Learning from co-expression networks: possibilities and challenges

EAR Serin, H Nijveen, HWM Hilhorst… - Frontiers in plant …, 2016 - frontiersin.org
Plants are fascinating and complex organisms. A comprehensive understanding of the
organization, function and evolution of plant genes is essential to disentangle important …

Unraveling gene function in agricultural species using gene co-expression networks

RJ Schaefer, JM Michno, CL Myers - Biochimica et Biophysica Acta (BBA) …, 2017 - Elsevier
Co-expression networks have been shown to be a powerful tool for inferring a gene's
function when little is known about it. With the advent of next generation sequencing …

High‐level hemicellulosic arabinose predominately affects lignocellulose crystallinity for genetically enhancing both plant lodging resistance and biomass enzymatic …

F Li, M Zhang, K Guo, Z Hu, R Zhang… - Plant Biotechnology …, 2015 - Wiley Online Library
Rice is a major food crop with enormous biomass residue for biofuels. As plant cell wall
recalcitrance basically decides a costly biomass process, genetic modification of plant cell …

The glucose 6-phosphate shunt around the Calvin–Benson cycle

TD Sharkey, SE Weise - Journal of experimental botany, 2016 - academic.oup.com
It is just over 60 years since a cycle for the regeneration of the CO2-acceptor used in
photosynthesis was proposed. In this opinion paper, we revisit the origins of the Calvin …

Characterization of the Early Events Leading to Totipotency in an Arabidopsis Protoplast Liquid Culture by Temporal Transcript Profiling

MC Chupeau, F Granier, O Pichon, JP Renou… - The plant …, 2013 - academic.oup.com
The molecular mechanisms underlying plant cell totipotency are largely unknown. Here, we
present a protocol for the efficient regeneration of plants from Arabidopsis thaliana …

Gene coexpression network alignment and conservation of gene modules between two grass species: maize and rice

SP Ficklin, FA Feltus - Plant Physiology, 2011 - academic.oup.com
One major objective for plant biology is the discovery of molecular subsystems underlying
complex traits. The use of genetic and genomic resources combined in a systems genetics …

Systematic identification of functional plant modules through the integration of complementary data sources

KS Heyndrickx, K Vandepoele - Plant physiology, 2012 - academic.oup.com
A major challenge is to unravel how genes interact and are regulated to exert specific
biological functions. The integration of genome-wide functional genomics data, followed by …

The association of multiple interacting genes with specific phenotypes in rice using gene coexpression networks

SP Ficklin, F Luo, FA Feltus - Plant physiology, 2010 - academic.oup.com
Discovering gene sets underlying the expression of a given phenotype is of great
importance, as many phenotypes are the result of complex gene-gene interactions. Gene …

Genetic enhancement of lodging resistance in rice due to the key cell wall polymer lignin, which affects stem characteristics

S Liu, Y Huang, H Xu, M Zhao, Q Xu, F Li - Breeding Science, 2018 - jstage.jst.go.jp
Lodging in crops seriously restricts plant growth and grain production. The genetic
modification of cell walls to enhance plant mechanical strength has been suggested as a …

Connectivity in gene coexpression networks negatively correlates with rates of molecular evolution in flowering plants

RR Masalia, AJ Bewick, JM Burke - PloS one, 2017 - journals.plos.org
Gene coexpression networks are a useful tool for summarizing transcriptomic data and
providing insight into patterns of gene regulation in a variety of species. Though there has …