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      FlyBase: genes and gene models

      research-article
      , 1
      Nucleic Acids Research
      Oxford University Press

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          Abstract

          FlyBase ( http://flybase.org) is the primary repository of genetic and molecular data of the insect family Drosophilidae. For the most extensively studied species, Drosophila melanogaster, a wide range of data are presented in integrated formats. Data types include mutant phenotypes, molecular characterization of mutant alleles and aberrations, cytological maps, wild-type expression patterns, anatomical images, transgenic constructs and insertions, sequence-level gene models and molecular classification of gene product functions. There is a growing body of data for other Drosophila species; this is expected to increase dramatically over the next year, with the completion of draft-quality genomic sequences of an additional 11 Drosphila species.

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          Most cited references9

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          The generic genome browser: a building block for a model organism system database.

          The Generic Model Organism System Database Project (GMOD) seeks to develop reusable software components for model organism system databases. In this paper we describe the Generic Genome Browser (GBrowse), a Web-based application for displaying genomic annotations and other features. For the end user, features of the browser include the ability to scroll and zoom through arbitrary regions of a genome, to enter a region of the genome by searching for a landmark or performing a full text search of all features, and the ability to enable and disable tracks and change their relative order and appearance. The user can upload private annotations to view them in the context of the public ones, and publish those annotations to the community. For the data provider, features of the browser software include reliance on readily available open source components, simple installation, flexible configuration, and easy integration with other components of a model organism system Web site. GBrowse is freely available under an open source license. The software, its documentation, and support are available at http://www.gmod.org.
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            MicroRNAs modulate hematopoietic lineage differentiation.

            C.-Z. Chen (2004)
            MicroRNAs (miRNAs) are an abundant class of approximately 22-nucleotide regulatory RNAs found in plants and animals. Some miRNAs of plants, Caenorhabditis elegans, and Drosophila play important gene-regulatory roles during development by pairing to target mRNAs to specify posttranscriptional repression of these messages. We identify three miRNAs that are specifically expressed in hematopoietic cells and show that their expression is dynamically regulated during early hematopoiesis and lineage commitment. One of these miRNAs, miR-181, was preferentially expressed in the B-lymphoid cells of mouse bone marrow, and its ectopic expression in hematopoietic stem/progenitor cells led to an increased fraction of B-lineage cells in both tissue-culture differentiation assays and adult mice. Our results indicate that microRNAs are components of the molecular circuitry that controls mouse hematopoiesis and suggest that other microRNAs have similar regulatory roles during other facets of vertebrate development.
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              The FlyBase database of the Drosophila genome projects and community literature.

              (2003)
              FlyBase (http://flybase.bio.indiana.edu/) provides an integrated view of the fundamental genomic and genetic data on the major genetic model Drosophila melanogaster and related species. FlyBase has primary responsibility for the continual reannotation of the D. melanogaster genome. The ultimate goal of the reannotation effort is to decorate the euchromatic sequence of the genome with as much biological information as is available from the community and from the major genome project centers. A complete revision of the annotations of the now-finished euchromatic genomic sequence has been completed. There are many points of entry to the genome within FlyBase, most notably through maps, gene products and ontologies, structured phenotypic and gene expression data, and anatomy.
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                Author and article information

                Journal
                Nucleic Acids Res
                Nucleic Acids Res
                Nucleic Acids Research
                Oxford University Press
                0305-1048
                1362-4962
                1 January 2005
                17 December 2004
                : 33
                : Database Issue
                : D390-D395
                Affiliations
                Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK and [1 ]The Biological Laboratories, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA
                Author notes
                [*]

                To whom correspondence should be addressed. Tel: +44 1223 333963; Fax: +44 1223 333992; Email: rd120@ 123456gen.cam.ac.uk

                [a]

                The FlyBase Consortium: W. Gelbart, K. Campbell, M. Crosby, D. Emmert, B. Matthews, S. Russo, A. Schroeder, F. Smutniak, P. Zhang, P. Zhou and M. Zytkovicz (Biological Laboratories, Harvard University, Cambridge, MA, USA); M. Ashburner, R. Drysdale, A. de Grey, R. Foulger, G. Millburn, D. Sutherland and C. Yamada (Department of Genetics, University of Cambridge, Cambridge, UK); T. Kaufman, K. Matthews, A. DeAngelo, R. K. Cook, D. Gilbert, J. Goodman, G. Grumbling, H. Sheth and V. Strelets (Department of Biology, Indiana University, Bloomington, IN, USA); G. Rubin, M. Gibson, N. Harris, S. Lewis, S. Misra and S. Q. Shu (University of California, Berkeley, CA, USA and Lawrence Berkeley National Laboratories, CA, USA)

                [a]

                The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use permissions, please contact journals.permissions@ 123456oupjournals.org .

                [a]

                © 2005, the authors

                Article
                gki046
                10.1093/nar/gki046
                540000
                15608223
                21d53b66-2504-43cb-b8d1-7cc7288dbd2d
                Copyright © 2005 Oxford University Press
                History
                : 15 September 2004
                : 28 September 2004
                : 28 September 2004
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                Genetics
                Genetics

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