Integrative inference of transcriptional networks in Arabidopsis yields novel ROS signalling regulators

I De Clercq, J Van de Velde, X Luo, L Liu, V Storme… - Nature Plants, 2021 - nature.com
Gene regulation is a dynamic process in which transcription factors (TFs) play an important
role in controlling spatiotemporal gene expression. To enhance our global understanding of …

TF2Network: predicting transcription factor regulators and gene regulatory networks in Arabidopsis using publicly available binding site information

SR Kulkarni, D Vaneechoutte… - Nucleic acids …, 2018 - academic.oup.com
A gene regulatory network (GRN) is a collection of regulatory interactions between
transcription factors (TFs) and their target genes. GRNs control different biological processes …

Specificity in ROS signaling and transcript signatures

L Vaahtera, M Brosche, M Wrzaczek… - Antioxidants & redox …, 2014 - liebertpub.com
Significance: Reactive oxygen species (ROS), important signaling molecules in plants, are
involved in developmental control and stress adaptation. ROS production can trigger broad …

ConnecTF: A platform to integrate transcription factor–gene interactions and validate regulatory networks

MD Brooks, CL Juang, MS Katari, JM Alvarez… - Plant …, 2021 - academic.oup.com
Deciphering gene regulatory networks (GRNs) is both a promise and challenge of systems
biology. The promise lies in identifying key transcription factors (TFs) that enable an …

Inference of plant gene regulatory networks using data-driven methods: A practical overview

SR Kulkarni, K Vandepoele - Biochimica et Biophysica Acta (BBA)-Gene …, 2020 - Elsevier
Transcriptional regulation is a complex and dynamic process that plays a vital role in plant
growth and development. A key component in the regulation of genes is transcription factors …

Gene regulatory network inference: connecting plant biology and mathematical modeling

L Van den Broeck, M Gordon, D Inzé, C Williams… - Frontiers in …, 2020 - frontiersin.org
Plant responses to environmental and intrinsic signals are tightly controlled by multiple
transcription factors (TFs). These TFs and their regulatory connections form gene regulatory …

Transcriptomic footprints disclose specificity of reactive oxygen species signaling in Arabidopsis

I Gadjev, S Vanderauwera, TS Gechev, C Laloi… - Plant …, 2006 - academic.oup.com
Reactive oxygen species (ROS) are key players in the regulation of plant development,
stress responses, and programmed cell death. Previous studies indicated that depending on …

Quantitative ROS bioreporters: A robust toolkit for studying biological roles of ROS in response to abiotic and biotic stresses

SD Lim, SH Kim, S Gilroy, JC Cushman… - Physiologia …, 2019 - Wiley Online Library
While the accumulation of reactive oxygen species (ROS) through spontaneous generation
or as the by‐products of aerobic metabolism can be toxic to plants, recent findings …

Stress signaling III: reactive oxygen species (ROS)

M Brosché, K Overmyer, M Wrzaczek… - Abiotic stress adaptation …, 2010 - Springer
Previously regarded merely as damaging agents, reactive oxygen species (ROS) are now
understood as important signal molecules vital to normal plant growth. This tutorial review …

A machine learning approach to predict gene regulatory networks in seed development in Arabidopsis

Y Ni, D Aghamirzaie, H Elmarakeby… - Frontiers in plant …, 2016 - frontiersin.org
Gene regulatory networks (GRNs) provide a representation of relationships between
regulators and their target genes. Several methods for GRN inference, both unsupervised …