Limits...
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.

Show MeSH

Related in: MedlinePlus

TrypanoCyc page for the 6-phosphogluconate dehydrogenase (1.1.1.44) reaction. (a) Reaction name and GeneDB link (specific to TrypanoCyc), (b) Detailed description of the reaction, (c) Localizations of the reactions as suggested by annotators, (d) Confidence score for the reaction (specific to TrypanoCyc), (e) Annotation tables displaying content of the TrypAnnot database (specific to TrypanoCyc).
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4384016&req=5

Figure 1: TrypanoCyc page for the 6-phosphogluconate dehydrogenase (1.1.1.44) reaction. (a) Reaction name and GeneDB link (specific to TrypanoCyc), (b) Detailed description of the reaction, (c) Localizations of the reactions as suggested by annotators, (d) Confidence score for the reaction (specific to TrypanoCyc), (e) Annotation tables displaying content of the TrypAnnot database (specific to TrypanoCyc).

Mentions: As a Pathway Tools-based website, TrypanoCyc provides a dedicated web page for each metabolic network entity (pathways, reactions, metabolites, enzymes, proteins and genes). The reaction page architecture was, however, modified in order to allow additional annotation information. These include the annotation confidence score (Figure 1d), stage specificity and compartmentation with links to key literature (Figure 1e). A comment box is also included, containing detailed free-text information on the reaction. Figure 1 shows the webpage for the pentose phosphate pathway enzyme, 6-phosphogluconate dehydrogenase (EC. 1.1.1.44).


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)

TrypanoCyc page for the 6-phosphogluconate dehydrogenase (1.1.1.44) reaction. (a) Reaction name and GeneDB link (specific to TrypanoCyc), (b) Detailed description of the reaction, (c) Localizations of the reactions as suggested by annotators, (d) Confidence score for the reaction (specific to TrypanoCyc), (e) Annotation tables displaying content of the TrypAnnot database (specific to TrypanoCyc).
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

Figure 1: TrypanoCyc page for the 6-phosphogluconate dehydrogenase (1.1.1.44) reaction. (a) Reaction name and GeneDB link (specific to TrypanoCyc), (b) Detailed description of the reaction, (c) Localizations of the reactions as suggested by annotators, (d) Confidence score for the reaction (specific to TrypanoCyc), (e) Annotation tables displaying content of the TrypAnnot database (specific to TrypanoCyc).
Mentions: As a Pathway Tools-based website, TrypanoCyc provides a dedicated web page for each metabolic network entity (pathways, reactions, metabolites, enzymes, proteins and genes). The reaction page architecture was, however, modified in order to allow additional annotation information. These include the annotation confidence score (Figure 1d), stage specificity and compartmentation with links to key literature (Figure 1e). A comment box is also included, containing detailed free-text information on the reaction. Figure 1 shows the webpage for the pentose phosphate pathway enzyme, 6-phosphogluconate dehydrogenase (EC. 1.1.1.44).

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