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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| Format: | Online |
| Language: | English |
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Oxford University Press
2015
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| Online Access: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4384016/ |
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pubmed-4384016 |
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pubmed-43840162015-04-08 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 Database Issue 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. Oxford University Press 2015-01-28 2014-10-09 /pmc/articles/PMC4384016/ /pubmed/25300491 http://dx.doi.org/10.1093/nar/gku944 Text en © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research. http://creativecommons.org/licenses/by-nc/4.0/ 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 |
| repository_type |
Open Access Journal |
| institution_category |
Foreign Institution |
| institution |
US National Center for Biotechnology Information |
| building |
NCBI PubMed |
| collection |
Online Access |
| language |
English |
| format |
Online |
| author |
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 |
| spellingShingle |
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 |
| author_facet |
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 |
| author_sort |
Shameer, Sanu |
| title |
TrypanoCyc: a community-led biochemical pathways database for Trypanosoma brucei |
| title_short |
TrypanoCyc: a community-led biochemical pathways database for Trypanosoma brucei |
| title_full |
TrypanoCyc: a community-led biochemical pathways database for Trypanosoma brucei |
| title_fullStr |
TrypanoCyc: a community-led biochemical pathways database for Trypanosoma brucei |
| title_full_unstemmed |
TrypanoCyc: a community-led biochemical pathways database for Trypanosoma brucei |
| title_sort |
trypanocyc: a community-led biochemical pathways database for trypanosoma brucei |
| description |
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. |
| publisher |
Oxford University Press |
| publishDate |
2015 |
| url |
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4384016/ |
| _version_ |
1613207159316676608 |