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

Par Conseil national de recherches du Canada

Téléchargement	Sera disponible ici le 31 mai 2024
DOI	Trouver le DOI : https://doi.org/10.1007/978-1-0716-3159-1_11
Auteur	Rechercher : Pan, Youlian¹; Rechercher : Surendra, Anuradha¹; Rechercher : Liu, Ziying¹; Rechercher : Ouellet, Thérèse; Rechercher : Foroud, Nora A.
Affiliation	Conseil national de recherches du Canada. Technologies numériques
Format	Texte, Chapitre de livre
Sujet	differential gene expression; differential expression feature extraction; RNA-seq; co-expression; gene regulation; wheat; Fusarium head blight; Fusarium graminearum; bioinformatics
Résumé	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
Date de publication	2023-05-31
Maison d’édition	Humana Press
Dans	Plant-Pathogen Interactions (31 mai 2023) : 137–159. https://doi.org/10.1007/978-1-0716-3159-1.
Série	Methods in Molecular Biology (MIMB), nº 2659.
Langue	anglais
Publications évaluées par des pairs	Oui
Exporter la notice	Exporter en format RIS
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Identificateur de l’enregistrement	c8f90c46-ae3f-43df-adf2-9e804220c4ec
Enregistrement créé	2023-06-06
Enregistrement modifié	2023-06-08

Date de modification :: 2024-04-16