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