Annotating and prioritizing human non-coding variants with RegulomeDB v.2

被引:68
作者
Dong, Shengcheng [1 ]
Zhao, Nanxiang [2 ]
Spragins, Emma [1 ]
Kagda, Meenakshi S. [1 ]
Li, Mingjie [1 ]
Assis, Pedro [1 ]
Jolanki, Otto [1 ]
Luo, Yunhai [1 ]
Cherry, J. Michael [1 ]
Boyle, Alan P. [2 ,3 ]
Hitz, Benjamin C. [1 ]
机构
[1] Stanford Univ, Dept Genet, Stanford, CA 94305 USA
[2] Univ Michigan, Dept Computat Med & Bioinformat, Ann Arbor, MI 48104 USA
[3] Univ Michigan, Dept Human Genet, Ann Arbor, MI 48104 USA
基金
美国国家卫生研究院;
关键词
D O I
10.1038/s41588-023-01365-3
中图分类号
Q3 [遗传学];
学科分类号
071007 ; 090102 ;
摘要
引用
收藏
页码:724 / 726
页数:3
相关论文
共 13 条
[1]   The GTEx Consortium atlas of genetic regulatory effects across human tissues [J].
Aguet, Francois ;
Barbeira, Alvaro N. ;
Bonazzola, Rodrigo ;
Brown, Andrew ;
Castel, Stephane E. ;
Jo, Brian ;
Kasela, Silva ;
Kim-Hellmuth, Sarah ;
Liang, Yanyu ;
Parsana, Princy ;
Flynn, Elise ;
Fresard, Laure ;
Gamazon, Eric R. ;
Hamel, Andrew R. ;
He, Yuan ;
Hormozdiari, Farhad ;
Mohammadi, Pejman ;
Munoz-Aguirre, Manuel ;
Ardlie, Kristin G. ;
Battle, Alexis ;
Bonazzola, Rodrigo ;
Brown, Christopher D. ;
Cox, Nancy ;
Dermitzakis, Emmanouil T. ;
Engelhardt, Barbara E. ;
Garrido-Martin, Diego ;
Gay, Nicole R. ;
Getz, Gad ;
Guigo, Roderic ;
Hamel, Andrew R. ;
Handsaker, Robert E. ;
He, Yuan ;
Hoffman, Paul J. ;
Hormozdiari, Farhad ;
Im, Hae Kyung ;
Jo, Brian ;
Kasela, Silva ;
Kashin, Seva ;
Kim-Hellmuth, Sarah ;
Kwong, Alan ;
Lappalainen, Tuuli ;
Li, Xiao ;
Liang, Yanyu ;
MacArthur, Daniel G. ;
Mohammadi, Pejman ;
Montgomery, Stephen B. ;
Munoz-Aguirre, Manuel ;
Rouhana, John M. ;
Hormozdiari, Farhad ;
Im, Hae Kyung .
SCIENCE, 2020, 369 (6509) :1318-1330
[2]   Epigenetic regulation of ACE2, the receptor of the SARS-CoV-2 virus [J].
Beacon, Tasnim H. ;
Delcuve, Genevieve P. ;
Davie, James R. .
GENOME, 2021, 64 (04) :386-399
[3]   Regulatory genomic circuitry of human disease loci by integrative epigenomics [J].
Boix, Carles A. ;
James, Benjamin T. ;
Park, Yongjin P. ;
Meuleman, Wouter ;
Kellis, Manolis .
NATURE, 2021, 590 (7845) :300-307
[4]   Annotation of functional variation in personal genomes using RegulomeDB [J].
Boyle, Alan P. ;
Hong, Eurie L. ;
Hariharan, Manoj ;
Cheng, Yong ;
Schaub, Marc A. ;
Kasowski, Maya ;
Karczewski, Konrad J. ;
Park, Julie ;
Hitz, Benjamin C. ;
Weng, Shuai ;
Cherry, J. Michael ;
Snyder, Michael .
GENOME RESEARCH, 2012, 22 (09) :1790-1797
[5]   Stathmin, a Gene Regulating Neural Plasticity, Affects Fear and Anxiety Processing in Humans [J].
Brocke, Burkhard ;
Lesch, Klaus-Peter ;
Armbruster, Diana ;
Moser, Dirk A. ;
Mueller, Anett ;
Strobel, Alexander ;
Kirschbaum, Clemens .
AMERICAN JOURNAL OF MEDICAL GENETICS PART B-NEUROPSYCHIATRIC GENETICS, 2010, 153B (01) :243-251
[6]   Predicting functional variants in enhancer and promoter elements using RegulomeDB [J].
Dong, Shengcheng ;
Boyle, Alan P. .
HUMAN MUTATION, 2019, 40 (09) :1292-1298
[7]   JASPAR 2020: update of the open-access database of transcription factor binding profiles [J].
Fornes, Oriol ;
Castro-Mondragon, Jaime A. ;
Khan, Aziz ;
van der Lee, Robin ;
Zhang, Xi ;
Richmond, Phillip A. ;
Modi, Bhavi P. ;
Correard, Solenne ;
Gheorghe, Marius ;
Baranasic, Damir ;
Santana-Garcia, Walter ;
Tan, Ge ;
Cheneby, Jeanne ;
Ballester, Benoit ;
Parcy, Francois ;
Sandelin, Albin ;
Lenhard, Boris ;
Wasserman, Wyeth W. ;
Mathelier, Anthony .
NUCLEIC ACIDS RESEARCH, 2020, 48 (D1) :D87-D92
[8]   Cardiac cell type-specific gene regulatory programs and disease risk association [J].
Hocker, James D. ;
Poirion, Olivier B. ;
Zhu, Fugui ;
Buchanan, Justin ;
Zhang, Kai ;
Chiou, Joshua ;
Wang, Tsui-Min ;
Zhang, Qingquan ;
Hou, Xiaomeng ;
Li, Yang E. ;
Zhang, Yanxiao ;
Farah, Elie N. ;
Wang, Allen ;
McCulloch, Andrew D. ;
Gaulton, Kyle J. ;
Ren, Bing ;
Chi, Neil C. ;
Preissl, Sebastian .
SCIENCE ADVANCES, 2021, 7 (20)
[9]   Genome-wide analysis provides genetic evidence that ACE2 influences COVID-19 risk and yields risk scores associated with severe disease [J].
Horowitz, Julie E. ;
Kosmicki, Jack A. ;
Damask, Amy ;
Sharma, Deepika ;
Roberts, Genevieve H. L. ;
Justice, Anne E. ;
Banerjee, Nilanjana ;
Coignet, Marie, V ;
Yadav, Ashish ;
Leader, Joseph B. ;
Marcketta, Anthony ;
Park, Danny S. ;
Lanche, Rouel ;
Maxwell, Evan ;
Knight, Spencer C. ;
Bai, Xiaodong ;
Guturu, Harendra ;
Sun, Dylan ;
Baltzell, Asher ;
Kury, Fabricio S. P. ;
Backman, Joshua D. ;
Girshick, Ahna R. ;
O'Dushlaine, Colm ;
McCurdy, Shannon R. ;
Partha, Raghavendran ;
Mansfield, Adam J. ;
Turissini, David A. ;
Li, Alexander H. ;
Zhang, Miao ;
Mbatchou, Joelle ;
Watanabe, Kyoko ;
Gurski, Lauren ;
McCarthy, Shane E. ;
Kang, Hyun M. ;
Dobbyn, Lee ;
Stahl, Eli ;
Verma, Anurag ;
Sirugo, Giorgio ;
Ritchie, Marylyn D. ;
Jones, Marcus ;
Balasubramanian, Suganthi ;
Siminovitch, Katherine ;
Salerno, William J. ;
Shuldiner, Alan R. ;
Rader, Daniel J. ;
Mirshahi, Tooraj ;
Locke, Adam E. ;
Marchini, Jonathan ;
Overton, John D. ;
Carey, David J. .
NATURE GENETICS, 2022, 54 (04) :382-+
[10]   An integrated analysis of public genomic data unveils a possible functional mechanism of psoriasis risk via a long-range ERRFI1 enhancer [J].
Kubota, Naoto ;
Suyama, Mikita .
BMC MEDICAL GENOMICS, 2020, 13 (01)