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Differential expression feature extraction (DEFE): a case study in wheat FHB RNA-seq data analysis

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DOIResolve DOI: https://doi.org/10.1007/978-1-0716-3159-1_11
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Name affiliation
  1. National Research Council of Canada. Digital Technologies
FormatText, Book Chapter
Subjectdifferential gene expression; differential expression feature extraction; RNA-seq; co-expression; gene regulation; wheat; Fusarium head blight; Fusarium graminearum; bioinformatics
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 ¼ up, 2 ¼ down, and 0 ¼ 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
Publication date
PublisherHumana Press
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  • Methods in Molecular Biology (MIMB), no. 2659.
LanguageEnglish
Peer reviewedYes
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Record created2023-06-06
Record modified2023-06-08
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