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Bioinformatics. 2016 Dec 1;32(23):3543-3551. Epub 2016 Aug 10.

EnhancerAtlas: a resource for enhancer annotation and analysis in 105 human cell/tissue types.

Gao T1, He B2,3, Liu S1, Zhu H4,5,6, Tan K2,3,7, Qian J1,4.

Author information

1
The Wilmer Eye Institute, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA.
2
Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.
3
Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.
4
The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA.
5
Department of Pharmacology and Molecular Science, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA.
6
Center for High-Throughput Biology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA.
7
Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.

Abstract

MOTIVATION:

Multiple high-throughput approaches have recently been developed and allowed the discovery of enhancers on a genome scale in a single experiment. However, the datasets generated from these approaches are not fully utilized by the research community due to technical challenges such as lack of consensus enhancer annotation and integrative analytic tools.

RESULTS:

We developed an interactive database, EnhancerAtlas, which contains an atlas of 2,534,123 enhancers for 105 cell/tissue types. A consensus enhancer annotation was obtained for each cell by summation of independent experimental datasets with the relative weights derived from a cross-validation approach. Moreover, EnhancerAtlas provides a set of useful analytic tools that allow users to query and compare enhancers in a particular genomic region or associated with a gene of interest, and assign enhancers and their target genes from a custom dataset.

AVAILABILITY AND IMPLEMENTATION:

The database with analytic tools is available at http://www.enhanceratlas.org/ CONTACT: jiang.qian@jhmi.edu or tank1@email.chop.eduSupplementary information: Supplementary data are available at Bioinformatics online.

PMID:
27515742
PMCID:
PMC5181530
DOI:
10.1093/bioinformatics/btw495
[Indexed for MEDLINE]
Free PMC Article

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