ArticleScientific reports2018
Identification of putative promoters in 48 eukaryotic genomes on the basis of DNA free energy.
Article in Scientific reports, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
24 citing papers in PubMed.
- Advancing bioinformatics with language models: components, applications, and perspectives.Briefings in bioinformatics · 2026Review
- DNA Sequence Perplexity Reveals Evolutionarily Conserved Patterns in cis-Regulatory Regions Across Diverse Species.Biochemical genetics · 2026Article
- Characterization of archaeal promoters using explainable and web-based CNN model.BMC genomics · 2025Article
- Article
- iProL: identifying DNA promoters from sequence information based on Longformer pre-trained model.BMC bioinformatics · 2024Article
- CDBProm: the Comprehensive Directory of Bacterial Promoters.NAR genomics and bioinformatics · 2024Article
- Physical Peculiarity of Two Sites in Human Promoters: Universality and Diverse Usage in Gene Function.International journal of molecular sciences · 2024Article
- DNA structural features and variability of complete MHC locus sequences.Frontiers in bioinformatics · 2024Review
- PromGER: Promoter Prediction Based on Graph Embedding and Ensemble Learning for Eukaryotic Sequence.Genes · 2023Article
- Transcriptome-based Mining of the Constitutive Promoters for Tuning Gene Expression in Aspergillus oryzae.Journal of microbiology (Seoul, Korea) · 2023Article
- Explainable artificial intelligence as a reliable annotator of archaeal promoter regions.Scientific reports · 2023Article
- Structural and functional analysis of stress-inducible genes and their promoters selected from young oil palm (Elaeis guineensis) under salt stress.BMC genomics · 2022Article
- Machine learning and statistics shape a novel path in archaeal promoter annotation.BMC bioinformatics · 2022Article
- Critical assessment of computational tools for prokaryotic and eukaryotic promoter prediction.Briefings in bioinformatics · 2022Article
- IMGTVaccines · 2022Article
- Article
- Genome-Wide Prediction of Transcription Start Sites in Conifers.International journal of molecular sciences · 2022Article
- Correlated Expression of the Opsin Retrogene LWS-R and its Host Gene in Two Poeciliid Fishes.Zoological studies · 2022Article
- TSSFinder-fast and accurate ab initio prediction of the core promoter in eukaryotic genomes.Briefings in bioinformatics · 2021Article
- Characterization of promoters in archaeal genomes based on DNA structural parameters.MicrobiologyOpen · 2021Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Transcription is an intricate mechanism and is orchestrated at the promoter region. The cognate motifs in the promoters are observed in only a subset of total genes across different domains of life. Hence, sequence-motif based promoter prediction may not be a holistic approach for whole genomes. Conversely, the DNA structural property, duplex stability is a characteristic of promoters and can be used to delineate them from other genomic sequences. In this study, we have used a DNA duplex stability based algorithm 'PromPredict' for promoter prediction in a broad range of eukaryotes, representing various species of yeast, worm, fly, fish, and mammal. Efficiency of the software has been tested in promoter regions of 48 eukaryotic systems. PromPredict achieves recall values, which range from 68 to 92% in various eukaryotes. PromPredict performs well in mammals, although their core promoter regions are GC rich. 'PromPredict' has also been tested for its ability to predict promoter regions for various transcript classes (coding and non-coding), TATA-containing and TATA-less promoters as well as on promoter sequences belonging to different gene expression variability categories. The results support the idea that differential DNA duplex stability is a potential predictor of promoter regions in various genomes.
Indexed as
Identifiers
What OpenQuestion holds
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.