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Showing search results (51–60 of 182):

  1. ERGR
    Resource Category : Databases -> Human Genes and Diseases -> Gene, system or disease specific databases

    Brief Description : Ethanol-related genes in human and model organisms

    Institute/s :
    Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, VA 23298, USA
    Address of Institute/s :
    Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, VA 23298, USA
    Country : USA

    Associated Institutes :

    • Department of Psychiatry and Virginia Institute for Psychiatric and Behavioral Genetics, Department of Pharmacy, Department of Pharmacology/Toxicology, Virginia Commonwealth University, Richmond, VA 23298
    • Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, VA 23284
    • Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, VA 23298, USA

    Associated Country : USA


    Authors/Contributors : An-Yuan Guo; Bradley T. Webb; Michael F. Miles; Mark P. Zimmerman; Kenneth S. Kendler; Zhongming Zhao
    Contact Email : zzhao@vcu.edu
    Year : 2008
    Language : English


  2. EVOG
    Resource Category : Databases -> Human and other Vertebrate Genomes -> Model organisms, comparative genomics

    Brief Description : Overlapping genes are defined as a pair of genes whose transcripts are overlapped. Recently, many cases of overlapped genes have been investigated in various eukaryotic organisms; however, their origin and transcriptional control mechanism has not yet been clearly determined. We have implemented EVOG (Evolution Visualizer for Overlapping Genes), a Web-based database with a novel visualization interface, to investigate the evolutionary relationship between overlapping genes. Here we study comparatively the extent of overlapping genes in thirteen genomes by analyzing the public databases of expressed sequences using a set of computational tools designed to identify overlapping genes on opposite DNA strands of the same genomic locus. Using this technique, we collected and analyzed all overlapping genes in human, chimpanzee, orangutan, marmoset, rhesus, cow, dog, mouse, rat, chicken, Xenopus, zebrafish, and Drosophila. This integrated service provides a manually curated database that displays the evolutionary features of overlapping genes. The EVOG database components included a number of overlapping genes (10074 in human, 10009 in chimpanzee, 67039 in orangutan, 51001 in marmoset, 219 in rhesus, 3627 in cow, 209 in dog, 10700 in mouse, 7987 in rat, 1439 in chicken, 597 in Xenopus, 2457 in zebrafish and 4115 in Drosophila). The EVOG database is very effective and easy to use for the analysis of the evolutionary process of overlapping genes when comparing different species. Therefore, EVOG could potentially be used as the main tool to investigate the evolution of the human genome in relation disease by comparing the expression profiles of overlapping genes.

    Institute/s :
    Pusan National University, Busan 609-735, Korea
    Address of Institute/s :
    Pusan National University, Busan 609-735, Korea
    Country : Korea

    Associated Institutes :

    • Korean BioInformation Center (KOBIC), KRIBB, Daejeon 305-806
    • School of Computer Science and Engineering, College of Engineering, Pusan National University, Busan 609-735, Korea
    • National Primate Research Center (NPRC), KRIBB, Ochang, Chungbuk 363-883, Republic of Korea
    • Division of Biological Sciences, College of Natural Sciences, Pusan National University, Busan 609-735, Korea

    Associated Country : Korea


    Authors/Contributors : Dae-Soo Kim; Chi-Young Cho; Jae-Won Huh; Heui-Soo Kim; Hwan-Gue Cho
    Contact Email : hgcho@pusan.ac.kr
    Year : 2008
    Language : English


  3. ExDom
    Resource Category : Databases -> Human and other Vertebrate Genomes -> Model organisms, comparative genomics

    Brief Description : Exon-intron structure of protein domains in seven eukaryotic genomes

    Institute/s :
    Genome International Corp, 8000 Excelsior Drive, Madison, WI 53717, USA
    Address of Institute/s :
    Genome International Corp, 8000 Excelsior Drive, Madison, WI 53717, USA
    Country : USA

    Associated Institutes :

    • Department of Human Genetics, Genome International Corp, 8000 Excelsior Drive, Madison, WI 53717, USA
    • Department of Bioinformatics, International Center for Advanced Genomics and Proteomics, 83, 1st Cross Street, Nehru Nagar, Chennai 600096, India

    Associated Country : USA; India


    Authors/Contributors : Ashwini Bhasi; Philge Philip; Vinu Manikandan; Periannan Senapathy
    Contact Email : ps@genome.com
    Year : 2008
    Language : English


  4. ExplorEnz
    Resource Category : Databases -> Metabolic and Signaling Pathways -> Enzymes and enzyme nomenclature

    Brief Description : Reference database of the IUBMB Enzyme Nomenclature

    Institute/s :
    Trinity College, Dublin 2, Ireland
    Address of Institute/s :
    Trinity College, Dublin 2, Ireland
    Country : Ireland

    Associated Institutes :

    • School of Biochemistry and Immunology, Trinity College, Dublin 2, Ireland

    Associated Country : Ireland


    Authors/Contributors : Andrew G. McDonald; Sinead Boyce; Keith F. Tipton
    Contact Email : amcdonld@tcd.ie
    Year : 2008
    Language : English


  5. FlyTED
    Resource Category : Databases -> Microarray Data and other Gene Expression Databases -> Microarray Data and other Gene Expression Databases

    Brief Description : Drosophila Testis Gene Expression Database

    Institute/s :
    Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK
    Address of Institute/s :
    Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, United Kingdom
    Country : United Kingdom

    Associated Institutes :

    • Image Bioinformatics Research Group, Drosophila Spermatogenesis Research Group, Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK

    Associated Country : United Kingdom


    Authors/Contributors : Jun Zhao; Graham Klyne; Elizabeth Benson; Elin Gudmannsdottir; Helen White-Cooper; David Shotton
    Contact Email : david.shotton@zoo.ox.ac.uk
    Year : 2009
    Language : English


  6. FunCoup
    Resource Category : Databases -> Metabolic and Signaling Pathways -> Protein-protein interactions

    Brief Description : Networks of Functional Coupling of proteins

    Institute/s :
    Stockholm University, Sweden
    Address of Institute/s :
    Stockholm University, Sweden
    Country : Sweden

    Associated Institutes :

    • School of Biotechnology, Royal Institute of Technology, Science for Life Laboratory, Box 1031, SE-17121 Solna, Sweden
    • Stockholm Bioinformatics Centre, Department of Biochemistry and Biophysics, Stockholm University

    Associated Country : Sweden


    Authors/Contributors : Andrey Alexeyenko; Thomas Schmitt; Andreas Tjarnberg; Dmitri Guala; Oliver Frings; Erik L. L. Sonnhammer
    Contact Email : Erik.Sonnhammer@sbc.su.se
    Year : 2011
    Language : English


  7. FunTree
    Resource Category : Databases -> Metabolic and Signaling Pathways -> Enzymes and enzyme nomenclature

    Brief Description : Evolution of novel enzyme functions in enzyme superfamilies

    Institute/s :
    European Bioinformatics Institute, United Kingdom
    Address of Institute/s :
    European Bioinformatics Institute, United Kingdom
    Country : United Kingdom

    Associated Institutes :

    • European Bioinformatics Institute, European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD
    • Institute of Structural and Molecular Biology, University College London, Darwin Building, Gower Street, London WC1E 6BT, UK

    Associated Country : United Kingdom


    Authors/Contributors : Nicholas Furnham; Ian Sillitoe; Gemma L. Holliday; Alison L. Cuff; Syed A. Rahman; Roman A. Laskowski; Christine A. Orengo; Janet M. Thornton
    Contact Email : nickf@ebi.ac.uk
    Year : 2011
    Language : English


  8. G2Cdb
    Resource Category : Databases -> Human Genes and Diseases -> Gene, system or disease specific databases

    Brief Description : Genes to Cognition

    Institute/s :
    Genes to Cognition Programme, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom
    Address of Institute/s :
    Genes to Cognition Programme, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom
    State : Cambridge
    Country : United Kingdom

    Associated Institutes :

    • Genes to Cognition Programme, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA
    • Institute for Adaptive and Neural Computation, School of Informatics, University of Edinburgh, 10 Crichton Street, Edinburgh EH8 9AB, UK

    Associated Country : United Kingdom


    Authors/Contributors : Mike D. R. Croning; Michael C. Marshall; Peter McLaren; J. Douglas Armstrong; Seth G. N. Grant
    Contact Email : sg3@sanger.ac.uk
    Year : 2008
    Language : English


  9. GABI-Kat SimpleSearch database
    Resource Category : Databases -> Plant databases -> Arabidopsis thaliana

    Brief Description : Insertional mutagenesis approaches, especially by T-DNA, play important roles in gene function studies of the model plant Arabidopsis thaliana. GABI-Kat SimpleSearch is a Flanking Sequence Tag (FST)-based database for T-DNA insertion mutants generated by the GABI-Kat project. Currently the database contains more than 108,000 mapped FSTs from about 64,000 lines which cover 64 percent of all annotated A. thaliana protein-coding genes. The web interface allows to search for relevant insertions by gene code, keyword, line identifier, GenBank accession number of the FST, and also by BLAST. A graphic display of the genome region around the gene or the FST location assists users to select insertion lines of their interests. About 3,800 insertions were confirmed in the offspring of the plant from which the original FST was generated, and the seeds of these lines are available from the Nottingham Arabidopsis Stock Centre. The database now also contains additional information such as segregation data, gene-specific primers and confirmation sequences. This information not only helps users to evaluate the usefulness of the mutant lines, but also covers a big part of the molecular characterization of the insertion alleles.

    Institute/s :
    Center for Biotechnology (CeBiTec), Bielefeld University, Universitaetsstrasse 25, D-33615 Bielefeld, Germany
    Address of Institute/s :
    Center for Biotechnology (CeBiTec), Bielefeld University, Universitaetsstrasse 25, D-33615 Bielefeld, Germany
    Country : Germany

    Associated Institutes :

    • Center for Biotechnology (CeBiTec), Bielefeld University, Universitaetsstrasse 25, D-33615 Bielefeld, Germany

    Associated Country : Germany


    Authors/Contributors : Nils Kleinboelting; Gunnar Huep; Andreas Kloetgen; Prisca Viehoever; Bernd Weisshaar
    Contact Email : bernd.weisshaar@uni-bielefeld.de
    Year : 2011
    Language : English


  10. GeMInA
    Resource Category : Databases -> Other Molecular Biology Databases -> Other Molecular Biology Databases

    Brief Description : The Gemina system (http://gemina.igs.umaryland.edu) identifies, standardizes and integrates the outbreak metadata for the breadth of NIAID category A–C viral and bacterial pathogens (http://www3.niaid.nih.gov/biodefense/PDF/cat.pdf), thereby providing an investigative and surveillance tool describing the Who [Host], What [Disease, Symptom], When [Date], Where [Location] and How [Pathogen, Environmental Source, Reservoir, Transmission Method] for each pathogen. The Gemina database (1) will provide a greater understanding of the interactions of viral and bacterial pathogens with their hosts and infectious diseases through in-depth literature text-mining, integrated outbreak metadata, outbreak surveillance tools, extensive ontology development (2), metadata curation and representative genomic sequence identification and standards development. The Gemina web interface provides metadata selection and retrieval of a pathogen\'s; Infection Systems (Pathogen, Host, Disease, Transmission Method and Anatomy) and Incidents (Location and Date) along with a hosts Age and Gender. The Gemina system provides an integrated investigative and geospatial surveillance system connecting pathogens, pathogen products and disease anchored on the taxonomic ID of the pathogen and host to identify the breadth of hosts and diseases known for these pathogens, to identify the extent of outbreak locations, and to identify unique genomic regions with the DNA Signature Insignia Detection Tool (3).

    Institute/s :
    Institute for Genome Sciences, University of Maryland School of Medicine
    Address of Institute/s :
    Baltimore
    Country : USA

    Associated Institutes :

    • Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore
    • National Center for Biotechnology Information, Bethesda, MD
    • University of Pittsburgh School of Medicine, Division of Infectious Diseases, Pittsburgh, PA, USA
    • University of Liverpool
    • School of Biological Sciences, UK

    Associated Country : USA; United Kingdom


    Authors/Contributors : Lynn M. Schriml; Cesar Arze; Suvarna Nadendla; Anu Ganapathy; Victor Felix; Anup Mahurkar; Katherine Phillippy; Aaron Gussman; Sam Angiuoli; Elodie Ghedin; Owen White; Neil Hall
    Contact Email : mailto:lschriml@som.umaryland.edu
    Year : 2009
    Language : English


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