EpiRegio: analysis and retrieval of regulatory elements linked to genes

被引:9
作者
Baumgarten, Nina [1 ,2 ,3 ,4 ]
Hecker, Dennis [1 ,2 ,3 ]
Karunanithi, Sivarajan [1 ,2 ,3 ]
Schmidt, Florian [3 ,4 ,5 ]
List, Markus [6 ]
Schulz, Marcel H. [1 ,2 ,3 ,4 ]
机构
[1] Goethe Univ Hosp, Inst Cardiovasc Regenerat, D-60590 Frankfurt, Germany
[2] Goethe Univ Hosp, Cardiopulm Inst, D-60590 Frankfurt, Germany
[3] German Ctr Cardiovasc Res, Partner Site Rhein Main, D-60590 Frankfurt, Germany
[4] Saarland Informat Campus, Cluster Excellence Multimodal Comp & Interact, D-66123 Saarbrucken, Germany
[5] Genome Inst Singapore, 60 Biopolis St, Singapore 138672, Singapore
[6] Tech Univ Munich, Data BioMed Grp, Chair Expt Bioinformat, TUM Sch Life Sci, Maximus von Imhof Forum 3, D-85354 Freising Weihenstephan, Germany
关键词
ENHANCER; TRANSITION; DYNAMICS;
D O I
10.1093/nar/gkaa382
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
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/.
引用
收藏
页码:W193 / W199
页数:7
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