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.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
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
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
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
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
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
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
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
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
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
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
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
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
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
Jaiswal P (2011) Gramene database: a hub for comparative plant genomics. Methods Mol Biol 678:247–275
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
Urbanczyk-Wochniak E, Sumner LW (2007) MedicCyc: a biochemical pathway database for Medicago truncatula. Bioinformatics 23(11):1418–1423
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
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
Ogata H, Goto S, Fujibuchi W, Kanehisa M (1998) Computation with the KEGG pathway database. Biosystems 47(1-2):119–128
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
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
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
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
Isserlin R, El-Badrawi RA, Bader GD (2011) The biomolecular interaction network database in PSI-MI 2.5. Database (Oxford) 2011:baq037
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
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights 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. https://doi.org/10.1007/978-1-4939-3167-5_4
Download citation
DOI: https://doi.org/10.1007/978-1-4939-3167-5_4
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