHRITIS RESEARCH & THERAPY 2009年第3期11卷 1-8页

作者： Lequerre, Thierry Bansard, Carine Vittecoq, Olivier Derambure, Celine Hiron, Martine Daveau, Maryvonne Tron, Francois Ayral, Xavier Biga, Norman Auquit-Auckbur, Isabelle Chiocchia, Gilles Le Loet, Xavier Salier, Jean-Philippe Univ Rouen Fac Med Pharm Inst Federatif Rech Multidisciplinaire Peptides 2 Inst Biomed ResINSERMU905 Rouen France Univ Rouen Inserm 905 F-76031 Rouen France Univ Rouen Rouen Univ Hosp Dept Rheumatol Rouen France Univ Paris 05 AP HP Cochin Hosp Dept Rheumatol F-75679 Paris 14 France Rouen Univ Hosp Dept Orthoped & Traumatol F-76031 Rouen France Rouen Univ Hosp Dept Plast & Reconstruct Surg F-76031 Rouen France Univ Paris 05 Inst Cochin INSERM CNRSU567UMR8104 Paris France

Introduction Rheumatoid arthritis (RA) is a heterogeneous disease and its underlying molecular mechanisms are still poorly understood. Because previous microarray studies have only focused on long-standing (LS) RA compared to osteoarthritis, we aimed to compare the molecular profiles of early and LS RA versus control synovia. Methods Synovial biopsies were obtained by arthroscopy from 15 patients (4 early untreated RA, 4 treated LS RA and 7 controls, who had traumatic or mechanical lesions). Extracted mRNAs were used for large-scale gene-expression profiling. The different gene-expression combinations identified by comparison of profiles of early, LS RA and healthy synovia were linked to the biological processes involved in each situation. Results Three combinations of 719, 116 and 52 transcripts discriminated, respectively, early from LS RA, and early or LS RA from healthy synovia. We identified several gene clusters and distinct molecular signatures specifically expressed during early or LS RA, thereby suggesting the involvement of different pathophysiological mechanisms during the course of RA. Conclusions Early and LS RA have distinct molecular signatures with different biological processes participating at different times during the course of the disease. These results suggest that better knowledge of the main biological processes involved at a given RA stage might help to choose the most appropriate treatment.

关键词： Rheumatoid Arthritis Rheumatoid Arthritis Patient additional data file Early Rheumatoid Arthritis Synovial Biopsy

来源：评论

学校读者我要写书评

暂无评论

Determining promoter location based on DNA structure first-principles calculations

引用

GENOME BIOLOGY 2007年第12期8卷 R263-R263页

作者： Goni, J. Ramon Perez, Alberto Torrents, David Orozco, Modesto Inst Biomed Res Barcelona 08028 Spain Univ Barcelona Fac Biol Dept Bioquim & Biol Mol E-08028 Barcelona Spain Univ Vic Laura Dept Biol Sistemes Grp Recerca Bioinformat & Estadist Med VIC 08500 Spain Barcelona Supercomp Ctr Computat Bioinformat Unit Barcelona 08028 Spain ICREA Barcelona 08010 Spain Struct Bioinformat Unit Inst Nacl Bioinformat Barcelona 08028 Spain

A new method for the prediction of promoter regions based on atomic molecular dynamics simulations of small oligonucleotides has been developed. The method works independently of gene structure conservation and orthology and of the presence of detectable sequence features. Results obtained with our method confirm the existence of a hidden physical code that modulates genome expression.

关键词： additional data file ProStar Encode Region Dinucleotide Step Base Step Pair

来源：评论

学校读者我要写书评

暂无评论

Towards the uniform distribution of null p-values on Affymetrix microarrays.

引用

GENOME BIOLOGY 2007年第5期8卷 R69-R69页

作者： Fodor, Anthony A. Tickle, Timothy L. Richardson, Christine Univ N Carolina Bioinformat Resource Ctr Charlotte NC 28223 USA Univ N Carolina Dept Biol Charlotte NC 28223 USA

Methods controlling false positive rates require that p-values of genes that are not differentially expressed follow a uniform distribution. Commonly used microarray statistics can generate p-values that do not meet this assumption. We show that poorly characterized variance, imperfect normalization and cross-hybridization are among the many causes of this non-uniform distribution. We demonstrate a simple technique that produces p-values that are close to uniform for non-differentially expressed genes in control data sets.

关键词： False Discovery Rate Microarray Experiment additional data file Embryoid Body Robust Multichip Average

来源：评论

学校读者我要写书评

暂无评论

Genome-wide gene expression in response to parasitoid attack in Drosophila -: art. no. R94

引用

GENOME BIOLOGY 2005年第11期6卷 1-20页

作者： Wertheim, B Kraaijeveld, AR Schuster, E Blanc, E Hopkins, M Pletcher, SD Strand, MR Partridge, L Godfray, HCJ UCL Ctr Evolutionary Genom Dept Biol London WC1E 6BT England Univ Georgia Dept Entomol Athens GA 30602 USA Baylor Coll Med Huffington Ctr Aging & Mol & Human Genet Houston TX 77030 USA European Bioinformat Inst Cambridge CB10 1SD England Univ London Imperial Coll Sci Technol & Med NERC Ctr Populat Biol Div Biol Ascot SL5 7PY Berks England

Background: Parasitoids are insect parasites whose larvae develop in the bodies of other insects. The main immune defense against parasitoids is encapsulation of the foreign body by blood cells, which subsequently often melanize. The capsule sequesters and kills the parasite. The molecular processes involved are still poorly understood, especially compared with insect humoral immunity. Results: We explored the transcriptional response to parasitoid attack in Drosophila larvae at nine time points following parasitism, hybridizing five biologic replicates per time point to whole-genome microarrays for both parasitized and control larvae. We found significantly different expression profiles for 159 probe sets (representing genes), and we classified them into 16 clusters based on patterns of co-expression. A series of functional annotations were nonrandomly associated with different clusters, including several involving immunity and related functions. We also identified nonrandom associations of transcription factor binding sites for three main regulators of innate immune responses (GATA/srp-like, NF-kappa B/Rel-like and Stat), as well as a novel putative binding site for an unknown transcription factor. The appearance or absence of candidate genes previously associated with insect immunity in our differentially expressed gene set was surveyed. Conclusion: Most genes that exhibited altered expression following parasitoid attack differed from those induced during antimicrobial immune responses, and had not previously been associated with defense. Applying bioinformatic techniques contributed toward a description of the encapsulation response as an integrated system, identifying putative regulators of co-expressed and functionally related genes. Genome-wide studies such as ours are a powerful first approach to investigating novel genes involved in invertebrate immunity.

关键词： additional data file Hemocyte Control Larva Parasitoid Attack Encapsulation Response

来源：评论

学校读者我要写书评

暂无评论

Finding disease candidate genes by liquid association

引用

GENOME BIOLOGY 2007年第10期8卷 R205-R205页

作者： Li, Ker-Chau Palotie, Aarno Yuan, Shinsheng Bronnikov, Denis Chen, Daniel Wei, Xuelian Choi, Oi-Wa Saarela, Janna Peltonen, Leena Univ Calif Los Angeles Dept Stat Los Angeles CA 90095 USA Acad Sinica Inst Stat Sci Taipei 115 Taiwan Univ Helsinki Finnish Genome Ctr FIN-00290 Helsinki Finland Univ Helsinki Dept Clin Chem FIN-00290 Helsinki Finland MIT Cambridge Ctr Cambridge MA 02142 USA MIT Broad Inst Harvard Cambridge MA 02142 USA Univ Calif Los Angeles Gonda Res Ctr Dept Pathol & Lab Med Los Angeles CA 90095 USA Univ Calif Los Angeles Dept Human Genet Los Angeles CA 90095 USA Natl Publ Hlth Inst Helsinki Finland Univ Helsinki Biomed Helsinki Dept Med Genet FIN-00290 Helsinki Finland

A novel approach to finding candidate genes by using gene expression data through liquid association is developed and used to identify multiple sclerosis susceptibility candidate genes.

关键词： Multiple Sclerosis Multiple Sclerosis Patient Myelin Basic Protein additional data file Experimental Allergic Encephalomyelitis

来源：评论

学校读者我要写书评

暂无评论

Genomic linkage map of the human blood fluke Schistosoma mansoni

引用

GENOME BIOLOGY 2009年第6期10卷 R71-R71页

作者： Criscione, Charles D. Valentim, Claudia L. L. Hirai, Hirohisa LoVerde, Philip T. Anderson, Timothy J. C. Texas A&M Univ Dept Biol College Stn TX 77843 USA Univ Texas Hlth Sci Ctr San Antonio Dept Biochem San Antonio TX 78229 USA Univ Texas Hlth Sci Ctr San Antonio Dept Pathol San Antonio TX 78229 USA SW Fdn Biomed Res Dept Genet San Antonio TX 78245 USA Kyoto Univ Primate Res Inst Aichi 4848506 Japan

Background: Schistosoma mansoni is a blood fluke that infects approximately 90 million people. The complete life cycle of this parasite can be maintained in the laboratory, making this one of the few experimentally tractable human helminth infections, and a rich literature reveals heritable variation in important biomedical traits such as virulence, host-specificity, transmission and drug resistance. However, there is a current lack of tools needed to study S. mansoni's molecular, quantitative, and population genetics. Our goal was to construct a genetic linkage map for S. mansoni, and thus provide a new resource that will help stimulate research on this neglected pathogen. Results: We genotyped grandparents, parents and 88 progeny to construct a 5.6 cM linkage map containing 243 microsatellites positioned on 203 of the largest scaffolds in the genome sequence. The map allows 70% of the estimated 300 Mb genome to be ordered on chromosomes, and highlights where scaffolds have been incorrectly assembled. The markers fall into eight main linkage groups, consistent with seven pairs of autosomes and one pair of sex chromosomes, and we were able to anchor linkage groups to chromosomes using fluorescent in situ hybridization. The genome measures 1,228.6 cM. Marker segregation reveals higher female recombination, confirms ZW inheritance patterns, and identifies recombination hotspots and regions of segregation distortion. Conclusions: The genetic linkage map presented here is the first for S. mansoni and the first for a species in the phylum Platyhelminthes. The map provides the critical tool necessary for quantitative genetic analysis, aids genome assembly, and furnishes a framework for comparative flatworm genomics and field-based molecular epidemiological studies.

关键词： Linkage Group Genome Assembly additional data file Segregation Distortion Pseudoautosomal Region

来源：评论

学校读者我要写书评

暂无评论

Harnessing naturally randomized transcription to infer regulatory relationships among genes

引用

GENOME BIOLOGY 2007年第10期8卷 R219-R219页

作者： Chen, Lin S. Emmert-Streib, Frank Storey, John D. Univ Washington Dept Biostat Seattle WA 98195 USA Univ Washington Dept Gen Sci Seattle WA 98195 USA

We develop an approach utilizing randomized genotypes to rigorously infer causal regulatory relationships among genes at the transcriptional level, based on experiments in which genotyping and expression profiling are performed. This approach can be used to build transcriptional regulatory networks and to identify putative regulators of genes. We apply the method to an experiment in yeast, in which genes known to be in the same processes and functions are recovered in the resulting transcriptional regulatory network.

关键词： Gene Ontology False Discovery Rate additional data file Hide Variable Regulatory Relationship

来源：评论

学校读者我要写书评

暂无评论

建议与咨询留下您的常用邮箱和电话号码，以便我们向您反馈解决方案和替代方法

时间限定

文献类型

馆藏选择

核心期刊

语言

文献类型

帮助

文字说明：

检索规则说明：

检索范例：

分类表

所选分类

限定检索结果

文献类型

馆藏范围

日期分布

学科分类号

主题

机构

作者

语言

请选择保存的检索档案：

请选择收藏分类：

通借通还

建议与咨询 留下您的常用邮箱和电话号码，以便我们向您反馈解决方案和替代方法

时间限定

文献类型

馆藏选择

核心期刊

语言

文献类型

帮助

文字说明：

检索规则说明：

检索范例：

分类表

所选分类

限定检索结果

文献类型

馆藏范围

日期分布

学科分类号

主题

机构

作者

语言

请选择保存的检索档案： 新增检索档案 确定 取消

请选择收藏分类： 新增自定义分类 确定 取消

通借通还

建议与咨询留下您的常用邮箱和电话号码，以便我们向您反馈解决方案和替代方法

请选择保存的检索档案：

请选择收藏分类：