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

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 MA, Ginger ML, Hertz-Fowler C, Kerkhoven EJ, Mäser P, Michels PA, Nayak A, Nes DW, Nolan DP, Olsen C, Silva-Franco F, Smith TK, Taylor MC, Tielens AG, Urbaniak MD, van Hellemond JJ, Vincent IM, Wilkinson SR, Wyllie S, Opperdoes FR, Barrett MP, Jourdan F - Nucleic Acids Res. (2014)

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Institut National de la Recherche Agronomique (INRA), UMR1331, TOXALIM (Research Centre in Food Toxicology), Université de Toulouse, Toulouse, France.

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Navigation between pathway and network representation using MetExplore and TrypanoCyc. (a) Each pathway page has an hyperlink allowing to load and visualize the pathway in MetExplore (circled in red on the pathway page screenshot). (b) When clicking on this link in the Glycolysis page, it is loaded in MetExplore; the red box corresponds to the cytosolic part and the green one to the glycosomal part. (c) Using MetExplore, it is then possible to generate a combination of various pathways. TCA cycle, succinate shunt, glycolysis and the pentose phosphate pathway were selected. (d) All reactions of these pathways are added to the cart (red box on the right). A third compartment, mitochondrion, appears (purple box). A reaction allowing transport between cytosol and glycosome appears in the network (red arrow). (e) In the tabular view of MetExplore, a TrypanoCyc button (visible in the third column of [c] table) allows to link back to TrypanoCyc.
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Figure 3: Navigation between pathway and network representation using MetExplore and TrypanoCyc. (a) Each pathway page has an hyperlink allowing to load and visualize the pathway in MetExplore (circled in red on the pathway page screenshot). (b) When clicking on this link in the Glycolysis page, it is loaded in MetExplore; the red box corresponds to the cytosolic part and the green one to the glycosomal part. (c) Using MetExplore, it is then possible to generate a combination of various pathways. TCA cycle, succinate shunt, glycolysis and the pentose phosphate pathway were selected. (d) All reactions of these pathways are added to the cart (red box on the right). A third compartment, mitochondrion, appears (purple box). A reaction allowing transport between cytosol and glycosome appears in the network (red arrow). (e) In the tabular view of MetExplore, a TrypanoCyc button (visible in the third column of [c] table) allows to link back to TrypanoCyc.

Mentions: To complement the classical pathway-oriented BioCyc representation of data, we also offer a novel way to visualize the content of TrypanoCyc via our MetExplore web server (21) (for step by step instructions see Supplementary Data S3). Each pathway page contains a hyperlink (Figure 3a), that opens MetExplore with the selected pathway (Figure 3b). Importantly, the MetExplore viewer takes into account the localization of reactions. For example, Figure 3b shows how the glycolytic pathway is divided into two compartments (glycosome and cytosol represented by green and red boxes, respectively).


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

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 MA, Ginger ML, Hertz-Fowler C, Kerkhoven EJ, Mäser P, Michels PA, Nayak A, Nes DW, Nolan DP, Olsen C, Silva-Franco F, Smith TK, Taylor MC, Tielens AG, Urbaniak MD, van Hellemond JJ, Vincent IM, Wilkinson SR, Wyllie S, Opperdoes FR, Barrett MP, Jourdan F - Nucleic Acids Res. (2014)

Navigation between pathway and network representation using MetExplore and TrypanoCyc. (a) Each pathway page has an hyperlink allowing to load and visualize the pathway in MetExplore (circled in red on the pathway page screenshot). (b) When clicking on this link in the Glycolysis page, it is loaded in MetExplore; the red box corresponds to the cytosolic part and the green one to the glycosomal part. (c) Using MetExplore, it is then possible to generate a combination of various pathways. TCA cycle, succinate shunt, glycolysis and the pentose phosphate pathway were selected. (d) All reactions of these pathways are added to the cart (red box on the right). A third compartment, mitochondrion, appears (purple box). A reaction allowing transport between cytosol and glycosome appears in the network (red arrow). (e) In the tabular view of MetExplore, a TrypanoCyc button (visible in the third column of [c] table) allows to link back to TrypanoCyc.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4384016&req=5

Figure 3: Navigation between pathway and network representation using MetExplore and TrypanoCyc. (a) Each pathway page has an hyperlink allowing to load and visualize the pathway in MetExplore (circled in red on the pathway page screenshot). (b) When clicking on this link in the Glycolysis page, it is loaded in MetExplore; the red box corresponds to the cytosolic part and the green one to the glycosomal part. (c) Using MetExplore, it is then possible to generate a combination of various pathways. TCA cycle, succinate shunt, glycolysis and the pentose phosphate pathway were selected. (d) All reactions of these pathways are added to the cart (red box on the right). A third compartment, mitochondrion, appears (purple box). A reaction allowing transport between cytosol and glycosome appears in the network (red arrow). (e) In the tabular view of MetExplore, a TrypanoCyc button (visible in the third column of [c] table) allows to link back to TrypanoCyc.
Mentions: To complement the classical pathway-oriented BioCyc representation of data, we also offer a novel way to visualize the content of TrypanoCyc via our MetExplore web server (21) (for step by step instructions see Supplementary Data S3). Each pathway page contains a hyperlink (Figure 3a), that opens MetExplore with the selected pathway (Figure 3b). Importantly, the MetExplore viewer takes into account the localization of reactions. For example, Figure 3b shows how the glycolytic pathway is divided into two compartments (glycosome and cytosol represented by green and red boxes, respectively).

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Institut National de la Recherche Agronomique (INRA), UMR1331, TOXALIM (Research Centre in Food Toxicology), Université de Toulouse, Toulouse, France.

Show MeSH
Related in: MedlinePlus