Plant Pathway Databases

  • Pankaj JaiswalEmail author
  • Björn Usadel
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 pathways Plant pathwaydatabases Molecular interactions Metabolic Pathways Signaling pathways Regulatory pathways Transport pathways WikiPathways MapMan RiceCyc MaizeCyc Gramene database Comparative pathway analysis 



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


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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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