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

Shameer, S. et al. (2015) TrypanoCyc: a community-led biochemical pathways database for Trypanosoma brucei. Nucleic Acids Research, 43(D1), D637-D644. (doi:10.1093/nar/gku944) (PMID:25300491) (PMCID:PMC4384016)

Shameer, S. et al. (2015) TrypanoCyc: a community-led biochemical pathways database for Trypanosoma brucei. Nucleic Acids Research, 43(D1), D637-D644. (doi:10.1093/nar/gku944) (PMID:25300491) (PMCID:PMC4384016)

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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 (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.

Item Type:Articles
Additional Information: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].
Status:Published
Refereed:Yes
Glasgow Author(s) Enlighten ID:Achcar, Dr Fiona and De Koning, Professor Harry and Kerkhoven, Mr Eduard and Barrett, Professor Michael and Vincent, Dr Isabel and Breitling, Professor Rainer and Crouch, Dr Kathryn and Cattanach, Dr Amy
Authors: Shameer, S., Logan-Klumpler, F. J., Vinson, F., Cottret, L., Merlet, B., Achcar, F., Boshart, M., Berriman, M., Breitling, R., Bringaud, F., Bütikofer, P., Cattanach, A. M., Bannerman-Chukualim, B., Creek, D. J., Crouch, K., De Koning, H. P., Denise, H., Ebikeme, C., Fairlamb, A. H., Ferguson, M. A.J., Ginger, M. L., Hertz-Fowler, C., Kerkhoven, E. J., Mäser, P., Michels, P. A.M., Nayak, A., Nes, D. W., Nolan, D. P., Olsen, C., Silva-Franco, F., Smith, T. K., Taylor, M. C., Tielens, A. G.M., Urbaniak, M. D., van Hellemond, J. J., Vincent, I. M., Wilkinson, S. R., Wyllie, S., Opperdoes, F. R., Barrett, M. P., and Jourdan, F.
Subjects:Q Science > QR Microbiology
College/School:College of Medical Veterinary and Life Sciences > Institute of Infection Immunity and Inflammation
College of Medical Veterinary and Life Sciences > Institute of Molecular Cell and Systems Biology
Journal Name:Nucleic Acids Research
Publisher:Oxford University Press
ISSN:1362-4962
ISSN (Online):1362-4962
Published Online:09 October 2014
Copyright Holders:Copyright © 2014 The Authors
First Published:First published in Nucleic Acids Research 43(DatabaseIssue):D637-D644
Publisher Policy:Reproduced under a creative commons license

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Project CodeAward NoProject NamePrincipal InvestigatorFunder's NameFunder RefLead Dept
571301ParaMet - A systematic approach to understanding parasite metabolism.Sylke MullerEuropean Commission (EC)ParaMet290080-FIII - PARASITOLOGY
371796The Wellcome Centre for Molecular Parasitology ( Core Support )Andrew WatersWellcome Trust (WELLCOME)085349/Z/08/ZIII - PARASITOLOGY