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; 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

doi:10.1093/nar/gku944

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 FergusonMichael 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

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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.

Original language	English
Pages (from-to)	D637-D644
Number of pages	8
Journal	Nucleic Acids Research
Volume	43
Early online date	9 Oct 2014
DOIs	https://doi.org/10.1093/nar/gku944
Publication status	Published - 28 Jan 2015

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10.1093/nar/gku944

shameer2014nucleicacidresD637
© 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 [email protected]
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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., ... Jourdan, F. (2015). TrypanoCyc: a community-led biochemical pathways database for Trypanosoma brucei. Nucleic Acids Research, 43, D637-D644. https://doi.org/10.1093/nar/gku944

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title = "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.",

author = "Sanu Shameer and Logan-Klumpler, {Flora J} 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 Cattanach, {Amy M} and Bridget Bannerman-Chukualim and Creek, {Darren J} and Kathryn Crouch and {de Koning}, {Harry P} and Hubert Denise and Charles Ebikeme and Fairlamb, {Alan H} and Ferguson, {Michael A J} and Ginger, {Michael L} and Christiane Hertz-Fowler and Kerkhoven, {Eduard J} and Pascal M{\"a}ser and Michels, {Paul A M} and Archana Nayak and Nes, {David W} and Nolan, {Derek P} and Christian Olsen and Fatima Silva-Franco 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 Susan Wyllie and Opperdoes, {Fred R} and Barrett, {Michael P} and Fabien Jourdan",

note = "European Commission FP7 Marie Curie Initial Training Network {\textquoteleft}ParaMet{\textquoteright} [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 {\textquoteleft}ParaMet{\textquoteright} [290080]. ",

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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, pp. D637-D644. https://doi.org/10.1093/nar/gku944

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

N1 - 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].

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 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.

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 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.

U2 - 10.1093/nar/gku944

DO - 10.1093/nar/gku944

M3 - Article

C2 - 25300491

SN - 0305-1048

VL - 43

SP - D637-D644

JO - Nucleic Acids Research

JF - Nucleic Acids Research

ER -

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

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