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TrypanoCyc: a community-led biochemical pathways database for Trypanosoma brucei

Sanu Shameer 1 Flora J. Logan-Klumpler 2 Florence Vinson 3 Ludovic Cottret 4 Benjamin Merlet 1 Fiona Achcar 5 Michael Boshart 6 Matthew Berriman 2 Rainer Breitling 7 Frédéric Bringaud 8 Peter Bütikofer 9 Amy M. Cattanach 5 Bridget Bannerman-Chukualim 2 Darren J. Creek 10 Kathryn Crouch 5 Harry P. de Koning 5 Hubert Denise 11 Charles Ebikeme 12 Alan H. Fairlamb 13 Michael A. J. Ferguson 13 Michael L. Ginger 14 Christiane Hertz-Fowler 15 Eduard J. Kerkhoven 16 Pascal Maeser 17 Paul A. M. Michels 18 Archana Nayak 5 David W. Nes 19 Derek P. Nolan 20 Christian Olsen 21 Fatima Silva-Franco 15 Terry K. Smith 22 Martin C. Taylor 23 Aloysius G. M. Tielens 24, 25 Michael D. Urbaniak 14 Jaap J. van Hellemond 25 Isabel M. Vincent 5 Shane R. Wilkinson 26 Susan Wyllie 13 Fred R. Opperdoes 27 Michael P. Barrett 5 Fabien Jourdan 3
Abstract : 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 ( ext-link-type="uri" xlink:href="" xlink:type="simple">, 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.
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Nucl. Acids Res.-2015-Shameer-...
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Sanu Shameer, Flora J. Logan-Klumpler, Florence Vinson, Ludovic Cottret, Benjamin Merlet, et al.. TrypanoCyc: a community-led biochemical pathways database for Trypanosoma brucei. Nucleic Acids Research, Oxford University Press, 2015, 43 (D1), pp.D637 - D644. ⟨10.1093/nar/gku944⟩. ⟨hal-02631222⟩



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