ArticleGenome research2009
High-resolution human core-promoter prediction with CoreBoost_HM.
Article in Genome research, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 57 papers.
What it found
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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.
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Who cites it
57 citing papers in PubMed, 106 citations in OpenAlex.
- Review
- PromGER: Promoter Prediction Based on Graph Embedding and Ensemble Learning for Eukaryotic Sequence.Genes · 2023Article
- Critical assessment of computational tools for prokaryotic and eukaryotic promoter prediction.Briefings in bioinformatics · 2022Article
- Assessing the functional association of intronic miRNAs with their host genes.RNA (New York, N.Y.) · 2018Article
- MicroRNA duplication accelerates the recruitment of new targets during vertebrate evolution.RNA (New York, N.Y.) · 2018Article
- DNA methylation regulates discrimination of enhancers from promoters through a H3K4me1-H3K4me3 seesaw mechanism.BMC genomics · 2017Article
- Functional polymorphisms in the promoter region of miR-17-92 cluster are associated with a decreased risk of colorectal cancer.Oncotarget · 2017Article
- Identification of active miRNA promoters from nuclear run-on RNA sequencing.Nucleic acids research · 2017Article
- Novel promoters and coding first exons in DLG2 linked to developmental disorders and intellectual disability.Genome medicine · 2017Article
- Methods of MicroRNA Promoter Prediction and Transcription Factor Mediated Regulatory Network.BioMed research international · 2017Review
- microRNAs in the Same Clusters Evolve to Coordinately Regulate Functionally Related Genes.Molecular biology and evolution · 2016Article
- MicroRNA Promoter Identification in Arabidopsis Using Multiple Histone Markers.BioMed research international · 2015Article
- Article
- Large-scale modeling of condition-specific gene regulatory networks by information integration and inference.Nucleic acids research · 2014Article
- Characterizing the Retinoblastoma 1 locus: putative elements for Rb1 regulation by in silico analysis.Frontiers in genetics · 2014Article
- Biogenesis of intronic miRNAs located in clusters by independent transcription and alternative splicing.RNA (New York, N.Y.) · 2014Article
- Rule-based knowledge acquisition method for promoter prediction in human and Drosophila species.TheScientificWorldJournal · 2014Article
- Nonparametric Bayesian Bi-Clustering for Next Generation Sequencing Count Data.Bayesian analysis · 2013Article
- Regulation of microRNA biogenesis and turnover by animals and their viruses.Cellular and molecular life sciences : CMLS · 2013Review
- PROmiRNA: a new miRNA promoter recognition method uncovers the complex regulation of intronic miRNAs.Genome biology · 2013Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors at 2 institutions in 2 countries.
Funding
Abstract
Correctly locating the gene transcription start site and the core-promoter is important for understanding transcriptional regulation mechanism. Here we have integrated specific genome-wide histone modification and DNA sequence features together to predict RNA polymerase II core-promoters in the human genome. Our new predictor CoreBoost_HM outperforms existing promoter prediction algorithms by providing significantly higher sensitivity and specificity at high resolution. We demonstrated that even though the histone modification data used in this study are from a specific cell type (CD4+ T-cell), our method can be used to identify both active and repressed promoters. We have applied it to search the upstream regions of microRNA genes, and show that CoreBoost_HM can accurately identify the known promoters of the intergenic microRNAs. We also identified a few intronic microRNAs that may have their own promoters. This result suggests that our new method can help to identify and characterize the core-promoters of both coding and noncoding genes.
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.