epiTAD: a web application for visualizing chromosome conformation capture data in the context of genetic epidemiology

被引：0
作者：
Creed, Jordan H. [1 ]
Aden-Buie, Garrick [1 ]
Monteiro, Alvaro N. [1 ]
Gerke, Travis A. [1 ]
机构：
[1] H Lee Moffitt Canc Ctr & Res Inst, Dept Canc Epidemiol, Tampa, FL 33612 USA
来源：
BIOINFORMATICS | 2019年 / 35卷 / 21期
关键词：
ASSOCIATION; RISK;
D O I：
10.1093/bioinformatics/btz387
中图分类号：
Q5 [生物化学];
学科分类号：
071010 ; 081704 ;
摘要：
Complementary advances in genomic technology and public data resources have created opportunities for researchers to conduct multifaceted examination of the genome on a large scale. To meet the need for integrative genome wide exploration, we present epiTAD. This web-based tool enables researchers to compare genomic 3D organization and annotations across multiple databases in an interactive manner to facilitate in silico discovery.
引用
收藏
页码：4462 / 4464
页数：3
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  • [1] Genetic effects on gene expression across human tissues
    Aguet, Francois
    Brown, Andrew A.
    Castel, Stephane E.
    Davis, Joe R.
    He, Yuan
    Jo, Brian
    Mohammadi, Pejman
    Park, Yoson
    Parsana, Princy
    Segre, Ayellet V.
    Strober, Benjamin J.
    Zappala, Zachary
    Cummings, Beryl B.
    Gelfand, Ellen T.
    Hadley, Kane
    Huang, Katherine H.
    Lek, Monkol
    Li, Xiao
    Nedzel, Jared L.
    Nguyen, Duyen Y.
    Noble, Michael S.
    Sullivan, Timothy J.
    Tukiainen, Taru
    MacArthur, Daniel G.
    Getz, Gad
    Management, Nih Program
    Addington, Anjene
    Guan, Ping
    Koester, Susan
    Little, A. Roger
    Lockhart, Nicole C.
    Moore, Helen M.
    Rao, Abhi
    Struewing, Jeffery P.
    Volpi, Simona
    Collection, Biospecimen
    Brigham, Lori E.
    Hasz, Richard
    Hunter, Marcus
    Johns, Christopher
    Johnson, Mark
    Kopen, Gene
    Leinweber, William F.
    Lonsdale, John T.
    McDonald, Alisa
    Mestichelli, Bernadette
    Myer, Kevin
    Roe, Bryan
    Salvatore, Michael
    Shad, Saboor
    [J]. NATURE, 2017, 550 (7675) : 204 - +
  • [2] A Novel Approach to High-Quality Postmortem Tissue Procurement: The GTEx Project
    Carithers, Latarsha J.
    Ardlie, Kristin
    Barcus, Mary
    Branton, Philip A.
    Britton, Angela
    Buia, Stephen A.
    Compton, Carolyn C.
    DeLuca, David S.
    Peter-Demchok, Joanne
    Gelfand, Ellen T.
    Guan, Ping
    Korzeniewski, Greg E.
    Lockhart, Nicole C.
    Rabiner, Chana A.
    Rao, Abhi K.
    Robinson, Karna L.
    Roche, Nancy V.
    Sawyer, Sherilyn J.
    Segre, Ayellet V.
    Shive, Charles E.
    Smith, Anna M.
    Sobin, Leslie H.
    Undale, Anita H.
    Valentino, Kimberly M.
    Vaught, Jim
    Young, Taylor R.
    Moore, Helen M.
    [J]. BIOPRESERVATION AND BIOBANKING, 2015, 13 (05) : 311 - 319
  • [3] Topological domains in mammalian genomes identified by analysis of chromatin interactions
    Dixon, Jesse R.
    Selvaraj, Siddarth
    Yue, Feng
    Kim, Audrey
    Li, Yan
    Shen, Yin
    Hu, Ming
    Liu, Jun S.
    Ren, Bing
    [J]. NATURE, 2012, 485 (7398) : 376 - 380
  • [4] Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt
    Durinck, Steffen
    Spellman, Paul T.
    Birney, Ewan
    Huber, Wolfgang
    [J]. NATURE PROTOCOLS, 2009, 4 (08) : 1184 - 1191
  • [5] Genomewide Association Studies and Assessment of the Risk of Disease
    Manolio, Teri A.
    [J]. NEW ENGLAND JOURNAL OF MEDICINE, 2010, 363 (02) : 166 - 176
  • [6] Association of Prostate Cancer Risk Variants with Gene Expression in Normal and Tumor Tissue
    Penney, Kathryn L.
    Sinnott, Jennifer A.
    Tyekucheva, Svitlana
    Gerke, Travis
    Shui, Irene M.
    Kraft, Peter
    Sesso, Howard D.
    Freedman, Matthew L.
    Loda, Massimo
    Mucci, Lorelei A.
    Stampfer, Meir J.
    [J]. CANCER EPIDEMIOLOGY BIOMARKERS & PREVENTION, 2015, 24 (01) : 255 - 260
  • [7] Sushi.R: flexible, quantitative and integrative genomic visualizations for publication-quality multi-panel figures
    Phanstiel, Douglas H.
    Boyle, Alan P.
    Araya, Carlos L.
    Snyder, Michael P.
    [J]. BIOINFORMATICS, 2014, 30 (19) : 2808 - 2810
  • [8] Quantifying the similarity of topological domains across normal and cancer human cell types
    Sauerwald, Natalie
    Kingsford, Carl
    [J]. BIOINFORMATICS, 2018, 34 (13) : 475 - 483
  • [9] HiTC: exploration of high-throughput 'C' experiments
    Servant, Nicolas
    Lajoie, Bryan R.
    Nora, Elphege P.
    Giorgetti, Luca
    Chen, Chong-Jian
    Heard, Edith
    Dekker, Job
    Barillot, Emmanuel
    [J]. BIOINFORMATICS, 2012, 28 (21) : 2843 - 2844
  • [10] The 3D Genome Browser: a web-based browser for visualizing 3D genome organization and long-range chromatin interactions
    Wang, Yanli
    Song, Fan
    Zhang, Bo
    Zhang, Lijun
    Xu, Jie
    Kuang, Da
    Li, Daofeng
    Choudhary, Mayank N. K.
    Li, Yun
    Hu, Ming
    Hardison, Ross
    Wang, Ting
    Yue, Feng
    [J]. GENOME BIOLOGY, 2018, 19
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