Differential Expression Feature Extraction (DEFE): A Case Study in Wheat FHB RNA-Seq Data Analysis

• Published in: Methods in molecular biology (Clifton, N.J.) Vol. 2659; p. 137
• Main Authors: Pan, Youlian, Surendra, Anuradha, Liu, Ziying, Ouellet, Thérèse, Foroud, Nora A
• Format: Journal Article
• Language: English
• Published: United States 2023
• Subjects: Fusarium - genetics; Fusarium - metabolism; Plant Diseases - genetics; Plant Diseases - microbiology; RNA-Seq; Triticum - microbiology; Fusarium graminearum; RNA-seq; Differential gene expression; Gene regulation; Co-expression; Differential expression feature extraction; Bioinformatics; Wheat; Fusarium head blight
• ISSN: 1940-6029
• DOI: 10.1007/978-1-0716-3159-1_11

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 3 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.