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

Shameer, Sanu and Logan-Klumpler, Flora J. and Vinson, Florence and Cottret, Ludovic and Merlet, Benjamin and Achcar, Fiona and Boshart, Michael and Berriman, Matthew and Breitling, Rainer and Bringaud, Frédéric and Bütikofer, Peter and Cattanach, Amy M. and Bannerman-Chukualim, Bridget and Creek, Darren J. and Crouch, Kathryn and de Koning, Harry P. and Denise, Hubert and Ebikeme, Charles and Fairlamb, Alan H. and Ferguson, Michael A. J. and Ginger, Michael L. and Hertz-Fowler, Christiane and Kerkhoven, Eduard J. and Mäser, Pascal and Michels, Paul A. M. and Nayak, Archana and Nes, David W. and Nolan, Derek P. and Olsen, Christian and Silva-Franco, Fatima and Smith, Terry K. and Taylor, Martin C. and Tielens, Aloysius G. M. and Urbaniak, Michael D. and van Hellemond, Jaap J. and Vincent, Isabel M. and Wilkinson, Shane R. and Wyllie, Susan and Opperdoes, Fred R. and Barrett, Michael P. and Jourdan, Fabien (2015) TrypanoCyc:a community-led biochemical pathways database for Trypanosoma brucei. Nucleic Acids Research, 43 (D1). D637-D644. ISSN 0305-1048

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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:
Journal Article
Journal or Publication Title:
Nucleic Acids Research
Additional Information:
C 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
Uncontrolled Keywords:
/dk/atira/pure/subjectarea/asjc/1300/1311
Subjects:
ID Code:
71781
Deposited By:
Deposited On:
14 Nov 2014 11:48
Refereed?:
Yes
Published?:
Published
Last Modified:
08 Jul 2020 04:23