ArticleNucleic acids research2018
TF2Network: predicting transcription factor regulators and gene regulatory networks in Arabidopsis using publicly available binding site information.
Article in Nucleic acids research, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 72 papers, 1 of them a synthesis that pooled it.
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72 citing papers in PubMed, 1 synthesis or guideline pooled it, 144 citations in OpenAlex.
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- SeedMatExplorer: the transcriptome atlas of Arabidopsis seed maturation.BMC plant biology · 2026Article
- Deciphering acclimation to sublethal combined and sequential abiotic stresses in Arabidopsis thaliana.Plant physiology · 2026Article
- Integrated Gene Regulatory Network Analysis Reveals Coordinated Transcriptional Reprogramming in thePlants (Basel, Switzerland) · 2026Article
- Loss of the plastidial signaling molecule, ppGpp, accumulation alters nuclear gene expression during nitrogen starvation.Frontiers in plant science · 2026Article
- A Practical Guide to Gene Regulatory Networks in Plants: From RNA Sequencing to Identification of Transcription Factor Binding Sites.Methods in molecular biology (Clifton, N.J.) · 2026Article
- INTACT-based guard cell transcriptomes from a progressive drought time course reveal targets for modifying stomatal responses.The Plant cell · 2025Article
- An Introduction to Network Analysis in Plant Biology.Plant direct · 2025Article
- A map of integrated cis-regulatory elements enhances gene-regulatory analysis in maize.Plant communications · 2025Article
- Characterization and functional analysis of conserved non-coding sequences among poaceae: insights into gene regulation and phenotypic variation in maize.BMC genomics · 2025Article
- BADDADAN: Mechanistic modelling of time-series gene module expression.Quantitative plant biology · 2025Article
- Weighted gene co-expression network analysis identifies functional modules related to bovine respiratory disease.PloS one · 2025Article
- A Model for the Gene Regulatory Network Along the Arabidopsis Fruit Medio-Lateral Axis: Rewiring the Pod Shatter Process.Plants (Basel, Switzerland) · 2024Article
- Arabidopsis transcription factor ANAC102 predominantly expresses a nuclear protein and acts as a negative regulator of methyl viologen-induced oxidative stress responses.Journal of experimental botany · 2024Article
- Integrative phenotyping analyses reveal the relevance of the phyB-PIF4 pathway in Arabidopsis thaliana reproductive organs at high ambient temperature.BMC plant biology · 2024Article
- Computational Reconstruction of the Transcription Factor Regulatory Network Induced by Auxin inPlants (Basel, Switzerland) · 2024Article
- Identification of Novel Regulators of Leaf Senescence Using a Deep Learning Model.Plants (Basel, Switzerland) · 2024Article
- Transcription Factors behindPlants (Basel, Switzerland) · 2024Article
- Identification of gene biomarkers for brain diseases via multi-network topological semantics extraction and graph convolutional network.BMC genomics · 2024Article
12 more citing papers are in PubMed but not listed here.
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Authors and funding
4 authors at 2 institutions in 1 country.
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No grant is acknowledged in the PubMed record.
Abstract
A gene regulatory network (GRN) is a collection of regulatory interactions between transcription factors (TFs) and their target genes. GRNs control different biological processes and have been instrumental to understand the organization and complexity of gene regulation. Although various experimental methods have been used to map GRNs in Arabidopsis thaliana, their limited throughput combined with the large number of TFs makes that for many genes our knowledge about regulating TFs is incomplete. We introduce TF2Network, a tool that exploits the vast amount of TF binding site information and enables the delineation of GRNs by detecting potential regulators for a set of co-expressed or functionally related genes. Validation using two experimental benchmarks reveals that TF2Network predicts the correct regulator in 75-92% of the test sets. Furthermore, our tool is robust to noise in the input gene sets, has a low false discovery rate, and shows a better performance to recover correct regulators compared to other plant tools. TF2Network is accessible through a web interface where GRNs are interactively visualized and annotated with various types of experimental functional information. TF2Network was used to perform systematic functional and regulatory gene annotations, identifying new TFs involved in circadian rhythm and stress response.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.