dbSUPER: a database of super-enhancers in mouse and human genome

被引：289

作者：

Khan, Aziz ^{[1
,2
]}

Zhang, Xuegong ^{[1
,2
,3
]}

机构：

[1] Tsinghua Univ, Bioinformat Div, MOE Key Lab Bioinformat, Beijing 100084, Peoples R China

[2] Tsinghua Univ, Ctr Synthet & Syst Biol, TNLIST Dept Automat, Beijing 100084, Peoples R China

[3] Tsinghua Univ, Sch Life Sci, Beijing 100084, Peoples R China

来源：

NUCLEIC ACIDS RESEARCH | 2016年 / 44卷 / D1期

关键词：

CELL IDENTITY; TRANSCRIPTION; GENE; CANCER; EXPRESSION; DYNAMICS;

D O I：

10.1093/nar/gkv1002

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：

Super-enhancers are clusters of transcriptional enhancers that drive cell-type-specific gene expression and are crucial to cell identity. Many disease-associated sequence variations are enriched in super-enhancer regions of disease-relevant cell types. Thus, super-enhancers can be used as potential biomarkers for disease diagnosis and therapeutics. Current studies have identified super-enhancers in more than 100 cell types and demonstrated their functional importance. However, a centralized resource to integrate all these findings is not currently available. We developed dbSUPER (http://bioinfo.au.tsinghua.edu.cn/dbsuper/), the first integrated and interactive database of super-enhancers, with the primary goal of providing a resource for assistance in further studies related to transcriptional control of cell identity and disease. dbSUPER provides a responsive and user-friendly web interface to facilitate efficient and comprehensive search and browsing. The data can be easily sent to Galaxy instances, GREAT and Cistrome web-servers for downstream analysis, and can also be visualized in the UCSC genome browser where custom tracks can be added automatically. The data can be downloaded and exported in variety of formats. Furthermore, dbSUPER lists genes associated with super-enhancers and also links to external databases such as GeneCards, UniProt and Entrez. dbSUPER also provides an overlap analysis tool to annotate user-defined regions. We believe dbSUPER is a valuable resource for the biology and genetic research communities.

引用

页码：D164 / D171

页数：8

共 51 条

[1] Re-Place Your BETs: The Dynamics of Super Enhancers [J].

Amaral, Paulo P. ;

Bannister, Andrew J. .

MOLECULAR CELL, 2014, 56 (02) :187-189

[2] Treating Transcriptional Addiction in Small Cell Lung Cancer [J].

Augert, Arnaud ;

MacPherson, David .

CANCER CELL, 2014, 26 (06) :783-784

[3] EXPRESSION OF A BETA-GLOBIN GENE IS ENHANCED BY REMOTE SV40 DNA-SEQUENCES [J].

BANERJI, J ;

RUSCONI, S ;

SCHAFFNER, W .

CELL, 1981, 27 (02) :299-308

[4] UniProt: a hub for protein information [J].

Bateman, Alex ;

Martin, Maria Jesus ;

O'Donovan, Claire ;

Magrane, Michele ;

Apweiler, Rolf ;

Alpi, Emanuele ;

Antunes, Ricardo ;

Arganiska, Joanna ;

Bely, Benoit ;

Bingley, Mark ;

Bonilla, Carlos ;

Britto, Ramona ;

Bursteinas, Borisas ;

Chavali, Gayatri ;

Cibrian-Uhalte, Elena ;

Da Silva, Alan ;

De Giorgi, Maurizio ;

Dogan, Tunca ;

Fazzini, Francesco ;

Gane, Paul ;

Cas-tro, Leyla Garcia ;

Garmiri, Penelope ;

Hatton-Ellis, Emma ;

Hieta, Reija ;

Huntley, Rachael ;

Legge, Duncan ;

Liu, Wudong ;

Luo, Jie ;

MacDougall, Alistair ;

Mutowo, Prudence ;

Nightin-gale, Andrew ;

Orchard, Sandra ;

Pichler, Klemens ;

Poggioli, Diego ;

Pundir, Sangya ;

Pureza, Luis ;

Qi, Guoying ;

Rosanoff, Steven ;

Saidi, Rabie ;

Sawford, Tony ;

Shypitsyna, Aleksandra ;

Turner, Edward ;

Volynkin, Vladimir ;

Wardell, Tony ;

Watkins, Xavier ;

Zellner, Hermann ;

Cowley, Andrew ;

Figueira, Luis ;

Li, Weizhong ;

McWilliam, Hamish .

NUCLEIC ACIDS RESEARCH, 2015, 43 (D1) :D204-D212

[5] Integrating diverse databases into an unified analysis framework: a Galaxy approach [J].

Blankenberg, Daniel ;

Coraor, Nathan ;

Von Kuster, Gregory ;

Taylor, James ;

Nekrutenko, Anton .

DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION, 2011,

[6] NF-κB Directs Dynamic Super Enhancer Formation in Inflammation and Atherogenesis [J].

Brown, Jonathan D. ;

Lin, Charles Y. ;

Duan, Qiong ;

Griffin, Gabriel ;

Federation, Alexander J. ;

Paranal, Ronald M. ;

Bair, Steven ;

Newton, Gail ;

Lichtman, Andrew H. ;

Kung, Andrew L. ;

Yang, Tianlun ;

Wang, Hong ;

Luscinskas, Francis W. ;

Croce, Kevin J. ;

Bradner, James E. ;

Plutzky, Jorge .

MOLECULAR CELL, 2014, 56 (02) :219-231

[7] Discovery and Characterization of Super-Enhancer-Associated Dependencies in Diffuse Large B Cell Lymphoma [J].

Chapuy, Bjoern ;

McKeown, Michael R. ;

Lin, Charles Y. ;

Monti, Stefano ;

Roemer, Margaretha G. M. ;

Qi, Jun ;

Rahl, Peter B. ;

Sun, Heather H. ;

Yeda, Kelly T. ;

Doench, John G. ;

Reichert, Elaine ;

Kung, Andrew L. ;

Rodig, Scott J. ;

Young, Richard A. ;

Shipp, Margaret A. ;

Bradner, James E. .

CANCER CELL, 2013, 24 (06) :777-790

[8] Characterization of genome-wide enhancer-promoter interactions reveals co-expression of interacting genes and modes of higher order chromatin organization [J].

Chepelev, Iouri ;

Wei, Gang ;

Wangsa, Dara ;

Tang, Qingsong ;

Zhao, Keji .

CELL RESEARCH, 2012, 22 (03) :490-503

[9] Targeting Transcriptional Addictions in Small Cell Lung Cancer with a Covalent CDK7 Inhibitor [J].

Christensen, Camilla L. ;

Kwiatkowski, Nicholas ;

Abraham, Brian J. ;

Carretero, Julian ;

Al-Shahrour, Fatima ;

Zhang, Tinghu ;

Chipumuro, Edmond ;

Herter-Sprie, Grit S. ;

Akbay, Esra A. ;

Altabef, Abigail ;

Zhang, Jianming ;

Shimamura, Takeshi ;

Capelletti, Marzia ;

Reibel, Jakob B. ;

Cavanaugh, Jillian D. ;

Gao, Peng ;

Liu, Yan ;

Michaelsen, Signe R. ;

Poulsen, Hans S. ;

Aref, Amir R. ;

Barbie, David A. ;

Bradner, James E. ;

George, Rani E. ;

Gray, Nathanael S. ;

Young, Richard A. ;

Won, Kwok-Kin .

CANCER CELL, 2014, 26 (06) :909-922

[10] Histone H3K27ac separates active from poised enhancers and predicts developmental state [J].

Creyghton, Menno P. ;

Cheng, Albert W. ;

Welstead, G. Grant ;

Kooistra, Tristan ;

Carey, Bryce W. ;

Steine, Eveline J. ;

Hanna, Jacob ;

Lodato, Michael A. ;

Frampton, Garrett M. ;

Sharp, Phillip A. ;

Boyer, Laurie A. ;

Young, Richard A. ;

Jaenisch, Rudolf .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2010, 107 (50) :21931-21936

← 1 2 3 4 5 6 →