ReviewMethods (San Diego, Calif.)2015
Computational schemes for the prediction and annotation of enhancers from epigenomic assays.
Review in Methods (San Diego, Calif.), 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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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.
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Who cites it
17 citing papers in PubMed.
- Article
- Predict long-range enhancer regulation based on protein-protein interactions between transcription factors.Nucleic acids research · 2021Article
- Functional effects of variation in transcription factor binding highlight long-range gene regulation by epromoters.Nucleic acids research · 2020Article
- Enhancer Domains Predict Gene Pathogenicity and Inform Gene Discovery in Complex Disease.American journal of human genetics · 2020Article
- Aberrant activation of CYR61 enhancers in colorectal cancer development.Journal of experimental & clinical cancer research : CR · 2019Article
- Applications of ENCODE data to Systematic Analyses via Data Integration.Current opinion in systems biology · 2018Article
- Systems biology in the central nervous system: a brief perspective on essential recent advancements.Current opinion in systems biology · 2017Article
- Transcription factor-associated combinatorial epigenetic pattern reveals higher transcriptional activity of TCF7L2-regulated intragenic enhancers.BMC genomics · 2017Article
- GeneHancer: genome-wide integration of enhancers and target genes in GeneCards.Database : the journal of biological databases and curation · 2017Article
- Review
- LBH Gene Transcription Regulation by the Interplay of an Enhancer Risk Allele and DNA Methylation in Rheumatoid Arthritis.Arthritis & rheumatology (Hoboken, N.J.) · 2016Article
- In silico identification of enhancers on the basis of a combination of transcription factor binding motif occurrences.Scientific reports · 2016Article
- Peak-valley-peak pattern of histone modifications delineates active regulatory elements and their directionality.Nucleic acids research · 2016Article
- Integrative genomic deconvolution of rheumatoid arthritis GWAS loci into gene and cell type associations.Genome biology · 2016Article
- Constructing 3D interaction maps from 1D epigenomes.Nature communications · 2016Article
- Demystifying the secret mission of enhancers: linking distal regulatory elements to target genes.Critical reviews in biochemistry and molecular biology · 2015Review
- Integrative omics analysis of rheumatoid arthritis identifies non-obvious therapeutic targets.PloS one · 2015Article
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
Identifying and annotating distal regulatory enhancers is critical to understand the mechanisms that control gene expression and cell-type-specific activities. Next-generation sequencing techniques have provided us an exciting toolkit of genome-wide assays that can be used to predict and annotate enhancers. However, each assay comes with its own specific set of analytical needs if enhancer prediction is to be optimal. Furthermore, integration of multiple genome-wide assays allows for different genomic features to be combined, and can improve predictive performance. Herein, we review the genome-wide assays and analysis schemes that are used to predict and annotate enhancers. In particular, we focus on three key computational topics: predicting enhancer locations, determining the cell-type-specific activity of enhancers, and linking enhancers to their target genes.
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