ArticleNucleic acids research2006
Identification of core promoter modules in Drosophila and their application in accurate transcription start site prediction.
Article in Nucleic acids research, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 73 papers.
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Who cites it
73 citing papers in PubMed, 113 citations in OpenAlex.
- Decoding promoter activity from DNA sequence using pre-trained language models.Scientific reports · 2026Article
- Characterization of core promoter activation by the Drosophila insulator-binding protein BEAF.Scientific reports · 2025Article
- Non-Random Distribution of EMS-Induced Mutations Reveals Preference for Open Chromatin and Expressed Genes in Rice.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Developmental and Housekeeping Genes: Two Types of Genetic Organization in theInternational journal of molecular sciences · 2024Review
- Identifying promoter sequence architectures via a chunking-based algorithm using non-negative matrix factorisation.PLoS computational biology · 2023Article
- Genomic benchmarks: a collection of datasets for genomic sequence classification.BMC genomic data · 2023Article
- Deep learning and support vector machines for transcription start site identification.PeerJ. Computer science · 2023Article
- Critical assessment of computational tools for prokaryotic and eukaryotic promoter prediction.Briefings in bioinformatics · 2022Article
- Large-scale analysis of Drosophila core promoter function using synthetic promoters.Molecular systems biology · 2022Article
- Computational identification and experimental characterization of preferred downstream positions in human core promoters.PLoS computational biology · 2021Article
- Computational identification of eukaryotic promoters based on cascaded deep capsule neural networks.Briefings in bioinformatics · 2021Article
- Episodes of Rapid Recovery of the Functional Activity of theFrontiers in genetics · 2021Article
- Embryonic tissue differentiation is characterized by transitions in cell cycle dynamic-associated core promoter regulation.Nucleic acids research · 2020Article
- Post-transcriptional modulation of cytochrome P450s, Cyp6g1 and Cyp6g2, by miR-310s cluster is associated with DDT-resistant Drosophila melanogaster strain 91-R.Scientific reports · 2020Article
- Predictive features of gene expression variation reveal mechanistic link with differential expression.Molecular systems biology · 2020Article
- Article
- iProEP: A Computational Predictor for Predicting Promoter.Molecular therapy. Nucleic acids · 2019Article
- Promoter-proximal pausing of RNA polymerase II: a nexus of gene regulation.Genes & development · 2019Review
- The landscape of transcription initiation across latent and lytic KSHV genomes.PLoS pathogens · 2019Article
- Integrative genomic analysis reveals novel regulatory mechanisms of eyeless during Drosophila eye development.Nucleic acids research · 2018Article
13 more citing papers are in PubMed but not listed here.
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1 author at 1 institution in 1 country.
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No grant is acknowledged in the PubMed record.
Abstract
The reliable recognition of eukaryotic RNA polymerase II core promoters, and the associated transcription start sites (TSSs) of genes, has been an ongoing challenge for computational biology. High throughput experimental methods such as tiling arrays or 5' SAGE/EST sequencing have recently lead to much larger datasets of core promoters, and to the assessment that the well-known core promoter sequence elements such as the TATA box appear to be much less frequent than thought. Here, we address the co-occurrence of several previously identified core promoter sequence motifs in Drosophila melanogaster to determine frequently occurring core promoter modules. We then use this in a new strategy to model core promoters as a set of alternative submodels for different core promoter architectures reflecting these different motif modules. We show that this system improves greatly on computational promoter recognition and leads to highly accurate in silico TSS prediction. Our results indicate that at least for the case of the fruit fly, we are getting closer to an understanding of how the beginning of a gene is defined in a eukaryotic genome.
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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.