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        Using the MetaCyc Pathway Database and the BioCyc Database Collection

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        2405
        • Abstract
        • Table of Contents
        • Figures
        • Literature Cited

        Abstract

         

        The MetaCyc database (http://metacyc.org) is a collection of more than a thousand metabolic pathways from a wide variety of organisms, collected from the literature by manual curation. BioCyc contains more than 370 Pathway/Genome Databases, each of which describes the genome and predicted metabolic pathways of a single organism, as computationally predicted from the annotated genomes, using MetaCyc data as a reference. The protocols in this unit introduce the user to the extensive data content available in MetaCyc and BioCyc, and to mechanisms for querying, visualizing, and analyzing these data using the Pathway Tools software. Curr. Protoc. Bioinform. 20:1.17.1?1.17.51. © 2007 by John Wiley & Sons, Inc.

        Keywords: metabolism; pathways; omics viewer; expression analysis tools; pathway comparison; genomics

             
         
        GO TO THE FULL PROTOCOL:
        PDF or HTML at Wiley Online Library

        Table of Contents

        • Introduction
        • Basic Protocol 1: The MetaCyc Pathway Database Home Page
        • Basic Protocol 2: Browsing the Database
        • Basic Protocol 3: Searching Using the Query Page Through the Web Server
        • Alternate Protocol 1: Searching the Database Using the Desktop Version
        • Basic Protocol 4: Searching the Database Using the Advanced Query Form
        • Basic Protocol 5: Finding Information About Enzymes
        • Basic Protocol 6: Finding Information About Pathways
        • Basic Protocol 7: Using the Genome Browser
        • Basic Protocol 8: Performing a Cross‐Species Pathway and Gene Comparison
        • Basic Protocol 9: Using the Cellular Overview Diagram Through the Web Server
        • Alternate Protocol 2: Using the Cellular Overview in the Desktop Version of Pathway Tools
        • Basic Protocol 10: Using the Regulatory Overview in the Desktop Version
        • Basic Protocol 11: Using the Genome Overview in the Desktop Version
        • Basic Protocol 12: Using the Cellular Omics Viewer Through the Web Server
        • Alternate Protocol 3: Using the Cellular Omics Viewer in the Desktop Version of Pathway Tools
        • Basic Protocol 13: Generating Posters from PGDBs
        • Basic Protocol 14: Downloading PGDBs from the PGDB Registry
        • Commentary
        • Literature Cited
        • Figures
        • Tables
             
         
        GO TO THE FULL PROTOCOL:
        PDF or HTML at Wiley Online Library

        Materials

         
        GO TO THE FULL PROTOCOL:
        PDF or HTML at Wiley Online Library

        Figures

        •   Figure Figure 1.17.1 MetaCyc.org home page.
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        •   Figure Figure 1.17.2 Browsing MetaCyc reactions.
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        •   Figure Figure 1.17.3 Example for a MetaCyc reactions class: tRNA‐Charging‐Reactions.
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        •   Figure Figure 1.17.4 Example MetaCyc reaction page.
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        •   Figure Figure 1.17.5 BioCyc Query Page.
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        •   Figure Figure 1.17.6 Searching for Pathways by the organisms in which they occur.
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        •   Figure Figure 1.17.7 Pathway Selection dialog window.
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        •   Figure Figure 1.17.8 Searching for reactions that consume ethanol.
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        •   Figure Figure 1.17.9 Searching for enzymes based on their modulation by chemical compounds.
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        •   Figure Figure 1.17.10 Searching for compounds based on molecular substructure.
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        •   Figure Figure 1.17.11 Structured Advanced Query Page.
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        •   Figure Figure 1.17.12 Example for an Advanced Query.
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        •   Figure Figure 1.17.13 Upper part of a MetaCyc enzyme page.
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        •   Figure Figure 1.17.14 Enzymatic activities part of a MetaCyc enzyme page.
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        •   Figure Figure 1.17.15 Evidence Codes.
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        •   Figure Figure 1.17.16 Gene‐Reaction schematic.
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        •   Figure Figure 1.17.17 Genome browser.
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        •   Figure Figure 1.17.18 Adding external tracks to the Genome Browser.
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        •   Figure Figure 1.17.19 Cross‐species pathway comparison.
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        •   Figure Figure 1.17.20 Cross‐species gene comparison.
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        •   Figure Figure 1.17.21 Metabolic Overview.
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        •   Figure Figure 1.17.22 Zooming options for the Metabolic Overview.
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        •   Figure Figure 1.17.23 Regulatory overview.
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        •   Figure Figure 1.17.24 Regulatory relationship among all E. coli genes that are involved in drug resistance/sensitivity. The ftsI gene and its direct regulators are highlighted.
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        •   Figure Figure 1.17.25 E. coli rcsB gene and its direct regulates.
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        •   Figure Figure 1.17.26 Genome Overview.
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        •   Figure Figure 1.17.27 Metabolic Omic Viewer.
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        •   Figure Figure 1.17.28 Pathway display with superimposed gene transcription data.
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        •   Figure Figure 1.17.29 Table describing pathways that include genes with expression values above a defined cutoff.
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        •   Figure Figure 1.17.30 Metabolic Overview histogram including animation controls.
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        •   Figure Figure 1.17.31 Omics Viewer settings window (desktop version of Pathway Tools).
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        •   Figure Figure 1.17.32 PGDB Registry.
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        Videos

        Literature Cited

           Caspi, R., Foerster, H., Fulcher, C.A., Hopkinson, R., Ingraham, J., Kaipa, P., Krummenacker, M., Paley, S., Pick, J., Rhee, S.Y., Tissier, C., Zhang, P., and Karp, P.D. 2006. MetaCyc: A multiorganism database of metabolic pathways and enzymes. Nucleic Acids Res. 34:D1‐D6.
           Green, M.L. and Karp, P.D. 2004. A Bayesian method for identifying missing enzymes in predicted metabolic pathway databases. BMC Bioinformatics 5:76.
           Karp, P.D., Ouzounis, C.A., Moore‐Kochlacs, C., Goldovsky, L., Kaipa, P., Ahrén, D., Tsoka, S., Darzentas, N., Kunin, V., and López‐Bigas, N. 2005. Expansion of the BioCyc collection of pathway/genome databases to 160 genomes. Nucleic Acids Res. 33:6083‐6089.
           Karp, P.D., Paley, S., and Romero, P. 2002. The Pathway Tools software. Bioinformatics 18;S225‐S232.
           Krieger, C.J., Zhang, P., Mueller, L.A., Wang, A., Paley, S., Arnaud, M., Pick, J., Rhee, S.Y., and Karp, P.D. 2004. MetaCyc: A multiorganism database of metabolic pathways and enzymes. Nucleic Acids Res. 32:D438‐D442.
           Paley, S.M. and Karp, P.D. 2006. The Pathway Tools cellular overview diagram and Omics Viewer Nucleic Acids Res. 34:3771‐3778.
        Internet Resources
           http:/metacyc.org
           MetaCyc home page
           http:/biocyc.org
           BioCyc home page
           http:/ecocyc.org
           EcoCyc home page
           http:/humancyc.org
           HumanCyc home page
           http://bioinformatics.ai.sri.com/ptools/
           Pathway Tools information site
           http://biocyc.org/biocyc‐pgdb‐list.shtml
           List of all BioCyc Pathway/Genome Databases
        GO TO THE FULL PROTOCOL:
        PDF or HTML at Wiley Online Library
         
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