Abstract
Metabolic databases such as The Plant Metabolic Network/MetaCyc and KEGG PATHWAY are publicly accessible resources providing organism-specific information on reactions and metabolites. KEGG PATHWAY depicts metabolic networks as wired, electronic circuit-like maps, whereas the MetaCyc family of databases uses a canonical textbook-like representation. The first MetaCyc-based database for a plant species was AraCyc, which describes metabolism in the model plant Arabidopsis. This database was created over 10 years ago and has since then undergone extensive manual curation to reflect updated information on enzymes and pathways in Arabidopsis. This chapter describes accessing and using AraCyc and its underlying Pathway Tools software. Specifically, methods for (1) navigating Pathway Tools, (2) visualizing omics data and superimposing the data on a metabolic pathway map, and (3) creating pathways and pathway components are discussed.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Kanehisa M (1996) Toward pathway engineering: a new database of genetic and molecular pathways. Sci Technol Jpn 59:34–38
Karp PD, Riley M, Paley SM, Pelligrini-Toole A (1996) EcoCyc: an encyclopedia of Escherichia coli genes and metabolism. Nucleic Acids Res 24:32–39
Kanehisa M, Goto S, Furumichi M, Tanabe M, Hirakawa M (2010) KEGG for representation and analysis of molecular networks involving diseases and drugs. Nucleic Acids Res 38:D355–D360
Karp PD, Riley M, Saier M, Paulsen IT, Paley SM, Pellegrini-Toole A (2000) The EcoCyc and MetaCyc databases. Nucleic Acids Res 28:56–59
Caspi R, Altman T, Dale JM, Dreher K, Fulcher CA, Gilham F, Kaipa P, Karthikeyan AS, Kothari A, Krummenacker M et al (2010) The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases. Nucleic Acids Res 38:D473–D479
Jaiswal P (2011) Gramene database: a hub for comparative plant genomics [Internet]. In: Pereira A (ed) Plant reverse genetics. Humana Press, Totowa, NJ, pp 247–275
Youens-Clark K, Buckler E, Casstevens T, Chen C, DeClerck G, Derwent P, Dharmawardhana P, Jaiswal P, Kersey P, Karthikeyan AS et al (2011) Gramene database in 2010: updates and extensions. Nucleic Acids Res 39:D1085–D1094
Zhang P, Dreher K, Karthikeyan A, Chi A, Pujar A, Caspi R, Karp P, Kirkup V, Latendresse M, Lee C et al (2010) Creation of a genome-wide metabolic pathway database for Populus trichocarpa using a new approach for reconstruction and curation of metabolic pathways for plants. Plant Physiol 153:1479–1491
May P, Christian J-O, Kempa S, Walther D (2009) ChlamyCyc: an integrative systems biology database and web-portal for Chlamydomonas reinhardtii. BMC Genomics 10:209
Urbanczyk-Wochniak E, Sumner LW (2007) MedicCyc: a biochemical pathway database for Medicago truncatula. Bioinformatics 23:1418–1423
Mazourek M, Pujar A, Borovsky Y, Paran I, Mueller L, Jahn MM (2009) A dynamic interface for capsaicinoid systems biology. Plant Physiol 150:1806–1821
Mueller LA, Zhang P, Rhee SY (2003) AraCyc: a biochemical pathway database for Arabidopsis. Plant Physiol 132:453–460
Grafahrend-Belau E, Weise S, Koschützki D, Scholz U, Junker BH, Schreiber F (2008) MetaCrop: a detailed database of crop plant metabolism. Nucleic Acids Res 36:D954–D958
Matthews L, Gopinath G, Gillespie M, Caudy M, Croft D, de Bono B, Garapati P, Hemish J, Hermjakob H, Jassal B et al (2009) Reactome knowledgebase of human biological pathways and processes. Nucleic Acids Res 37:D619–D622
Thimm O, Bläsing O, Gibon Y, Nagel A, Meyer S, Krüger P, Selbig J, Müller LA, Rhee SY, Stitt M (2004) MAPMAN a user-driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes. Plant J 37:914–939
Yan J, Zhang C, Gu M, Bai Z, Zhang W, Qi T, Cheng Z, Peng W, Luo H, Nan F et al (2009) The Arabidopsis CORONATINE INSENSITIVE1 protein is a jasmonate receptor. Plant Cell 21:2220–2236
Gidda SK, Miersch O, Levitin A, Schmidt J, Wasternack C, Varin L (2003) Biochemical and molecular characterization of a hydroxyjasmonate sulfotransferase from Arabidopsis thaliana. J Biol Chem 278:17895–17900
Acknowledgments
The author would like to thank George Dreher for testing the protocols and improving the manuscript as well as Peifen Zhang, Sue Rhee, the members of the Rhee lab, and all of the members of the Pathways Tools/MetaCyc group. This work was funded by the US National Science Foundation (awards NSF DBI-0640769 and IOS-1026003).
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2014 Springer Science+Business Media, New York
About this protocol
Cite this protocol
Dreher, K. (2014). Putting the Plant Metabolic Network Pathway Databases to Work: Going Offline to Gain New Capabilities. In: Sriram, G. (eds) Plant Metabolism. Methods in Molecular Biology, vol 1083. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-661-0_10
Download citation
DOI: https://doi.org/10.1007/978-1-62703-661-0_10
Published:
Publisher Name: Humana Press, Totowa, NJ
Print ISBN: 978-1-62703-660-3
Online ISBN: 978-1-62703-661-0
eBook Packages: Springer Protocols