ArticleNucleic acids research2020
EpiRegio: analysis and retrieval of regulatory elements linked to genes.
Article in Nucleic acids research, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed, 35 citations in OpenAlex.
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- CVD-associated SNPs with regulatory potential reveal novel non-coding disease genes.Human genomics · 2023Article
- The endothelial-enriched lncRNA LINC00607 mediates angiogenic function.Basic research in cardiology · 2023Article
- Multimodal analysis methods in predictive biomedicine.Computational and structural biotechnology journal · 2023Review
- De novo annotation of lncRNA HOTAIR transcripts by long-read RNA capture-seq reveals a differentiation-driven isoform switch.BMC genomics · 2022Article
- Nuclear receptor activation shapes spatial genome organization essential for gene expression control: lessons learned from the vitamin D receptor.Nucleic acids research · 2022Article
- Multivariate genomic and transcriptomic determinants of imaging-derived personalized therapeutic needs in Parkinson's disease.Scientific reports · 2022Article
- Integrative analysis of epigenetics data identifies gene-specific regulatory elements.Nucleic acids research · 2021Article
- Clinical epigenetics settings for cancer and cardiovascular diseases: real-life applications of network medicine at the bedside.Clinical epigenetics · 2021Review
- A hierarchical regulatory network analysis of the vitamin D induced transcriptome reveals novel regulators and complete VDR dependency in monocytes.Scientific reports · 2021Article
- Single cell sequencing reveals endothelial plasticity with transient mesenchymal activation after myocardial infarction.Nature communications · 2021Article
- HRT Atlas v1.0 database: redefining human and mouse housekeeping genes and candidate reference transcripts by mining massive RNA-seq datasets.Nucleic acids research · 2021Article
- ATACdb: a comprehensive human chromatin accessibility database.Nucleic acids research · 2021Article
Corrections and comments
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Authors and funding
6 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
A current challenge in genomics is to interpret non-coding regions and their role in transcriptional regulation of possibly distant target genes. Genome-wide association studies show that a large part of genomic variants are found in those non-coding regions, but their mechanisms of gene regulation are often unknown. An additional challenge is to reliably identify the target genes of the regulatory regions, which is an essential step in understanding their impact on gene expression. Here we present the EpiRegio web server, a resource of regulatory elements (REMs). REMs are genomic regions that exhibit variations in their chromatin accessibility profile associated with changes in expression of their target genes. EpiRegio incorporates both epigenomic and gene expression data for various human primary cell types and tissues, providing an integrated view of REMs in the genome. Our web server allows the analysis of genes and their associated REMs, including the REM's activity and its estimated cell type-specific contribution to its target gene's expression. Further, it is possible to explore genomic regions for their regulatory potential, investigate overlapping REMs and by that the dissection of regions of large epigenomic complexity. EpiRegio allows programmatic access through a REST API and is freely available at https://epiregio.de/.
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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.