ArticleNucleic acids research2017
TSSPlant: a new tool for prediction of plant Pol II promoters.
Article in Nucleic acids research, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 61 papers.
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61 citing papers in PubMed, 126 citations in OpenAlex.
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- A systematic guide for identifying transcription factors that directly regulate the expression of a gene of interest.Genome research · 2026Review
- Synthetic Biology of Plants and Microbes for Agriculture, Environment, and Future Applications.Chemical reviews · 2026Review
- TEITbase: a database for transposable element (TE)-initiated transcripts in human cancers.Database : the journal of biological databases and curation · 2026Article
- Transcription start site aware catalogue of microRNA encoded peptides in tomato (Solanum lycopersicum).Discover plants · 2026Article
- Functional Characterization of a Root-Preferential and Stress-Inducible Promoter of Eca-miR482f inPlants (Basel, Switzerland) · 2025Article
- Genetic Variability of Gene Expression in Tomato Fruits Ripened on and off the Vine: Cis-Regulatory Elements Associated with Differential Transcription Patterns in the Most Discrepant Variety.Plants (Basel, Switzerland) · 2025Article
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- Characterization of archaeal promoters using explainable and web-based CNN model.BMC genomics · 2025Article
- Innovations, Challenges and Future Directions of T7RNA Polymerase in Microbial Cell Factories.ACS synthetic biology · 2025Review
- Harnessing promoter elements to enhance gene editing in plants: perspectives and advances.Plant biotechnology journal · 2025Review
- Recent advances in designing synthetic plant regulatory modules.Frontiers in plant science · 2025Review
- CRISPR-Activation: Boosting Expression of Plant MIRs.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Noncanonical transcription initiation is primarily tissue specific and epigenetically tuned in paleopolyploid plants.The Plant cell · 2024Article
- Detection and classification of long terminal repeat sequences in plant LTR-retrotransposons and their analysis using explainable machine learning.BioData mining · 2024Article
- Identification of CAP genes in finger lime (Citrus australasica) and their role in plant responses to abiotic and biotic stress.Scientific reports · 2024Article
- Isolation and Characterization ofPlants (Basel, Switzerland) · 2023Article
- From qualitative to quantitative: the state of the art and challenges for plant synthetic biology.Quantitative biology (Beijing, China) · 2023Review
1 more citing papers are in PubMed but not listed here.
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Our current knowledge of eukaryotic promoters indicates their complex architecture that is often composed of numerous functional motifs. Most of known promoters include multiple and in some cases mutually exclusive transcription start sites (TSSs). Moreover, TSS selection depends on cell/tissue, development stage and environmental conditions. Such complex promoter structures make their computational identification notoriously difficult. Here, we present TSSPlant, a novel tool that predicts both TATA and TATA-less promoters in sequences of a wide spectrum of plant genomes. The tool was developed by using large promoter collections from ppdb and PlantProm DB. It utilizes eighteen significant compositional and signal features of plant promoter sequences selected in this study, that feed the artificial neural network-based model trained by the backpropagation algorithm. TSSPlant achieves significantly higher accuracy compared to the next best promoter prediction program for both TATA promoters (MCC≃0.84 and F1-score≃0.91 versus MCC≃0.51 and F1-score≃0.71) and TATA-less promoters (MCC≃0.80, F1-score≃0.89 versus MCC≃0.29 and F1-score≃0.50). TSSPlant is available to download as a standalone program at http://www.cbrc.kaust.edu.sa/download/.
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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.