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

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.

DOI: 10.1093/nar/gku944

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@inproceedings{Shameer2015TrypanoCycAC, title={TrypanoCyc: a community-led biochemical pathways database for Trypanosoma brucei}, author={Sanu Shameer and Flora J. Logan-Klumpler and Florence Vinson and Ludovic Cottret and Benjamin Merlet and Fiona Achcar and Michael Boshart and Matthew Berriman and Rainer Breitling and Fr{\'e}d{\'e}ric Bringaud and Peter B{\"{u}tikofer and Amy M. Cattanach and Bridget Bannerman-Chukualim and Darren J. Creek and Kathryn Crouch and Harry P. de Koning and Hubert Denise and Charles Ebikeme and Alan H. Fairlamb and Michael A. J. Ferguson and Michael L. Ginger and Christiane Hertz-Fowler and Eduard J. Kerkhoven and Pascal M{\"a}ser and Paul A. M. Michels and Archana Nayak and David W. Nes and Derek P. Nolan and Christian Olsen and Fatima Silva-Franco and Terry K. Smith and Martin C. Taylor and Aloysius G. M. Tielens and Michael D. Urbaniak and Jaap J. van Hellemond and Isabel M. Vincent and Shane R. Wilkinson and Susan Wyllie and Fred R. Opperdoes and Michael P. Barrett and Fabien Jourdan}, booktitle={Nucleic Acids Research}, year={2015} }