Chapter title |
Pathway Analysis and Omics Data Visualization Using Pathway Genome Databases: FragariaCyc, a Case Study.
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Chapter number | 14 |
Book title |
Plant Genomics Databases
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Published in |
Methods in molecular biology, January 2017
|
DOI | 10.1007/978-1-4939-6658-5_14 |
Pubmed ID | |
Book ISBNs |
978-1-4939-6656-1, 978-1-4939-6658-5
|
Authors |
Sushma Naithani, Pankaj Jaiswal |
Editors |
Aalt D.J van Dijk |
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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Geographical breakdown
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United States | 1 | 14% |
Unknown | 6 | 86% |
Demographic breakdown
Readers by professional status | Count | As % |
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Student > Bachelor | 2 | 29% |
Student > Ph. D. Student | 1 | 14% |
Student > Postgraduate | 1 | 14% |
Unknown | 3 | 43% |
Readers by discipline | Count | As % |
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Computer Science | 2 | 29% |
Chemistry | 1 | 14% |
Design | 1 | 14% |
Unknown | 3 | 43% |