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The MetaCyc Database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases.

Caspi R, Foerster H, Fulcher CA, Kaipa P, Krummenacker M, Latendresse M, Paley S, Rhee SY, Shearer AG, Tissier C, Walk TC, Zhang P, Karp PD - Nucleic Acids Res. (2007)

Bottom Line: Each BioCyc PGDB contains the predicted metabolic network of one organism, including metabolic pathways, enzymes, metabolites and reactions predicted by the Pathway Tools software using MetaCyc as a reference database.The BioCyc website offers many tools for computational analysis of PGDBs, including comparative analysis and analysis of omics data in a pathway context.The BioCyc PGDBs generated by SRI are offered for adoption by any interested party for the ongoing integration of metabolic and genome-related information about an organism.

View Article: PubMed Central - PubMed

Affiliation: SRI International, 333 Ravenswood, Menlo Park, CA 94025, USA.

ABSTRACT
MetaCyc (MetaCyc.org) is a universal database of metabolic pathways and enzymes from all domains of life. The pathways in MetaCyc are curated from the primary scientific literature, and are experimentally determined small-molecule metabolic pathways. Each reaction in a MetaCyc pathway is annotated with one or more well-characterized enzymes. Because MetaCyc contains only experimentally elucidated knowledge, it provides a uniquely high-quality resource for metabolic pathways and enzymes. BioCyc (BioCyc.org) is a collection of more than 350 organism-specific Pathway/Genome Databases (PGDBs). Each BioCyc PGDB contains the predicted metabolic network of one organism, including metabolic pathways, enzymes, metabolites and reactions predicted by the Pathway Tools software using MetaCyc as a reference database. BioCyc PGDBs also contain predicted operons and predicted pathway hole fillers-predictions of which enzymes may catalyze pathway reactions that have not been assigned to an enzyme. The BioCyc website offers many tools for computational analysis of PGDBs, including comparative analysis and analysis of omics data in a pathway context. The BioCyc PGDBs generated by SRI are offered for adoption by any interested party for the ongoing integration of metabolic and genome-related information about an organism.

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The regulatory overview. The diagram is composed of three nested ellipses. The innermost ellipse comprises genes that are regulating other genes, but that are not regulated by any genes. The middle ellipse comprises genes that are both regulators and regulatees (= regulated by some entity), and the outermost ellipse comprises genes that are regulated, but do not regulate. The triangles that extend outward from the outer ellipse are collections of many genes that share the same set of regulator genes-although genes within a triangle may respond to those regulators in different ways. They are drawn within triangles simply to keep the size of the outer ellipse manageable.
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Figure 2: The regulatory overview. The diagram is composed of three nested ellipses. The innermost ellipse comprises genes that are regulating other genes, but that are not regulated by any genes. The middle ellipse comprises genes that are both regulators and regulatees (= regulated by some entity), and the outermost ellipse comprises genes that are regulated, but do not regulate. The triangles that extend outward from the outer ellipse are collections of many genes that share the same set of regulator genes-although genes within a triangle may respond to those regulators in different ways. They are drawn within triangles simply to keep the size of the outer ellipse manageable.

Mentions: This tool displays the transcriptional regulatory network of an organism that is defined in a PGDB (Figure 2). The network can be queried in several ways, for instance by highlighting all genes under a specified Gene Ontology class or all genes regulated by a specified transcription factor. The Regulatory Overview is currently available in desktop mode only and will be available through the Web in a later release of Pathway Tools.Figure 2.


The MetaCyc Database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases.

Caspi R, Foerster H, Fulcher CA, Kaipa P, Krummenacker M, Latendresse M, Paley S, Rhee SY, Shearer AG, Tissier C, Walk TC, Zhang P, Karp PD - Nucleic Acids Res. (2007)

The regulatory overview. The diagram is composed of three nested ellipses. The innermost ellipse comprises genes that are regulating other genes, but that are not regulated by any genes. The middle ellipse comprises genes that are both regulators and regulatees (= regulated by some entity), and the outermost ellipse comprises genes that are regulated, but do not regulate. The triangles that extend outward from the outer ellipse are collections of many genes that share the same set of regulator genes-although genes within a triangle may respond to those regulators in different ways. They are drawn within triangles simply to keep the size of the outer ellipse manageable.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2238876&req=5

Figure 2: The regulatory overview. The diagram is composed of three nested ellipses. The innermost ellipse comprises genes that are regulating other genes, but that are not regulated by any genes. The middle ellipse comprises genes that are both regulators and regulatees (= regulated by some entity), and the outermost ellipse comprises genes that are regulated, but do not regulate. The triangles that extend outward from the outer ellipse are collections of many genes that share the same set of regulator genes-although genes within a triangle may respond to those regulators in different ways. They are drawn within triangles simply to keep the size of the outer ellipse manageable.
Mentions: This tool displays the transcriptional regulatory network of an organism that is defined in a PGDB (Figure 2). The network can be queried in several ways, for instance by highlighting all genes under a specified Gene Ontology class or all genes regulated by a specified transcription factor. The Regulatory Overview is currently available in desktop mode only and will be available through the Web in a later release of Pathway Tools.Figure 2.

Bottom Line: Each BioCyc PGDB contains the predicted metabolic network of one organism, including metabolic pathways, enzymes, metabolites and reactions predicted by the Pathway Tools software using MetaCyc as a reference database.The BioCyc website offers many tools for computational analysis of PGDBs, including comparative analysis and analysis of omics data in a pathway context.The BioCyc PGDBs generated by SRI are offered for adoption by any interested party for the ongoing integration of metabolic and genome-related information about an organism.

View Article: PubMed Central - PubMed

Affiliation: SRI International, 333 Ravenswood, Menlo Park, CA 94025, USA.

ABSTRACT
MetaCyc (MetaCyc.org) is a universal database of metabolic pathways and enzymes from all domains of life. The pathways in MetaCyc are curated from the primary scientific literature, and are experimentally determined small-molecule metabolic pathways. Each reaction in a MetaCyc pathway is annotated with one or more well-characterized enzymes. Because MetaCyc contains only experimentally elucidated knowledge, it provides a uniquely high-quality resource for metabolic pathways and enzymes. BioCyc (BioCyc.org) is a collection of more than 350 organism-specific Pathway/Genome Databases (PGDBs). Each BioCyc PGDB contains the predicted metabolic network of one organism, including metabolic pathways, enzymes, metabolites and reactions predicted by the Pathway Tools software using MetaCyc as a reference database. BioCyc PGDBs also contain predicted operons and predicted pathway hole fillers-predictions of which enzymes may catalyze pathway reactions that have not been assigned to an enzyme. The BioCyc website offers many tools for computational analysis of PGDBs, including comparative analysis and analysis of omics data in a pathway context. The BioCyc PGDBs generated by SRI are offered for adoption by any interested party for the ongoing integration of metabolic and genome-related information about an organism.

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