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

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...

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Published inNucleic acids research Vol. 43; no. Database issue; pp. D637 - D644
Main Authors Shameer, Sanu, Logan-Klumpler, Flora J, Vinson, Florence, Cottret, Ludovic, Merlet, Benjamin, Achcar, Fiona, Boshart, Michael, Berriman, Matthew, Breitling, Rainer, Bringaud, Frédéric, Bütikofer, Peter, Cattanach, Amy M, Bannerman-Chukualim, Bridget, Creek, Darren J, Crouch, Kathryn, de Koning, Harry P, Denise, Hubert, Ebikeme, Charles, Fairlamb, Alan H, Ferguson, Michael A J, Ginger, Michael L, Hertz-Fowler, Christiane, Kerkhoven, Eduard J, Mäser, Pascal, Michels, Paul A M, Nayak, Archana, Nes, David W, Nolan, Derek P, Olsen, Christian, Silva-Franco, Fatima, Smith, Terry K, Taylor, Martin C, Tielens, Aloysius G M, Urbaniak, Michael D, van Hellemond, Jaap J, Vincent, Isabel M, Wilkinson, Shane R, Wyllie, Susan, Opperdoes, Fred R, Barrett, Michael P, Jourdan, Fabien
Format Journal Article
LanguageEnglish
Published England Oxford University Press 2015
Subjects
Data Mining
Database Issue
Databases, Chemical
Internet
Life Sciences
Metabolic Networks and Pathways
Proteomics
Trypanosoma brucei brucei - genetics
Trypanosoma brucei brucei - metabolism
Vegetal Biology
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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.
AbstractList 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 ( ext-link-type="uri" xlink:href="www.metexplore.fr/trypanocyc/" xlink:type="simple">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.
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.
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.
The metabolic network of a cell represents thecatabolic and anabolic reactions that interconvertsmall molecules (metabolites) through the activity ofenzymes, transporters and non-catalyzed chemicalreactions. Our understanding of individual metabolicnetworks is increasing as we learn more aboutthe enzymes that are active in particular cells underparticular conditions and as technologies advanceto allow detailed measurements of the cellularmetabolome. Metabolic network databases areof increasing importance in allowing us to contextualisedata sets emerging from transcriptomic,proteomic and metabolomic experiments. Here wepresent a dynamic database, TrypanoCyc (http://www.metexplore.fr/trypanocyc/), which describesthe generic and condition-specific metabolic networkof Trypanosoma brucei, a parasitic protozoan responsiblefor human and animal African trypanosomiasis.In addition to enabling navigation through the BioCyc-based TrypanoCyc interface, we have alsoimplemented a network-based representation of theinformation through MetExplore, yielding a novel environmentin which to visualise the metabolism ofthis important parasite.
Author Bannerman-Chukualim, Bridget
Hertz-Fowler, Christiane
Nes, David W
Breitling, Rainer
Creek, Darren J
Achcar, Fiona
Vinson, Florence
Fairlamb, Alan H
Taylor, Martin C
Boshart, Michael
Nolan, Derek P
Berriman, Matthew
Mäser, Pascal
Bütikofer, Peter
Shameer, Sanu
Vincent, Isabel M
Jourdan, Fabien
Opperdoes, Fred R
Cottret, Ludovic
Urbaniak, Michael D
Ebikeme, Charles
Olsen, Christian
Wilkinson, Shane R
Wyllie, Susan
Tielens, Aloysius G M
Ginger, Michael L
Crouch, Kathryn
Kerkhoven, Eduard J
Silva-Franco, Fatima
Denise, Hubert
Barrett, Michael P
Bringaud, Frédéric
Logan-Klumpler, Flora J
Nayak, Archana
van Hellemond, Jaap J
Ferguson, Michael A J
de Koning, Harry P
Smith, Terry K
Cattanach, Amy M
Michels, Paul A M
Merlet, Benjamin
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  organization: Ludwig-Maximilians-Universität München, Biocenter, 82152-Martinsried, Germany
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  organization: CNRS, Bordeaux, 33076, France
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  organization: University of Bern, Bern, CH-3012, Switzerland
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  fullname: Creek, Darren J
  organization: Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Australia
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  surname: Crouch
  fullname: Crouch, Kathryn
  organization: University of Glasgow, Glasgow, Scotland, G12 8QQ, UK
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  surname: de Koning
  fullname: de Koning, Harry P
  organization: University of Glasgow, Glasgow, Scotland, G12 8QQ, UK
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  fullname: Denise, Hubert
  organization: European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridge, CB10 1SD, UK
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  organization: ISSC, UNESCO, F-75732 CEDEX 15, Paris, France
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  givenname: Paul A M
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  surname: Vincent
  fullname: Vincent, Isabel M
  organization: University of Glasgow, Glasgow, Scotland, G12 8QQ, UK
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  fullname: Wilkinson, Shane R
  organization: Queen Mary University of London, London E1 4NS, UK
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  organization: University of Dundee, Dundee, Scotland, DD1 4HN, UK
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  surname: Barrett
  fullname: Barrett, Michael P
  email: Fabien.Jourdan@toulouse.inra.fr
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  surname: Jourdan
  fullname: Jourdan, Fabien
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  organization: Institut National de la Recherche Agronomique (INRA), UMR1331, TOXALIM (Research Centre in Food Toxicology), Université de Toulouse, Toulouse, France Fabien.Jourdan@toulouse.inra.fr
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ContentType Journal Article
Copyright The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.
Distributed under a Creative Commons Attribution 4.0 International License
The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research. 2015
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Snippet The metabolic network of a cell represents the catabolic and anabolic reactions that interconvert small molecules (metabolites) through the activity of...
The metabolic network of a cell represents thecatabolic and anabolic reactions that interconvertsmall molecules (metabolites) through the activity ofenzymes,...
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SubjectTerms Data Mining
Database Issue
Databases, Chemical
Internet
Life Sciences
Metabolic Networks and Pathways
Proteomics
Trypanosoma brucei brucei - genetics
Trypanosoma brucei brucei - metabolism
Vegetal Biology
Title TrypanoCyc: a community-led biochemical pathways database for Trypanosoma brucei
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