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Pathway Analysis and Omics Data Visualization Using Pathway Genome Databases: FragariaCyc, a Case Study

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Plant Genomics Databases

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1533))

Abstract

The species-specific plant Pathway Genome Databases (PGDBs) based on the BioCyc platform provide a conceptual model of the cellular metabolic network of an organism. Such frameworks allow analysis of the genome-scale expression data to understand changes in the overall metabolisms of an organism (or organs, tissues, and cells) in response to various extrinsic (e.g. developmental and differentiation) and/or extrinsic signals (e.g. pathogens and abiotic stresses) from the surrounding environment. Using FragariaCyc, a pathway database for the diploid strawberry Fragaria vesca, we show (1) the basic navigation across a PGDB; (2) a case study of pathway comparison across plant species; and (3) an example of RNA-Seq data analysis using Omics Viewer tool. The protocols described here generally apply to other Pathway Tools-based PGDBs.

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Acknowledgement

We are grateful to Peter Karp and his staff from SRI International for providing excellent Pathway Tools support. The FragariaCyc development was partially supported by funds provided to SN by Oregon State University and through collaboration with Dr. Pankaj Jaiswal. PJ acknowledges NSF IOS #1127112 grant.

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Authors and Affiliations

  1. Department of Botany and Plant Pathology, Oregon State University, 2082 Cordley Hall, Corvallis, OR, 97331-2902, USA

    Sushma Naithani & Pankaj Jaiswal

Authors
  1. Sushma Naithani
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  2. Pankaj Jaiswal
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Corresponding author

Correspondence to Sushma Naithani .

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Editors and Affiliations

  1. PRI Bioscience, Biometris and Bioinformatics, Wageningen University & Research Wageningen, Wageningen, The Netherlands

    Aalt D.J van Dijk

1 Electronic Supplementary Material

Supplementary Table 1

Biocyc-protocol-fragaria-16316 genes-1 (TXT 1196 KB)

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Naithani, S., Jaiswal, P. (2017). Pathway Analysis and Omics Data Visualization Using Pathway Genome Databases: FragariaCyc, a Case Study. In: van Dijk, A. (eds) Plant Genomics Databases. Methods in Molecular Biology, vol 1533. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-6658-5_14

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  • DOI: https://doi.org/10.1007/978-1-4939-6658-5_14

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-6656-1

  • Online ISBN: 978-1-4939-6658-5

  • eBook Packages: Springer Protocols

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