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Plant Pathway Databases

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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 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

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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

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Correspondence to Pankaj Jaiswal .

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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

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  • 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