Diurnal Transcriptome and Gene Network Represented through Sparse Modeling in Brachypodium distachyon.

ABSTRACT: We report the comprehensive identification of periodic genes and their network inference, based on a gene co-expression analysis and an Auto-Regressive eXogenous (ARX) model with a group smoothly clipped absolute deviation (SCAD) method using a time-series transcriptome dataset in a model grass, Brachypodium distachyon. To reveal the diurnal changes in the transcriptome in B. distachyon, we performed RNA-seq analysis of its leaves sampled through a diurnal cycle of over 48 h at 4 h intervals using three biological replications, and identified 3,621 periodic genes through our wavelet analysis. The expression data are feasible to infer network sparsity based on ARX models. We found that genes involved in biological processes such as transcriptional regulation, protein degradati

SUBMITTER: Koda S 

PROVIDER: S-EPMC5712366 | biostudies-literature | 2017

REPOSITORIES: biostudies-literature