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Nucleic Acids Res. 2015 Jan;43(Database issue):D637-44. doi: 10.1093/nar/gku944. Epub 2014 Oct 9.

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

Author information

1
Institut National de la Recherche Agronomique (INRA), UMR1331, TOXALIM (Research Centre in Food Toxicology), Université de Toulouse, Toulouse, France.
2
The Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK.
3
Institut National de la Recherche Agronomique (INRA), UMR441, Laboratoire des Interactions Plantes-Microorganismes (LIPM), Auzeville, France.
4
University of Glasgow, Glasgow, Scotland, G12 8QQ, UK.
5
Ludwig-Maximilians-Universität München, Biocenter, 82152-Martinsried, Germany.
6
Manchester Institute of Biotechnology, Faculty of Life Sciences, University of Manchester, Manchester, UK.
7
CNRS, Bordeaux, 33076, France.
8
University of Bern, Bern, CH-3012, Switzerland.
9
Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Australia.
10
European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridge, CB10 1SD, UK.
11
ISSC, UNESCO, F-75732 CEDEX 15, Paris, France.
12
University of Dundee, Dundee, Scotland, DD1 4HN, UK.
13
Divisionof Biomedical and Life Sciences, Lancaster University, Bailrigg, Lancaster, LA1 4YG, UK.
14
University of Liverpool, Liverpool, Merseyside L69 3BX, UK.
15
Chalmers University of Technology, Kemivägen 10, 412 96, Göteborg, Sweden.
16
Swiss Tropical and Public Health Institute, Socinstr. 57, Basel 4051, Switzerland.
17
University of Edinburgh, Mayfield Road, Edinburgh EH9 3JU, UK.
18
Texas Tech University, Lubbock, TX, USA.
19
Trinity College Dublin, Dublin 2, Ireland.
20
Biomatters Inc. 60 Park Place, Suite 2100, Newark, NJ, USA.
21
University of St Andrews, St Andrews, Scotland, KY16 9ST, UK.
22
LSHTM, London, WC1E 7HT, UK.
23
Utrecht University, Utrecht, 3508 TD, The Netherlands Erasmus University Medical Center, Rotterdam, 3015 CE, The Netherlands.
24
Erasmus University Medical Center, Rotterdam, 3015 CE, The Netherlands.
25
Queen Mary University of London, London E1 4NS, UK.
26
University of Louvain, Brussels, B-1200, Belgium.
27
University of Glasgow, Glasgow, Scotland, G12 8QQ, UK Fabien.Jourdan@toulouse.inra.fr.
28
Institut National de la Recherche Agronomique (INRA), UMR1331, TOXALIM (Research Centre in Food Toxicology), Université de Toulouse, Toulouse, France Fabien.Jourdan@toulouse.inra.fr.

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.

PMID:
25300491
PMCID:
PMC4384016
DOI:
10.1093/nar/gku944
[Indexed for MEDLINE]
Free PMC Article

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