TrypanoCyc

A community-led biochemical pathways database for Trypanosoma brucei

Sanu Shameer, Flora J. Logan-Klumpler, Florence Vinson, Ludovic Cottret, Benjamin Merlet, Fiona Achcar, Michael Boshart, Matthew Berriman, Rainer Breitling, Frédéric Bringaud, Peter Bütikofer, Amy M. Cattanach, Bridget Bannerman-Chukualim, Darren J. Creek, Kathryn Crouch, Harry P. De Koning, Hubert Denise, Charles Ebikeme, Alan H. Fairlamb, Michael A J Ferguson & 21 others Michael L. Ginger, Christiane Hertz-Fowler, Eduard J. Kerkhoven, Pascal Mäser, Paul A M Michels, Archana Nayak, David W. Nes, Derek P. Nolan, Christian Olsen, Fatima Silva-Franco, Terry K. Smith, Martin C. Taylor, Aloysius G M Tielens, Michael D. Urbaniak, Jaap J. Van Hellemond, Isabel M. Vincent, Shane R. Wilkinson, Susan Wyllie, Fred R. Opperdoes, Michael P. Barrett, Fabien Jourdan

Research output: Contribution to journalArticle

17 Citations (Scopus)

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 individualmetabolic 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.

Original languageEnglish
Pages (from-to)D637-D644
Number of pages8
JournalNucleic Acids Research
Volume43
Issue numberD1
Early online date9 Oct 2014
DOIs
Publication statusPublished - 28 Jan 2015
Externally publishedYes

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Trypanosoma brucei brucei
Metabolic Networks and Pathways
Databases
African Trypanosomiasis
Metabolomics
Metabolome
Enzymes
Proteomics
Parasites
Technology

Cite this

Shameer, S., Logan-Klumpler, F. J., Vinson, F., Cottret, L., Merlet, B., Achcar, F., ... Jourdan, F. (2015). TrypanoCyc: A community-led biochemical pathways database for Trypanosoma brucei. Nucleic Acids Research, 43(D1), D637-D644. https://doi.org/10.1093/nar/gku944
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. / TrypanoCyc : A community-led biochemical pathways database for Trypanosoma brucei. In: Nucleic Acids Research. 2015 ; Vol. 43, No. D1. pp. D637-D644.
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Shameer, S, Logan-Klumpler, FJ, Vinson, F, Cottret, L, Merlet, B, Achcar, F, Boshart, M, Berriman, M, Breitling, R, Bringaud, F, Bütikofer, P, Cattanach, AM, Bannerman-Chukualim, B, Creek, DJ, Crouch, K, De Koning, HP, Denise, H, Ebikeme, C, Fairlamb, AH, Ferguson, MAJ, Ginger, ML, Hertz-Fowler, C, Kerkhoven, EJ, Mäser, P, Michels, PAM, Nayak, A, Nes, DW, Nolan, DP, Olsen, C, Silva-Franco, F, Smith, TK, Taylor, MC, Tielens, AGM, Urbaniak, MD, Van Hellemond, JJ, Vincent, IM, Wilkinson, SR, Wyllie, S, Opperdoes, FR, Barrett, MP & Jourdan, F 2015, 'TrypanoCyc: A community-led biochemical pathways database for Trypanosoma brucei', Nucleic Acids Research, vol. 43, no. D1, pp. D637-D644. https://doi.org/10.1093/nar/gku944

TrypanoCyc : A community-led biochemical pathways database for Trypanosoma brucei. / 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.

In: Nucleic Acids Research, Vol. 43, No. D1, 28.01.2015, p. D637-D644.

Research output: Contribution to journalArticle

TY - JOUR

T1 - TrypanoCyc

T2 - A community-led biochemical pathways database for Trypanosoma brucei

AU - Shameer, Sanu

AU - Logan-Klumpler, Flora J.

AU - Vinson, Florence

AU - Cottret, Ludovic

AU - Merlet, Benjamin

AU - Achcar, Fiona

AU - Boshart, Michael

AU - Berriman, Matthew

AU - Breitling, Rainer

AU - Bringaud, Frédéric

AU - Bütikofer, Peter

AU - Cattanach, Amy M.

AU - Bannerman-Chukualim, Bridget

AU - Creek, Darren J.

AU - Crouch, Kathryn

AU - De Koning, Harry P.

AU - Denise, Hubert

AU - Ebikeme, Charles

AU - Fairlamb, Alan H.

AU - Ferguson, Michael A J

AU - Ginger, Michael L.

AU - Hertz-Fowler, Christiane

AU - Kerkhoven, Eduard J.

AU - Mäser, Pascal

AU - Michels, Paul A M

AU - Nayak, Archana

AU - Nes, David W.

AU - Nolan, Derek P.

AU - Olsen, Christian

AU - Silva-Franco, Fatima

AU - Smith, Terry K.

AU - Taylor, Martin C.

AU - Tielens, Aloysius G M

AU - Urbaniak, Michael D.

AU - Van Hellemond, Jaap J.

AU - Vincent, Isabel M.

AU - Wilkinson, Shane R.

AU - Wyllie, Susan

AU - Opperdoes, Fred R.

AU - Barrett, Michael P.

AU - Jourdan, Fabien

PY - 2015/1/28

Y1 - 2015/1/28

N2 - 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 individualmetabolic 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.

AB - 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 individualmetabolic 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.

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U2 - 10.1093/nar/gku944

DO - 10.1093/nar/gku944

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SP - D637-D644

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JF - Nucleic Acids Research

SN - 0305-1048

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Shameer S, Logan-Klumpler FJ, Vinson F, Cottret L, Merlet B, Achcar F et al. TrypanoCyc: A community-led biochemical pathways database for Trypanosoma brucei. Nucleic Acids Research. 2015 Jan 28;43(D1):D637-D644. https://doi.org/10.1093/nar/gku944