EnhancerAtlas

A resource for enhancer annotation and analysis in 105 human cell/tissue types

Tianshun Gao, Bing He, Sheng Liu, Heng Zhu, Kai Tan, Jiang Qian

Research output: Contribution to journalArticle

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.

Original languageEnglish (US)
Pages (from-to)3543-3551
Number of pages9
JournalBioinformatics
Volume32
Issue number23
DOIs
StatePublished - 2016

Fingerprint

Annotation
Genes
Cells
Tissue
Gene
Resources
Atlas
Cell
Cross-validation
Summation
High Throughput
Genomics
Assign
Genome
Atlases
Query
Target
Throughput
Databases
Experiment

ASJC Scopus subject areas

  • Statistics and Probability
  • Medicine(all)
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Computational Theory and Mathematics
  • Computational Mathematics

Cite this

EnhancerAtlas : A resource for enhancer annotation and analysis in 105 human cell/tissue types. / Gao, Tianshun; He, Bing; Liu, Sheng; Zhu, Heng; Tan, Kai; Qian, Jiang.

In: Bioinformatics, Vol. 32, No. 23, 2016, p. 3543-3551.

Research output: Contribution to journalArticle

Gao, Tianshun ; He, Bing ; Liu, Sheng ; Zhu, Heng ; Tan, Kai ; Qian, Jiang. / EnhancerAtlas : A resource for enhancer annotation and analysis in 105 human cell/tissue types. In: Bioinformatics. 2016 ; Vol. 32, No. 23. pp. 3543-3551.
@article{5874f3a6fee147349a6ec8f0be5b6ed7,
title = "EnhancerAtlas: A resource for enhancer annotation and analysis in 105 human cell/tissue types",
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.",
author = "Tianshun Gao and Bing He and Sheng Liu and Heng Zhu and Kai Tan and Jiang Qian",
year = "2016",
doi = "10.1093/bioinformatics/btw495",
language = "English (US)",
volume = "32",
pages = "3543--3551",
journal = "Bioinformatics",
issn = "1367-4803",
publisher = "Oxford University Press",
number = "23",

}

TY - JOUR

T1 - EnhancerAtlas

T2 - A resource for enhancer annotation and analysis in 105 human cell/tissue types

AU - Gao, Tianshun

AU - He, Bing

AU - Liu, Sheng

AU - Zhu, Heng

AU - Tan, Kai

AU - Qian, Jiang

PY - 2016

Y1 - 2016

N2 - 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.

AB - 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.

UR - http://www.scopus.com/inward/record.url?scp=85016229211&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85016229211&partnerID=8YFLogxK

U2 - 10.1093/bioinformatics/btw495

DO - 10.1093/bioinformatics/btw495

M3 - Article

VL - 32

SP - 3543

EP - 3551

JO - Bioinformatics

JF - Bioinformatics

SN - 1367-4803

IS - 23

ER -