Identifying stress responsive genes using overlapping communities in co-expression networks

Background: This paper proposes a workflow to identify genes that respond to specific treatments in plants. The workflow takes as input the RNA sequencing read counts and phenotypical data of different genotypes, measured under control and treatment conditions. It outputs a reduced group of genes ma...

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Bibliographic Details
Main Authors:	Finke, J. (Author), Riccio-Rengifo, C. (Author), Rocha, C. (Author)
Format:	Article
Language:	English
Published:	BioMed Central Ltd 2021
Subjects:	Agronomy article biomass Co-expression network Co-expression networks gene expression Genes Genetic engineering genetics genotype Genotype LASSO nonhuman Oryza Oryza sativa Overlapping communities Phenotypic traits physiological stress rice Rice RNA sequencing root weight Salinity salt stress Salt stresss salt tolerance Salt Tolerance sequence analysis Sequence Analysis, RNA shoot Stress, Physiological Stress-responsive gene Stress-responsive genes treatment response workflow Work-flows
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Identifying stress responsive genes using overlapping communities in co-expression networks

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