Putting the Plant Metabolic Network Pathway Databases to Work: Going Offline to Gain New Capabilities

Kate Dreher

doi:10.1007/978-1-62703-661-0_10

Plant Metabolism pp 151-171

Part of the Methods in Molecular Biology book series (MIMB, volume 1083)

Putting the Plant Metabolic Network Pathway Databases to Work: Going Offline to Gain New Capabilities

Authors
Authors and affiliations

Kate Dreher

Protocol

First Online:: 10 October 2013

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.

Key words

Plant metabolism Omics data analysis Biochemical pathway databases

References

1.
Kanehisa M (1996) Toward pathway engineering: a new database of genetic and molecular pathways. Sci Technol Jpn 59:34–38Google Scholar
2.
Karp PD, Riley M, Paley SM, Pelligrini-Toole A (1996) EcoCyc: an encyclopedia of Escherichia coli genes and metabolism. Nucleic Acids Res 24:32–39PubMedCrossRefGoogle Scholar
3.
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–D360PubMedCrossRefGoogle Scholar
4.
Karp PD, Riley M, Saier M, Paulsen IT, Paley SM, Pellegrini-Toole A (2000) The EcoCyc and MetaCyc databases. Nucleic Acids Res 28:56–59PubMedCrossRefGoogle Scholar
5.
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–D479PubMedCrossRefGoogle Scholar
6.
Jaiswal P (2011) Gramene database: a hub for comparative plant genomics [Internet]. In: Pereira A (ed) Plant reverse genetics. Humana Press, Totowa, NJ, pp 247–275CrossRefGoogle Scholar
7.
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–D1094PubMedCrossRefGoogle Scholar
8.
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 153:1479–1491PubMedCrossRefGoogle Scholar
9.
May P, Christian J-O, Kempa S, Walther D (2009) ChlamyCyc: an integrative systems biology database and web-portal for Chlamydomonas reinhardtii. BMC Genomics 10:209PubMedCrossRefGoogle Scholar
10.
Urbanczyk-Wochniak E, Sumner LW (2007) MedicCyc: a biochemical pathway database for Medicago truncatula. Bioinformatics 23:1418–1423PubMedCrossRefGoogle Scholar
11.
Mazourek M, Pujar A, Borovsky Y, Paran I, Mueller L, Jahn MM (2009) A dynamic interface for capsaicinoid systems biology. Plant Physiol 150:1806–1821PubMedCrossRefGoogle Scholar
12.
Mueller LA, Zhang P, Rhee SY (2003) AraCyc: a biochemical pathway database for Arabidopsis. Plant Physiol 132:453–460PubMedCrossRefGoogle Scholar
13.
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–D958PubMedCrossRefGoogle Scholar
14.
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–D622PubMedCrossRefGoogle Scholar
15.
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 37:914–939PubMedCrossRefGoogle Scholar
16.
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 21:2220–2236PubMedCrossRefGoogle Scholar
17.
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 278:17895–17900PubMedCrossRefGoogle Scholar

Copyright information

Authors and Affiliations

Kate Dreher
- 1

1.Carnegie Institution for SciencePalo AltoUSA

About this protocol

Cite this protocol as:: 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 (Methods and Protocols), vol 1083. Humana Press, Totowa, NJ

DOI 10.1007/978-1-62703-661-0_10
Publisher Name Humana Press, Totowa, NJ
Print ISBN 978-1-62703-660-3
Online ISBN 978-1-62703-661-0
eBook Packages Springer Protocols

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Putting the Plant Metabolic Network Pathway Databases to Work: Going Offline to Gain New Capabilities

Abstract

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