Skip to main content

Plant Pathway Databases

  • Protocol

Part of the Methods in Molecular Biology book series (MIMB,volume 1374)


Pathway databases provide information about the role of chemicals, genes, and gene products in the form of protein or RNA, their interactions leading to the formulation of metabolic, transport, regulatory, and signaling reactions. The reactions can then be tethered by the principle of inputs and outputs of one or more reaction to create pathways. This chapter provides a list of various online databases that carry information about plant pathways and provides a brief overview of how to use the pathway databases such as WikiPathways Plants Portal, MapMan and the cereal crop pathway databases like RiceCyc and MaizeCyc, that were developed using the Pathway Tools software.

Key words

  • Biological pathway s
  • Plant pathway database s
  • Molecular interaction s
  • Metabolic Pathways
  • Signaling pathway s
  • Regulatory pathway s
  • Transport pathway s
  • WikiPathways
  • MapMan
  • RiceCyc
  • MaizeCyc
  • Gramene database
  • Comparative pathway analysis

This is a preview of subscription content, access via your institution.

Buying options

USD   49.95
Price excludes VAT (USA)
  • DOI: 10.1007/978-1-4939-3167-5_4
  • Chapter length: 17 pages
  • Instant PDF download
  • Readable on all devices
  • Own it forever
  • Exclusive offer for individuals only
  • Tax calculation will be finalised during checkout
USD   109.00
Price excludes VAT (USA)
  • ISBN: 978-1-4939-3167-5
  • Instant PDF download
  • Readable on all devices
  • Own it forever
  • Exclusive offer for individuals only
  • Tax calculation will be finalised during checkout
Softcover Book
USD   139.99
Price excludes VAT (USA)
Hardcover Book
USD   199.99
Price excludes VAT (USA)
Fig. 1
Fig. 2
Fig. 3
Fig. 4

Springer Nature is developing a new tool to find and evaluate Protocols. Learn more


  1. Dharmawardhana P, Ren L, Amarasinghe V, Monaco M, Thomason J, Ravenscroft D, McCouch S, Ware D, Jaiswal P (2013) A genome scale metabolic network for rice and accompanying analysis of tryptophan, auxin and serotonin biosynthesis regulation under biotic stress. Rice (N Y) 6(1):15

    Google Scholar 

  2. Monaco M, Sen TZ, Dharmawardhana P, Ren L, Schaeffer M, Naithani S, Amarasinghe V, Thomason J, Harper L, Gardiner J, Cannon E, Lawrence C, Ware D, Jaiswal P (2013) Maize metabolic network construction and transcriptome analysis. Plant Genome 6:1–12

    CrossRef  Google Scholar 

  3. Usadel B, Poree F, Nagel A, Lohse M, Czedik-Eysenberg A, Stitt M (2009) A guide to using MapMan to visualize and compare Omics data in plants: a case study in the crop species, Maize. Plant Cell Environ 32(9):1211–1229

    CrossRef  PubMed  Google Scholar 

  4. Hanumappa M, Preece J, Elser J, Nemeth D, Bono G, Wu K, Jaiswal P (2013) WikiPathways for plants: a community pathway curation portal and a case study in rice and Arabidopsis seed development networks. Rice (N Y) 6(1):14

    Google Scholar 

  5. Kelder T, van Iersel MP, Hanspers K, Kutmon M, Conklin BR, Evelo CT, Pico AR (2011) WikiPathways: building research communities on biological pathways. Nucleic Acids Res 40(Database issue):D1301–D1307

    PubMed Central  PubMed  Google Scholar 

  6. Caspi R, Altman T, Billington R, Dreher K, Foerster H, Fulcher CA, Holland TA, Keseler IM, Kothari A, Kubo A, Krummenacker M, Latendresse M, Mueller LA, Ong Q, Paley S, Subhraveti P, Weaver DS, Weerasinghe D, Zhang P, Karp PD (2014) The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases. Nucleic Acids Res 42(Database issue):D459–D471

    PubMed Central  CAS  CrossRef  PubMed  Google Scholar 

  7. Thimm BO, Gibon Y, Nagel A, Meyer S, Kruger P, Selbig J, Muller 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(6):914–939

    CAS  CrossRef  PubMed  Google Scholar 

  8. Lohse M, Nagel A, Herter T, May P, Schroda M, Zrenner R, Tohge T, Fernie AR, Stitt M, Usadel B (2014) Mercator: a fast and simple web server for genome scale functional annotation of plant sequence data. Plant Cell Environ 37(5):1250–1258

    CAS  CrossRef  PubMed  Google Scholar 

  9. Usadel B, Nagel A, Steinhauser D, Gibon Y, Blasing OE, Redestig H, Sreenivasulu N, Krall L, Hannah MA, Poree F, Fernie AR, Stitt M (2006) PageMan: an interactive ontology tool to generate, display, and annotate overview graphs for profiling experiments. BMC Bioinform 7:535

    CrossRef  Google Scholar 

  10. van Iersel MP, Kelder T, Pico AR, Hanspers K, Coort S, Conklin BR, Evelo C (2008) Presenting and exploring biological pathways with PathVisio. BMC Bioinform 9:399

    CrossRef  Google Scholar 

  11. Doniger SW, Salomonis N, Dahlquist KD, Vranizan K, Lawlor SC, Conklin BR (2003) MAPPFinder: using Gene Ontology and GenMAPP to create a global gene-expression profile from microarray data. Genome Biol 4(1):6

    CrossRef  Google Scholar 

  12. Gao J, Zhang C, van Iersel M, Zhang L, Xu D, Schultz N, Pico RA (2014) BridgeDb app: unifying identifier mapping services for Cytoscape. F1000Res 3:148

    PubMed Central  PubMed  Google Scholar 

  13. van Iersel MP, Pico AR, Kelder T, Gao J, Ho I, Hanspers K, Conklin BR, Evelo CT (2010) The BridgeDb framework: standardized access to gene, protein and metabolite identifier mapping services. BMC Bioinform 11:5

    CrossRef  Google Scholar 

  14. Jaiswal P (2011) Gramene database: a hub for comparative plant genomics. Methods Mol Biol 678:247–275

    CAS  CrossRef  PubMed  Google Scholar 

  15. Jaiswal P, Ni J, Yap I, Ware D, Spooner W, Youens-Clark K, Ren L, Liang C, Hurwitz B, Zhao W, Ratnapu K, Faga B, Canaran P, Fogleman M, Hebbard C, Avraham S, Schmidt S, Casstevens TM, Buckler ES, Stein L, McCouch S (2006) Gramene: a genomics and genetics resource for rice. Rice Genet Newslett 22(1):9–16

    Google Scholar 

  16. Urbanczyk-Wochniak E, Sumner LW (2007) MedicCyc: a biochemical pathway database for Medicago truncatula. Bioinformatics 23(11):1418–1423

    CAS  CrossRef  PubMed  Google Scholar 

  17. Zhang P, Dreher K, Karthikeyan A, Chi A, Pujar A, Caspi R, Karp P, Kirkup V, Latendresse M, Lee C, Mueller LA, Muller R, Rhee SY (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(4):1479–1491

    PubMed Central  CAS  CrossRef  PubMed  Google Scholar 

  18. Nakao M, Bono H, Kawashima S, Kamiya T, Sato K, Goto S, Kanehisa M (1999) Genome-scale gene expression analysis and pathway reconstruction in KEGG. Genome Inform Ser Workshop Genome Inform 10:94–103

    CAS  PubMed  Google Scholar 

  19. Ogata H, Goto S, Fujibuchi W, Kanehisa M (1998) Computation with the KEGG pathway database. Biosystems 47(1-2):119–128

    CAS  CrossRef  PubMed  Google Scholar 

  20. Monaco MK, Stein J, Naithani S, Wei S, Dharmawardhana P, Kumari S, Amarasinghe V, Youens-Clark K, Thomason J, Preece J, Pasternak S, Olson A, Jiao Y, Lu Z, Bolser D, Kerhornou A, Staines D, Walts B, Wu G, D’Eustachio P, Haw R, Croft D, Kersey PJ, Stein L, Jaiswal P, Ware D (2014) Gramene 2013: comparative plant genomics resources. Nucleic Acids Res 42(Database issue):D1193–D1199

    PubMed Central  CAS  CrossRef  PubMed  Google Scholar 

  21. Ling MH, Rabara RC, Tripathi P, Rushton PJ, Ge SX (2013) Extending MapMan ontology to tobacco for visualization of gene expression. Dataset Pap Biol 2013:pii: 706465

    Google Scholar 

  22. Toufighi K, Brady SM, Austin R, Ly E, Provart NJ (2005) The Botany Array Resource: e-Northerns, Expression Angling, and promoter analyses. Plant J 43(1):153–163

    CAS  CrossRef  PubMed  Google Scholar 

  23. Orchard S, Ammari M, Aranda B, Breuza L, Briganti L, Broackes-Carter F, Campbell NH, Chavali G, Chen C, del-Toro N, Duesbury M, Dumousseau M, Galeota E, Hinz U, Iannuccelli M, Jagannathan S, Jimenez R, Khadake J, Lagreid A, Licata L, Lovering RC, Meldal B, Melidoni AN, Milagros M, Peluso D, Perfetto L, Porras P, Raghunath A, Ricard-Blum S, Roechert B, Stutz A, Tognolli M, van Roey K, Cesareni G, Hermjakob H (2014) The MIntAct project--IntAct as a common curation platform for 11 molecular interaction databases. Nucleic Acids Res 42(Database issue):D358–D363

    PubMed Central  CAS  CrossRef  PubMed  Google Scholar 

  24. Isserlin R, El-Badrawi RA, Bader GD (2011) The biomolecular interaction network database in PSI-MI 2.5. Database (Oxford) 2011:baq037

    CrossRef  Google Scholar 

Download references


We kindly acknowledge current and former members of our respective laboratories and collaborative projects for their contribution to building pathway resources for the plant biology community. We also acknowledge the iPlant Collaborative ( for hosting the Gramene’s PGDB pathway databases ( We extend special thanks to numerous collaborators and domain experts who continue to contribute to the development and annotation of pathway databases. PJ acknowledges funding support by the US National Science Foundation (NSF) award IOS #1127112 and the funds made available by the Oregon State University. BU acknowledges funding support for the PlabiPD project FKZ 0315961

Author information

Authors and Affiliations


Corresponding author

Correspondence to Pankaj Jaiswal .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and Permissions

Copyright information

© 2016 Springer Science+Business Media New York

About this protocol

Cite this protocol

Jaiswal, P., Usadel, B. (2016). Plant Pathway Databases. In: Edwards, D. (eds) Plant Bioinformatics. Methods in Molecular Biology, vol 1374. Humana Press, New York, NY.

Download citation

  • DOI:

  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-3166-8

  • Online ISBN: 978-1-4939-3167-5

  • eBook Packages: Springer Protocols