Chapter title |
Differential Expression Feature Extraction (DEFE): A Case Study in Wheat FHB RNA-Seq Data Analysis
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Chapter number | 11 |
Book title |
Plant-Pathogen Interactions
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Published by |
Humana, New York, NY, May 2023
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DOI | 10.1007/978-1-0716-3159-1_11 |
Pubmed ID | |
Book ISBNs |
978-1-07-163158-4, 978-1-07-163159-1
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Authors |
Youlian Pan, Anuradha Surendra, Ziying Liu, Thérèse Ouellet, Nora A. Foroud |
Abstract |
In differential gene expression data analysis, one objective is to identify groups of co-expressed genes from a large dataset in order to detect the association between such a group of genes and an experimental condition. This is often done through a clustering approach, such as k-means or bipartition hierarchical clustering, based on particular similarity measures in the grouping process. In such a dataset, the gene differential expression itself is an innate attribute that can be used in the feature extraction process. For example, in a dataset consisting of multiple treatments versus their controls, the expression of a gene in each treatment would have three possible behaviors, upregulated, downregulated, or unchanged. We present in this chapter, a differential expression feature extraction (DEFE) method by using a string consisting of three numerical values at each character to denote such behavior, i.e., 1 = up, 2 = down, and 0 = unchanged, which results in up to 3B differential expression patterns across all B comparisons. This approach has been successfully applied in many research projects, and among these, we demonstrate the strength of DEFE in a case study on RNA-sequencing (RNA-seq) data analysis of wheat challenged with the phytopathogenic fungus, Fusarium graminearum. Combinations of multiple schemes of DEFE patterns revealed groups of genes putatively associated with resistance or susceptibility to FHB. |
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