ArticleProceedings of the National Academy of Sciences of the United States of America2017
Improved regulatory element prediction based on tissue-specific local epigenomic signatures.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 43 papers.
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Who cites it
43 citing papers in PubMed.
- Mapping cis- and trans-regulatory target genes of human-specific deletions.Nature communications · 2025Article
- Pig-eRNAdb: a comprehensive enhancer and eRNA dataset of pigs.Scientific data · 2024Article
- Mapping Chromatin Occupancy ofCells · 2023Article
- Mapping Chromatin Occupancy ofbioRxiv : the preprint server for biology · 2023Article
- Robust enhancer-gene regulation identified by single-cell transcriptomes and epigenomes.Cell genomics · 2023Article
- Computational methods for identifying enhancer-promoter interactions.Quantitative biology (Beijing, China) · 2023Review
- Deciphering transcription factors and their corresponding regulatory elements during inhibitory interneuron differentiation using deep neural networks.Frontiers in cell and developmental biology · 2023Article
- Accurate prediction of functional states of cis-regulatory modules reveals common epigenetic rules in humans and mice.BMC biology · 2022Article
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- ReFeaFi: Genome-wide prediction of regulatory elements driving transcription initiation.PLoS computational biology · 2021Article
- MOSTWAS: Multi-Omic Strategies for Transcriptome-Wide Association Studies.PLoS genetics · 2021Article
- A pitfall for machine learning methods aiming to predict across cell types.Genome biology · 2020Article
- Long-range chromatin interactions in pathogenic gene expression control.Transcription · 2020Review
- Supervised enhancer prediction with epigenetic pattern recognition and targeted validation.Nature methods · 2020Article
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- Article
- CAMIO: a transgenic CRISPR pipeline to create diverse targeted genome deletions in Drosophila.Nucleic acids research · 2020Article
- Integrative prediction of gene expression with chromatin accessibility and conformation data.Epigenetics & chromatin · 2020Article
- A curated benchmark of enhancer-gene interactions for evaluating enhancer-target gene prediction methods.Genome biology · 2020Article
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Authors and funding
11 authors.
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Abstract
Accurate enhancer identification is critical for understanding the spatiotemporal transcriptional regulation during development as well as the functional impact of disease-related noncoding genetic variants. Computational methods have been developed to predict the genomic locations of active enhancers based on histone modifications, but the accuracy and resolution of these methods remain limited. Here, we present an algorithm, regulatory element prediction based on tissue-specific local epigenetic marks (REPTILE), which integrates histone modification and whole-genome cytosine DNA methylation profiles to identify the precise location of enhancers. We tested the ability of REPTILE to identify enhancers previously validated in reporter assays. Compared with existing methods, REPTILE shows consistently superior performance across diverse cell and tissue types, and the enhancer locations are significantly more refined. We show that, by incorporating base-resolution methylation data, REPTILE greatly improves upon current methods for annotation of enhancers across a variety of cell and tissue types. REPTILE is available at https://github.com/yupenghe/REPTILE/.
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