1. TrypanoCyc: a community-led biochemical pathways database for Trypanosoma brucei
- Author
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Shameer, Sanu, Logan-Klumpler, Flora J, Vinson, Florence, Cottret, Ludovic, Merlet, Benjamin, Achcar, Fiona, Boshart, Michael, Berriman, Matthew, Breitling, Rainer, Bringaud, Frédéric, Bütikofer, Peter, Cattanach, Amy M, Bannerman-Chukualim, Bridget, Creek, Darren J, Crouch, Kathryn, de Koning, Harry P, Denise, Hubert, Ebikeme, Charles, Fairlamb, Alan H, Ferguson, Michael A J, Ginger, Michael L, Hertz-Fowler, Christiane, Kerkhoven, Eduard J, Mäser, Pascal, Michels, Paul A M, Nayak, Archana, Nes, David W, Nolan, Derek P, Olsen, Christian, Silva-Franco, Fatima, Smith, Terry K, Taylor, Martin C, Tielens, Aloysius G M, Urbaniak, Michael D, van Hellemond, Jaap J, Vincent, Isabel M, Wilkinson, Shane R, Wyllie, Susan, Opperdoes, Fred R, Barrett, Michael P, Jourdan, Fabien, LS Biochemie van parasieten, B&C BRC-SIB-TR, Regenerative Medicine, Stem Cells & Cancer, Medical Microbiology & Infectious Diseases, LS Biochemie van parasieten, B&C BRC-SIB-TR, Regenerative Medicine, Stem Cells & Cancer, ToxAlim (ToxAlim), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole d'Ingénieurs de Purpan (INPT - EI Purpan), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Recherche Agronomique (INRA), The Wellcome Trust Sanger Institute [Cambridge], Métabolisme et Xénobiotiques (ToxAlim-MeX), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3), Laboratoire des interactions plantes micro-organismes (LIPM), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), University of Glasgow, Ludwig Maximilians University of Munich, University of Manchester [Manchester], Centre National de la Recherche Scientifique (CNRS), University of Bern, Monash University, European Molecular Biology Laboratory European Bioinformatics Institute, United Nations Educational, Scientific and Cultural Organization (UNESCO), University of Dundee, Lancaster University, University of Liverpool, Chalmers University of Technology [Gothenburg, Sweden], Swiss Tropical and Public Health Institute [Basel], University of Edinburgh, TexasTech University, Trinity College Dublin, Biomatters Inc, Partenaires INRAE, University of St Andrews [Scotland], London School of Hygiene and Tropical Medicine (LSHTM), Utrecht University [Utrecht], Erasmus University Rotterdam, Queen Mary University of London (QMUL), Université Catholique de Louvain = Catholic University of Louvain (UCL), ANR project, European Project: 290080,EC:FP7:PEOPLE,FP7-PEOPLE-2011-ITN,PARAMET(2012), University of St Andrews. School of Biology, University of St Andrews. Biomedical Sciences Research Complex, Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Ecole d'Ingénieurs de Purpan (INP - PURPAN), Université de Toulouse (UT)-Université de Toulouse (UT), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3), and Ludwig-Maximilians University [Munich] (LMU)
- Subjects
Proteomics ,Anabolism ,QH301 Biology ,[SDV]Life Sciences [q-bio] ,Trypanosoma brucei brucei ,Metabolic network ,610 Medicine & health ,Biology ,Trypanosoma brucei ,computer.software_genre ,03 medical and health sciences ,QH301 ,Metabolomics ,Metabolome ,Genetics ,[SDV.BV]Life Sciences [q-bio]/Vegetal Biology ,Database Issue ,Data Mining ,030304 developmental biology ,base de données ,0303 health sciences ,Internet ,Database ,Catabolism ,030302 biochemistry & molecular biology ,DAS ,métabolisme cellulaire ,biology.organism_classification ,maladie parasitaire ,QR ,Metabolic pathway ,570 Life sciences ,biology ,computer ,trypanosoma brucei ,Databases, Chemical ,Metabolic Networks and Pathways - Abstract
European Commission FP7 Marie Curie Initial Training Network ‘ParaMet’ [290080 to S.S.]; ANR project MetaboHub [ANR-11-INBS-0010 to B.M.]; Wellcome Trust [085349]; The work of Fiona Achcar was part of the SysMO SilicoTryp project coordinated by R.B. Funding for open access charge: European Commission FP7 Marie Curie Initial Training Network ‘ParaMet’ [290080]. The metabolic network of a cell represents the catabolic and anabolic reactions that interconvert small molecules (metabolites) through the activity of enzymes, transporters and non-catalyzed chemical reactions. Our understanding of individual metabolic networks is increasing as we learn more about the enzymes that are active in particular cells under particular conditions and as technologies advance to allow detailed measurements of the cellular metabolome. Metabolic network databases are of increasing importance in allowing us to contextualise data sets emerging from transcriptomic, proteomic and metabolomic experiments. Here we present a dynamic database, TrypanoCyc (http://www.metexplore.fr/trypanocyc/), which describes the generic and condition-specific metabolic network of Trypanosoma brucei, a parasitic protozoan responsible for human and animal African trypanosomiasis. In addition to enabling navigation through the BioCyc-based TrypanoCyc interface, we have also implemented a network-based representation of the information through MetExplore, yielding a novel environment in which to visualise the metabolism of this important parasite. Publisher PDF
- Published
- 2015