ArticlePlant physiology2021
ConnecTF: A platform to integrate transcription factor-gene interactions and validate regulatory networks.
Article in Plant physiology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
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Who cites it
34 citing papers in PubMed, 57 citations in OpenAlex.
- Context matters: coordinated transcriptional regulation and root plasticity under multinutrient conditions.The New phytologist · 2026Article
- HHO5 orchestrates dose-dependent feedback regulation of organic versus inorganic nitrogen signaling in Arabidopsis.The Plant cell · 2026Article
- Integrated Gene Regulatory Network Analysis Reveals Coordinated Transcriptional Reprogramming in thePlants (Basel, Switzerland) · 2026Article
- Antagonistic regulation of nitrogen and drought signaling mediated by NIN-like protein 7 transcription factor inProceedings of the National Academy of Sciences of the United States of America · 2026Article
- Synthetic promoter design in plants: integration of computational and experimental approaches.Frontiers in plant science · 2026Review
- Chromatin state architecture governs transcription factor accessibility across plant genomes.PLoS genetics · 2026Article
- From binding to networks: methods for identifying transcription factor targets in plant systems.Frontiers in plant science · 2026Review
- A map of integrated cis-regulatory elements enhances gene-regulatory analysis in maize.Plant communications · 2025Article
- Chromatin accessibility dynamics and transcriptional regulatory networks underlying the primary nitrogen response in rice roots.Plant communications · 2025Article
- Conservation and divergence of regulatory architecture in nitrate-responsive plant gene circuits.The Plant cell · 2025Article
- Model-to-crop conserved NUE Regulons enhance machine learning predictions of nitrogen use efficiency.The Plant cell · 2025Article
- Shining light on Arabidopsis regulatory networks integrating nitrogen use and photosynthesis.The Plant journal : for cell and molecular biology · 2025Article
- Fruit sugar hub: gene regulatory network associated with soluble solids content (SSC) in Prunus persica.Biological research · 2024Article
- Identification of Novel Regulators of Leaf Senescence Using a Deep Learning Model.Plants (Basel, Switzerland) · 2024Article
- Nitrogen sensing and regulatory networks: it's about time and space.The Plant cell · 2024Review
- Organ-delimited gene regulatory networks provide high accuracy in candidate transcription factor selection across diverse processes.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Bipartite networks represent causality better than simple networks: evidence, algorithms, and applications.Frontiers in genetics · 2024Article
- Recent advances in exploring transcriptional regulatory landscape of crops.Frontiers in plant science · 2024Review
- Voice from both sides: a molecular dialogue between transcriptional activators and repressors in seed-to-seedling transition and crop adaptation.Frontiers in plant science · 2024Review
- Phloem-MobilePlants (Basel, Switzerland) · 2023Article
Corrections and comments
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Authors and funding
10 authors at 4 institutions in 2 countries.
Funding
Abstract
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 organism to react to changes in its environment. The challenge lies in validating GRNs that involve hundreds of TFs with hundreds of thousands of interactions with their genome-wide targets experimentally determined by high-throughput sequencing. To address this challenge, we developed ConnecTF, a species-independent, web-based platform that integrates genome-wide studies of TF-target binding, TF-target regulation, and other TF-centric omic datasets and uses these to build and refine validated or inferred GRNs. We demonstrate the functionality of ConnecTF by showing how integration within and across TF-target datasets uncovers biological insights. Case study 1 uses integration of TF-target gene regulation and binding datasets to uncover TF mode-of-action and identify potential TF partners for 14 TFs in abscisic acid signaling. Case study 2 demonstrates how genome-wide TF-target data and automated functions in ConnecTF are used in precision/recall analysis and pruning of an inferred GRN for nitrogen signaling. Case study 3 uses ConnecTF to chart a network path from NLP7, a master TF in nitrogen signaling, to direct secondary TF2s and to its indirect targets in a Network Walking approach. The public version of ConnecTF (https://ConnecTF.org) contains 3,738,278 TF-target interactions for 423 TFs in Arabidopsis, 839,210 TF-target interactions for 139 TFs in maize (Zea mays), and 293,094 TF-target interactions for 26 TFs in rice (Oryza sativa). The database and tools in ConnecTF will advance the exploration of GRNs in plant systems biology applications for model and crop species.
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Registered trials
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.