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

ABSTRACT:

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 marked as relevant for treatment response. Technically, the proposed approach is both a generalization and an extension of WGCNA. It aims to identify specific modules of overlapping communities underlying the co-expression network of genes. Module detection is achieved by using Hierarchical Link Clustering. The overlapping nature of the systems' regulatory domains that generate co-expression can be identified by such modules. LASSO regression is employed to analyze phenotypic responses of m

SUBMITTER: Riccio-Rengifo C 

PROVIDER: S-EPMC8574028 | biostudies-literature | 2021 Nov

REPOSITORIES: biostudies-literature