Gene regulatory network inference resources: A practical overview
D Mercatelli, L Scalambra, L Triboli, F Ray… - Biochimica et Biophysica …, 2020 - Elsevier
Transcriptional regulation is a fundamental molecular mechanism involved in almost every
aspect of life, from homeostasis to development, from metabolism to behavior, from reaction …
aspect of life, from homeostasis to development, from metabolism to behavior, from reaction …
Inferring interaction networks from multi-omics data
A major goal in systems biology is a comprehensive description of the entirety of all complex
interactions between different types of biomolecules—also referred to as the interactome …
interactions between different types of biomolecules—also referred to as the interactome …
PlantTFDB 4.0: toward a central hub for transcription factors and regulatory interactions in plants
With the goal of providing a comprehensive, high-quality resource for both plant transcription
factors (TFs) and their regulatory interactions with target genes, we upgraded plant TF …
factors (TFs) and their regulatory interactions with target genes, we upgraded plant TF …
iTAK: a program for genome-wide prediction and classification of plant transcription factors, transcriptional regulators, and protein kinases
Transcription factors (TFs) are proteins that regulate the expression of target genes by
binding to specific cis-elements in promoter regions. Transcriptional regulators (TRs) also …
binding to specific cis-elements in promoter regions. Transcriptional regulators (TRs) also …
Alternative splicing landscapes in Arabidopsis thaliana across tissues and stress conditions highlight major functional differences with animals
Background Alternative splicing (AS) is a widespread regulatory mechanism in multicellular
organisms. Numerous transcriptomic and single-gene studies in plants have investigated AS …
organisms. Numerous transcriptomic and single-gene studies in plants have investigated AS …
PlantTFDB 3.0: a portal for the functional and evolutionary study of plant transcription factors
With the aim to provide a resource for functional and evolutionary study of plant transcription
factors (TFs), we updated the plant TF database PlantTFDB to version 3.0 (http://planttfdb …
factors (TFs), we updated the plant TF database PlantTFDB to version 3.0 (http://planttfdb …
PlantPAN 2.0: an update of plant promoter analysis navigator for reconstructing transcriptional regulatory networks in plants
CN Chow, HQ Zheng, NY Wu, CH Chien… - Nucleic acids …, 2016 - academic.oup.com
Transcription factors (TFs) are sequence-specific DNA-binding proteins acting as critical
regulators of gene expression. The Plant P romoter A nalysis N avigator (PlantPAN; …
regulators of gene expression. The Plant P romoter A nalysis N avigator (PlantPAN; …
Temporal transcriptome profiling reveals expression partitioning of homeologous genes contributing to heat and drought acclimation in wheat (Triticum aestivum L.)
Z Liu, M Xin, J Qin, H Peng, Z Ni, Y Yao, Q Sun - BMC plant biology, 2015 - Springer
Abstract Background Hexaploid wheat (Triticum aestivum) is a globally important crop. Heat,
drought and their combination dramatically reduce wheat yield and quality, but the …
drought and their combination dramatically reduce wheat yield and quality, but the …
ChIP-Hub provides an integrative platform for exploring plant regulome
Plant genomes encode a complex and evolutionary diverse regulatory grammar that forms
the basis for most life on earth. A wealth of regulome and epigenome data have been …
the basis for most life on earth. A wealth of regulome and epigenome data have been …
Temporal transcriptional response to ethylene gas drives growth hormone cross-regulation in Arabidopsis
The gaseous plant hormone ethylene regulates a multitude of growth and developmental
processes. How the numerous growth control pathways are coordinated by the ethylene …
processes. How the numerous growth control pathways are coordinated by the ethylene …