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

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Date
28/01/2015
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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.
Citation
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 & Jourdan , F 2015 , ' TrypanoCyc : a community-led biochemical pathways database for Trypanosoma brucei ' Nucleic Acids Research , vol 43 , pp. D637-D644 . DOI: 10.1093/nar/gku944
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Publisher PDF
Publication
Nucleic Acids Research
Status
Peer reviewed
URI
http://hdl.handle.net/10023/5801
DOI
http://dx.doi.org/10.1093/nar/gku944
ISSN
0305-1048
Type
Journal article
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© The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
Description
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].
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