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 …

Integrative omics approaches for biosynthetic pathway discovery in plants

KS Singh, JJJ van der Hooft, SCM van Wees… - Natural product …, 2022 - pubs.rsc.org
Covering: up to 2022 With the emergence of large amounts of omics data, computational
approaches for the identification of plant natural product biosynthetic pathways and their …

Comparative and functional algal genomics

CE Blaby-Haas, SS Merchant - Annual Review of Plant Biology, 2019 - annualreviews.org
Over 100 whole-genome sequences from algae are published or soon to be published. The
rapidly increasing availability of these fundamental resources is changing how we …

Toward kingdom-wide analyses of gene expression

I Julca, QW Tan, M Mutwil - Trends in Plant Science, 2023 - cell.com
Gene expression data for Archaeplastida are accumulating exponentially, with more than
300 000 RNA-sequencing (RNA-seq) experiments available for hundreds of species. The …

A comparison of human and mouse gene co-expression networks reveals conservation and divergence at the tissue, pathway and disease levels

G Monaco, S van Dam, JL Casal Novo Ribeiro… - BMC evolutionary …, 2015 - Springer
Background A deeper understanding of differences and similarities in transcriptional
regulation between species can uncover important information about gene functions and the …

Convergent loss of an EDS1/PAD4 signaling pathway in several plant lineages reveals coevolved components of plant immunity and drought response

EL Baggs, JG Monroe, AS Thanki, R O'Grady… - The Plant …, 2020 - academic.oup.com
Plant innate immunity relies on nucleotide binding leucine-rich repeat receptors (NLRs) that
recognize pathogen-derived molecules and activate downstream signaling pathways. We …

Co-expression networks for plant biology: why and how

X Rao, RA Dixon - Acta biochimica et biophysica Sinica, 2019 - academic.oup.com
Co-expression network analysis is one of the most powerful approaches for interpretation of
large transcriptomic datasets. It enables characterization of modules of co-expressed genes …

The reduction in maize leaf growth under mild drought affects the transition between cell division and cell expansion and cannot be restored by elevated gibberellic …

H Nelissen, XH Sun, B Rymen… - Plant Biotechnology …, 2018 - Wiley Online Library
Growth is characterized by the interplay between cell division and cell expansion, two
processes that occur separated along the growth zone at the maize leaf. To gain further …

Phylogenomic analysis of gene co‐expression networks reveals the evolution of functional modules

C Ruprecht, S Proost… - The Plant …, 2017 - Wiley Online Library
Molecular evolutionary studies correlate genomic and phylogenetic information with the
emergence of new traits of organisms. These traits are, however, the consequence of …

Gene regulatory networks for lignin biosynthesis in switchgrass (Panicum virgatum)

X Rao, X Chen, H Shen, Q Ma, G Li… - Plant Biotechnology …, 2019 - Wiley Online Library
Cell wall recalcitrance is the major challenge to improving saccharification efficiency in
converting lignocellulose into biofuels. However, information regarding the transcriptional …