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Computational Metabolomics Operations at BioCyc.org.

Karp PD, Billington R, Holland TA, Kothari A, Krummenacker M, Weaver D, Latendresse M, Paley S - Metabolites (2015)

Bottom Line: That analysis operation identifies metabolite sets that are statistically over-represented for the substrates of specific metabolic pathways.BioCyc also enables visualization of metabolomics data on individual pathway diagrams and on the organism-specific metabolic map diagrams that are available for every BioCyc organism.Most of these operations are available both interactively and as programmatic web services.

View Article: PubMed Central - PubMed

Affiliation: Bioinformatics Research Group, SRI International, 333 Ravenswood Ave AE206, Menlo Park, CA 94025, USA. pkarp@ai.sri.com.

ABSTRACT
BioCyc.org is a genome and metabolic pathway web portal covering 5500 organisms, including Homo sapiens, Arabidopsis thaliana, Saccharomyces cerevisiae and Escherichia coli. These organism-specific databases have undergone variable degrees of curation. The EcoCyc (Escherichia coli Encyclopedia) database is the most highly curated; its contents have been derived from 27,000 publications. The MetaCyc (Metabolic Encyclopedia) database within BioCyc is a "universal" metabolic database that describes pathways, reactions, enzymes and metabolites from all domains of life. Metabolic pathways provide an organizing framework for analyzing metabolomics data, and the BioCyc website provides computational operations for metabolomics data that include metabolite search and translation of metabolite identifiers across multiple metabolite databases. The site allows researchers to store and manipulate metabolite lists using a facility called SmartTables, which supports metabolite enrichment analysis. That analysis operation identifies metabolite sets that are statistically over-represented for the substrates of specific metabolic pathways. BioCyc also enables visualization of metabolomics data on individual pathway diagrams and on the organism-specific metabolic map diagrams that are available for every BioCyc organism. Most of these operations are available both interactively and as programmatic web services.

No MeSH data available.


Related in: MedlinePlus

This metabolite SmartTable was derived from the SmartTable in Figure 1 by adding Column 3, which transforms the metabolites in Column 1 to the metabolic pathways containing those metabolites.
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f2-metabolites-05-00291: This metabolite SmartTable was derived from the SmartTable in Figure 1 by adding Column 3, which transforms the metabolites in Column 1 to the metabolic pathways containing those metabolites.

Mentions: Transformations are a more advanced set of SmartTable operations that compute a new column of information for a SmartTable based on a starting column. For example, in Figure 2, we have transformed our metabolite SmartTable by adding a column that lists all metabolic pathways in which each metabolite from Column 1 is a substrate within that PGDB. Other transformations available for metabolites include computing the set of reactions that a metabolite is involved in, computing the set of genes or enzymes regulated by the metabolite and computing the set of proteins known to bind the metabolite. Given a new column created by a transformation, clicking on the “+” at the top of the column will create a new SmartTable containing all objects in that column (i.e., the set of pathways in Figure 2).


Computational Metabolomics Operations at BioCyc.org.

Karp PD, Billington R, Holland TA, Kothari A, Krummenacker M, Weaver D, Latendresse M, Paley S - Metabolites (2015)

This metabolite SmartTable was derived from the SmartTable in Figure 1 by adding Column 3, which transforms the metabolites in Column 1 to the metabolic pathways containing those metabolites.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4495374&req=5

f2-metabolites-05-00291: This metabolite SmartTable was derived from the SmartTable in Figure 1 by adding Column 3, which transforms the metabolites in Column 1 to the metabolic pathways containing those metabolites.
Mentions: Transformations are a more advanced set of SmartTable operations that compute a new column of information for a SmartTable based on a starting column. For example, in Figure 2, we have transformed our metabolite SmartTable by adding a column that lists all metabolic pathways in which each metabolite from Column 1 is a substrate within that PGDB. Other transformations available for metabolites include computing the set of reactions that a metabolite is involved in, computing the set of genes or enzymes regulated by the metabolite and computing the set of proteins known to bind the metabolite. Given a new column created by a transformation, clicking on the “+” at the top of the column will create a new SmartTable containing all objects in that column (i.e., the set of pathways in Figure 2).

Bottom Line: That analysis operation identifies metabolite sets that are statistically over-represented for the substrates of specific metabolic pathways.BioCyc also enables visualization of metabolomics data on individual pathway diagrams and on the organism-specific metabolic map diagrams that are available for every BioCyc organism.Most of these operations are available both interactively and as programmatic web services.

View Article: PubMed Central - PubMed

Affiliation: Bioinformatics Research Group, SRI International, 333 Ravenswood Ave AE206, Menlo Park, CA 94025, USA. pkarp@ai.sri.com.

ABSTRACT
BioCyc.org is a genome and metabolic pathway web portal covering 5500 organisms, including Homo sapiens, Arabidopsis thaliana, Saccharomyces cerevisiae and Escherichia coli. These organism-specific databases have undergone variable degrees of curation. The EcoCyc (Escherichia coli Encyclopedia) database is the most highly curated; its contents have been derived from 27,000 publications. The MetaCyc (Metabolic Encyclopedia) database within BioCyc is a "universal" metabolic database that describes pathways, reactions, enzymes and metabolites from all domains of life. Metabolic pathways provide an organizing framework for analyzing metabolomics data, and the BioCyc website provides computational operations for metabolomics data that include metabolite search and translation of metabolite identifiers across multiple metabolite databases. The site allows researchers to store and manipulate metabolite lists using a facility called SmartTables, which supports metabolite enrichment analysis. That analysis operation identifies metabolite sets that are statistically over-represented for the substrates of specific metabolic pathways. BioCyc also enables visualization of metabolomics data on individual pathway diagrams and on the organism-specific metabolic map diagrams that are available for every BioCyc organism. Most of these operations are available both interactively and as programmatic web services.

No MeSH data available.


Related in: MedlinePlus