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Plant Pathway Databases

  • Pankaj Jaiswal
  • Björn Usadel
Part of the Methods in Molecular Biology book series (MIMB, volume 1374)

Abstract

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 pathways Plant pathwaydatabases Molecular interactions Metabolic Pathways Signaling pathways Regulatory pathways Transport pathways WikiPathways MapMan RiceCyc MaizeCyc Gramene database Comparative pathway analysis 

Notes

Acknowledgement

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 (http://www.iplantcollaborative.org/) for hosting the Gramene’s PGDB pathway databases (http://pathway.iplantcollaborative.org/). 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

References

  1. 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):15Google Scholar
  2. 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 6:1–12CrossRefGoogle Scholar
  3. 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):1211–1229CrossRefPubMedGoogle Scholar
  4. 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):14Google Scholar
  5. 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–D1307PubMedCentralPubMedGoogle Scholar
  6. 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–D471PubMedCentralCrossRefPubMedGoogle Scholar
  7. 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):914–939CrossRefPubMedGoogle Scholar
  8. 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):1250–1258CrossRefPubMedGoogle Scholar
  9. 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 7:535CrossRefGoogle Scholar
  10. 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 9:399CrossRefGoogle Scholar
  11. 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):6CrossRefGoogle Scholar
  12. 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 3:148PubMedCentralPubMedGoogle Scholar
  13. 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 11:5CrossRefGoogle Scholar
  14. 14.
    Jaiswal P (2011) Gramene database: a hub for comparative plant genomics. Methods Mol Biol 678:247–275CrossRefPubMedGoogle Scholar
  15. 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):9–16Google Scholar
  16. 16.
    Urbanczyk-Wochniak E, Sumner LW (2007) MedicCyc: a biochemical pathway database for Medicago truncatula. Bioinformatics 23(11):1418–1423CrossRefPubMedGoogle Scholar
  17. 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):1479–1491PubMedCentralCrossRefPubMedGoogle Scholar
  18. 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 10:94–103PubMedGoogle Scholar
  19. 19.
    Ogata H, Goto S, Fujibuchi W, Kanehisa M (1998) Computation with the KEGG pathway database. Biosystems 47(1-2):119–128CrossRefPubMedGoogle Scholar
  20. 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–D1199PubMedCentralCrossRefPubMedGoogle Scholar
  21. 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: 706465Google Scholar
  22. 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):153–163CrossRefPubMedGoogle Scholar
  23. 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–D363PubMedCentralCrossRefPubMedGoogle Scholar
  24. 24.
    Isserlin R, El-Badrawi RA, Bader GD (2011) The biomolecular interaction network database in PSI-MI 2.5. Database (Oxford) 2011:baq037CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media New York 2016

Authors and Affiliations

  1. 1.Department of Botany and Plant PathologyOregon State UniversityCorvallisUSA
  2. 2.IBMG: Institute for Biology IRWTH Aachen UniversityAachenGermany
  3. 3.Forschungszentrum Jülich IBG-2 Plant SciencesJülichGermany

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