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      PlasmoDB: a functional genomic database for malaria parasites

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          Abstract

          PlasmoDB ( http://PlasmoDB.org) is a functional genomic database for Plasmodium spp. that provides a resource for data analysis and visualization in a gene-by-gene or genome-wide scale. PlasmoDB belongs to a family of genomic resources that are housed under the EuPathDB ( http://EuPathDB.org) Bioinformatics Resource Center (BRC) umbrella. The latest release, PlasmoDB 5.5, contains numerous new data types from several broad categories—annotated genomes, evidence of transcription, proteomics evidence, protein function evidence, population biology and evolution. Data in PlasmoDB can be queried by selecting the data of interest from a query grid or drop down menus. Various results can then be combined with each other on the query history page. Search results can be downloaded with associated functional data and registered users can store their query history for future retrieval or analysis.

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          Gene Ontology: tool for the unification of biology

          Michael Ashburner, Catherine A. Ball, Judith Blake … (2002)
          Genomic sequencing has made it clear that a large fraction of the genes specifying the core biological functions are shared by all eukaryotes. Knowledge of the biological role of such shared proteins in one organism can often be transferred to other organisms. The goal of the Gene Ontology Consortium is to produce a dynamic, controlled vocabulary that can be applied to all eukaryotes even as knowledge of gene and protein roles in cells is accumulating and changing. To this end, three independent ontologies accessible on the World-Wide Web (http://www.geneontology.org) are being constructed: biological process, molecular function and cellular component.
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            The global distribution of clinical episodes of Plasmodium falciparum malaria.

            Robert W. Snow, Carlos Guerra, Abdisalan Noor … (2005)
            Interest in mapping the global distribution of malaria is motivated by a need to define populations at risk for appropriate resource allocation and to provide a robust framework for evaluating its global economic impact. Comparison of older and more recent malaria maps shows how the disease has been geographically restricted, but it remains entrenched in poor areas of the world with climates suitable for transmission. Here we provide an empirical approach to estimating the number of clinical events caused by Plasmodium falciparum worldwide, by using a combination of epidemiological, geographical and demographic data. We estimate that there were 515 (range 300-660) million episodes of clinical P. falciparum malaria in 2002. These global estimates are up to 50% higher than those reported by the World Health Organization (WHO) and 200% higher for areas outside Africa, reflecting the WHO's reliance upon passive national reporting for these countries. Without an informed understanding of the cartography of malaria risk, the global extent of clinical disease caused by P. falciparum will continue to be underestimated.
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              Discovery of gene function by expression profiling of the malaria parasite life cycle.

              Karine G Le Roch, Yingyao Zhou, Peter Blair … (2003)
              The completion of the genome sequence for Plasmodium falciparum, the species responsible for most malaria human deaths, has the potential to reveal hundreds of new drug targets and proteins involved in pathogenesis. However, only approximately 35% of the genes code for proteins with an identifiable function. The absence of routine genetic tools for studying Plasmodium parasites suggests that this number is unlikely to change quickly if conventional serial methods are used to characterize encoded proteins. Here, we use a high-density oligonucleotide array to generate expression profiles of human and mosquito stages of the malaria parasite's life cycle. Genes with highly correlated levels and temporal patterns of expression were often involved in similar functions or cellular processes.
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                Author and article information

                Journal
                Journal ID (nlm-ta): Nucleic Acids Res
                Journal ID (iso-abbrev): Nucleic Acids Res
                Journal ID (publisher-id): nar
                Journal ID (hwp): nar
                Title: Nucleic Acids Research
                Publisher: Oxford University Press
                ISSN (Print): 0305-1048
                ISSN (Electronic): 1362-4962
                Publication date Collection: January 2009
                Publication date (Print): January 2009
                Publication date (Electronic): 28 October 2008
                Publication date PMC-release: 28 October 2008
                Volume: 37
                Issue: Database issue , Database issue
                Pages: D539-D543
                Affiliations
                1Center for Tropical & Emerging Global Diseases, University of Georgia, Athens, GA 30602, 2Penn Center for Bioinformatics, University of Pennsylvania, Philadelphia, PA 19104, 3Center for Applied Genetic Technologies, University of Georgia, Athens, GA 30602, 4School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, 5Department of Genetics, 6Department of Computer Science, University of Georgia, Athens, GA 30602 and 7Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
                Author notes
                *To whom correspondence should be addressed. Tel: +1 215 746 7019; Fax: +1 215 573 3111; Email: oharb@ 123456pcbi.upenn.edu
                Correspondence may also be addressed to Brian P. Brunk. Tel: +1 215 573 3118; Fax: +1 215 573 3111; Email: brunkb@ 123456pcbi.upenn.edu ; Jessica C. Kissinger. Tel: +1 706 542 6562; Fax: +1 706 542 3582; Email: jkissing@ 123456uga.edu ; David S. Roos. Tel: +1 215 898 2118; Fax: +1 215 746 6697;Email: droos@ 123456sas.upenn.edu ; Christian J. Stoeckert. Tel: +1 215 573 4409; Fax: +1 215 573 3111; Email: stoeckrt@ 123456pcbi.upenn.edu
                Article
                Publisher ID: gkn814
                DOI: 10.1093/nar/gkn814
                PMC ID: 2686598
                PubMed ID: 18957442
                SO-VID: 71bb37c4-ae57-409b-8896-53c895c8df99
                Copyright © © 2008 The Author(s)
                License:

                This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License ( http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                Date received : 15 September 2008
                Date accepted : 3 October 2008
                Categories
                Subject: Articles

                ScienceOpen disciplines: Genetics
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                ScienceOpen disciplines: Genetics

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