TrypanoCyc: a community-led biochemical pathways database for Trypanosoma brucei
Journal article, 2015
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.
Author
S. Shameer
Universite de Toulouse
F. J. Logan-Klumpler
Wellcome Trust Sanger Institute
F. Vinson
Universite de Toulouse
L. Cottret
INRA Institut National de La Recherche Agronomique
B. Merlet
Universite de Toulouse
F. Achcar
University of Glasgow
M. Boshart
Ludwig-Maximilians-Universitat Munchen
M. Berriman
Wellcome Trust Sanger Institute
R. Breitling
University of Manchester
F. Bringaud
CNRS Centre National de la Recherche Scientifique
P. Butikofer
Universitat Bern
A. M. Cattanach
University of Glasgow
B. Bannerman-Chukualim
Wellcome Trust Sanger Institute
D. J. Creek
Monash University
K. Crouch
University of Glasgow
H. P. de Koning
University of Glasgow
H. Denise
European Bioinformatics Institute
C. Ebikeme
UNESCO United Nations Educational, Scientific and Cultural Organization
A. H. Fairlamb
University of Dundee
M. A. J. Ferguson
University of Dundee
M. L. Ginger
Lancaster University
C. Hertz-Fowler
University of Liverpool
Eduard Kerkhoven
Chalmers, Biology and Biological Engineering, Systems and Synthetic Biology
P. Maser
Swiss Tropical and Public Health Institute (Swiss TPH)
P. A. M. Michels
University of Edinburgh
A. Nayak
University of Glasgow
D. W. Nes
Texas Tech University at Lubbock
D. P. Nolan
Trinity College Dublin
C. Olsen
Biomatters Inc.
F. Silva-Franco
University of Liverpool
T. K. Smith
University of St Andrews
M. C. Taylor
London School of Hygiene & Tropical Medicine
A. G. M. Tielens
Erasmus University Medical Center
Utrecht University
M. D. Urbaniak
Lancaster University
J. J. van Hellemond
Erasmus University Medical Center
I. M. Vincent
University of Glasgow
S. R. Wilkinson
Queen Mary, University of London
S. Wyllie
University of Dundee
F. R. Opperdoes
Universite Catholique de Louvain
M. P. Barrett
University of Glasgow
F. Jourdan
Universite de Toulouse
Nucleic Acids Research
0305-1048 (ISSN) 1362-4962 (eISSN)
Vol. 43 D1 D637-D644Subject Categories (SSIF 2011)
Biochemistry and Molecular Biology
DOI
10.1093/nar/gku944