ArticleBioinformatics (Oxford, England)2024
ElemeNT 2023: an enhanced tool for detection and curation of core promoter elements.
Article in Bioinformatics (Oxford, England), 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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Who cites it
6 citing papers in PubMed.
- A systematic guide for identifying transcription factors that directly regulate the expression of a gene of interest.Genome research · 2026Review
- Heterogeneous NF-κB activation and enhancer features shape transcription in Drosophila immunity.Biophysical journal · 2026Article
- Dual promoter-enhancer activities reflect a unified regulatory logic.Nature communications · 2026Article
- RegRNA 3.0: expanding regulatory RNA analysis with new features for motif, interaction, and annotation.Nucleic acids research · 2025Article
- Heterogeneous NF-κB activation and enhancer features shape transcription inbioRxiv : the preprint server for biology · 2025Article
- Transcriptional induction by ecdysone in Drosophila salivary glands involves an increase in chromatin accessibility and acetylation.Nucleic acids research · 2025Article
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Authors and funding
8 authors.
Funding
Abstract
motivationPrediction and identification of core promoter elements and transcription factor binding sites is essential for understanding the mechanism of transcription initiation and deciphering the biological activity of a specific locus. Thus, there is a need for an up-to-date tool to detect and curate core promoter elements/motifs in any provided nucleotide sequences.
resultsHere, we introduce ElemeNT 2023-a new and enhanced version of the Elements Navigation Tool, which provides novel capabilities for assessing evolutionary conservation and for readily evaluating the quality of high-throughput transcription start site (TSS) datasets, leveraging preferential motif positioning. ElemeNT 2023 is accessible both as a fast web-based tool and via command line (no coding skills are required to run the tool). While this tool is focused on core promoter elements, it can also be used for searching any user-defined motif, including sequence-specific DNA binding sites. Furthermore, ElemeNT's CORE database, which contains predicted core promoter elements around annotated TSSs, is now expanded to cover 10 species, ranging from worms to human. In this applications note, we describe the new workflow and demonstrate a case study using ElemeNT 2023 for core promoter composition analysis of diverse species, revealing motif prevalence and highlighting evolutionary insights. We discuss how this tool facilitates the exploration of uncharted transcriptomic data, appraises TSS quality, and aids in designing synthetic promoters for gene expression optimization. Taken together, ElemeNT 2023 empowers researchers with comprehensive tools for meticulous analysis of sequence elements and gene expression strategies. AVAILABILITY AND IMPLEMENTATION: ElemeNT 2023 is freely available at https://www.juven-gershonlab.org/resources/element-v2023/. The source code and command line version of ElemeNT 2023 are available at https://github.com/OritAdato/ElemeNT. No coding skills are required to run the tool.
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