ArticleThe Plant journal : for cell and molecular biology2022
TDTHub, a web server tool for the analysis of transcription factor binding sites in plants.
Article in The Plant journal : for cell and molecular biology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed, 24 citations in OpenAlex.
- 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
- A map of integrated cis-regulatory elements enhances gene-regulatory analysis in maize.Plant communications · 2025Article
- Proteomic profiling reveals important regulators of photosynthate accumulation in wheat leaves during grain development.BMC plant biology · 2025Article
- Advances in Protein Kinase Regulation of Stress Responses in Fruits and Vegetables.International journal of molecular sciences · 2025Review
- The evaluation of transcription factor binding site prediction tools in human and Arabidopsis genomes.BMC bioinformatics · 2024Article
- The landscape of transcription factor promoter activity during vegetative development in Marchantia.The Plant cell · 2024Article
- Bioinformatic Analysis for Identifying Transcription Factors Involved in Protein Secretion and Vacuole Formation.Methods in molecular biology (Clifton, N.J.) · 2024Article
- From qualitative to quantitative: the state of the art and challenges for plant synthetic biology.Quantitative biology (Beijing, China) · 2023Review
- A translatome-transcriptome multi-omics gene regulatory network reveals the complicated functional landscape of maize.Genome biology · 2023Article
- TSPTFBS 2.0: trans-species prediction of transcription factor binding sites and identification of their core motifs in plants.Frontiers in plant science · 2023Article
- Genome-wide identification of BBX gene family and their expression patterns under salt stress in soybean.BMC genomics · 2022Article
- Decoding complexity: tackling the challenge of how many transcription factors regulate a plant gene.TranscriptionReview
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Authors and funding
2 authors at 1 institution in 1 country.
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Abstract
Transcriptional regulation underlies most developmental programs and physiological responses to environmental changes in plants. Transcription factors (TFs) play a key role in the regulation of gene expression by binding specifically to short DNA sequences in the regulatory regions of genes: the TF binding sites (TFBSs). In recent years, several bioinformatic tools have been developed to detect TFBSs in candidate genes, either by de novo prediction or by directly mapping experimentally known TFBSs. However, most of these tools contain information for only a few species or require multi-step procedures, and are not always intuitive for non-experienced researchers. Here we present TFBS-Discovery Tool Hub (TDTHub), a web server for quick and intuitive studies of transcriptional regulation in plants. TDTHub uses pre-computed TFBSs in 40 plant species and allows the choice of two mapping algorithms, providing a higher versatility. Besides the main TFBS enrichment tool, TDTHub includes additional tools to assist in the analysis and visualization of data. In order to demonstrate the effectiveness of TDTHub, we analyzed the transcriptional regulation of the anthocyanin biosynthesis pathway. We also analyzed the transcriptional cascades in response to jasmonate and wounding in Arabidopsis and tomato (Solanum lycopersicum), respectively. In these studies, TDTHub helped to verify the most relevant TF nodes and to propose new ones with a prominent role in these pathways. TDTHub is available at http://acrab.cnb.csic.es/TDTHub/, and it will be periodically upgraded and expanded for new species and gene annotations.
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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.