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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

HumanCyc adenosine nucleotide degradation pathway (SALVADEHYPOX-PWY) overlayed with metabolomics data. The data for each metabolite are shown in a separate “omics pop-up” window with eight time points provided for each metabolite. Data were derived from metabolomics data of Chen et al. acquired during the second infection period (diabetic onset and respiratory syncytial virus infection). Data shown represent the daily mean of negative-mode LC-MS peak intensities computed from observed compound peaks in three technical replicates and scaled by a factor of 1e-6.
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f4-metabolites-05-00291: HumanCyc adenosine nucleotide degradation pathway (SALVADEHYPOX-PWY) overlayed with metabolomics data. The data for each metabolite are shown in a separate “omics pop-up” window with eight time points provided for each metabolite. Data were derived from metabolomics data of Chen et al. acquired during the second infection period (diabetic onset and respiratory syncytial virus infection). Data shown represent the daily mean of negative-mode LC-MS peak intensities computed from observed compound peaks in three technical replicates and scaled by a factor of 1e-6.

Mentions: KEGG provides metabolomics visualization services for its pathway diagrams via the KEGG Mapper [18]. The KEGG Mapper is similar to the single-data-point tool we describe in Section 2.7.3, but KEGG Mapper cannot depict multiple data points, as Pathway Tools shows via pop-up windows (see Figure 4). It is also important to keep in mind the general differences between KEGG maps and BioCyc pathways discussed in a recent comparison [6]: KEGG maps tend to be significantly larger than BioCyc pathways, because KEGG maps are mosaics of multiple biological pathways across many species, whereas BioCyc pathways are single metabolic pathways found in specific organisms. For example, KEGG map MAP00270 combines individual pathways involved in biosynthesis and degradation of L-cysteine and L-methionine; therefore, metabolite matches to this KEGG map could be confused with several pathways.


Computational Metabolomics Operations at BioCyc.org.

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

HumanCyc adenosine nucleotide degradation pathway (SALVADEHYPOX-PWY) overlayed with metabolomics data. The data for each metabolite are shown in a separate “omics pop-up” window with eight time points provided for each metabolite. Data were derived from metabolomics data of Chen et al. acquired during the second infection period (diabetic onset and respiratory syncytial virus infection). Data shown represent the daily mean of negative-mode LC-MS peak intensities computed from observed compound peaks in three technical replicates and scaled by a factor of 1e-6.
© Copyright Policy
Related In: Results  -  Collection

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

f4-metabolites-05-00291: HumanCyc adenosine nucleotide degradation pathway (SALVADEHYPOX-PWY) overlayed with metabolomics data. The data for each metabolite are shown in a separate “omics pop-up” window with eight time points provided for each metabolite. Data were derived from metabolomics data of Chen et al. acquired during the second infection period (diabetic onset and respiratory syncytial virus infection). Data shown represent the daily mean of negative-mode LC-MS peak intensities computed from observed compound peaks in three technical replicates and scaled by a factor of 1e-6.
Mentions: KEGG provides metabolomics visualization services for its pathway diagrams via the KEGG Mapper [18]. The KEGG Mapper is similar to the single-data-point tool we describe in Section 2.7.3, but KEGG Mapper cannot depict multiple data points, as Pathway Tools shows via pop-up windows (see Figure 4). It is also important to keep in mind the general differences between KEGG maps and BioCyc pathways discussed in a recent comparison [6]: KEGG maps tend to be significantly larger than BioCyc pathways, because KEGG maps are mosaics of multiple biological pathways across many species, whereas BioCyc pathways are single metabolic pathways found in specific organisms. For example, KEGG map MAP00270 combines individual pathways involved in biosynthesis and degradation of L-cysteine and L-methionine; therefore, metabolite matches to this KEGG map could be confused with several pathways.

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