An integrated encyclopedia of DNA elements in the human genome.
The ENCODE Project Consortium; Overall coordination (data analysis coordination); Dunham, Ian 2; Kundaje, Anshul 3,82,+; Data production leads (data production); Aldred, Shelley F. 4; Collins, Patrick J. 4; Davis, Carrie A. 5; Doyle, Francis 6; Epstein, Charles B. 7; Frietze, Seth 8; Harrow, Jennifer 9; Kaul, Rajinder 10; Khatun, Jainab 11; Lajoie, Bryan R. 12; Landt, Stephen G. 13; Lee, Bum-Kyu 14; Pauli, Florencia 15; Rosenbloom, Kate R. 16; Sabo, Peter 17; Safi, Alexias 18; Sanyal, Amartya 12; Shoresh, Noam 7; Simon, Jeremy M. 19; Song, Lingyun 18; Trinklein, Nathan D. 4; Lead analysts (data analysis); Altshuler, Robert C. 20; Birney, Ewan 2,*; Brown, James B. 21; Cheng, Chao 22; Djebali, Sarah 23; Dong, Xianjun 24; Ernst, Jason 20,82,+; Furey, Terrence S. 25; Gerstein, Mark 22; Giardine, Belinda 26; Greven, Melissa 24; Hardison, Ross C. 26,27; Harris, Robert S. 26; Herrero, Javier 2; Hoffman, Michael M. 17; Iyer, Sowmya 28; Kellis, Manolis 20; Kheradpour, Pouya 20; Lassmann, Timo 29; Li, Qunhua 21,82,+; Lin, Xinying 24; Marinov, Georgi K. 30; Merkel, Angelika 23; Mortazavi, Ali 31; Parker, Stephen C. J. 32; Reddy, Timothy E. 15,82,+; Rozowsky, Joel 22; Schlesinger, Felix 5; Thurman, Robert E. 17; Wang, Jie 24; Ward, Lucas D. 20; Whitfield, Troy W. 24; Wilder, Steven P. 2; Wu, Weisheng 26; Xi, Hualin S. 33; Yip, Kevin Y. 22,82,+; Zhuang, Jiali 24; Writing group; Bernstein, Bradley E. 7,34; Green, Eric D. 35; Gunter, Chris 15; Snyder, Michael 13; NHGRI project management (scientific management); Pazin, Michael J. 36; Lowdon, Rebecca F. 36,82,+; Dillon, Laura A. L. 36,82,+; Adams, Leslie B. 36; Kelly, Caroline J. 36; Zhang, Julia 36,82,+; Wexler, Judith R. 36,82,+; Good, Peter J. 36; Feingold, Elise A. 36; Principal investigators (steering committee); Crawford, Gregory E. 18,37; Dekker, Job 12; Elnitski, Laura 38; Farnham, Peggy J. 8; Giddings, Morgan C. 11; Gingeras, Thomas R. 5,39; Guigo, Roderic 23,40; Hubbard, Timothy J. 9; James Kent, W. 16; Lieb, Jason D. 19; Margulies, Elliott H. 32,82,+; Myers, Richard M. 15; Stamatoyannopoulos, John A. 41; Tenenbaum, Scott A. 6; Weng, Zhiping 24; White, Kevin P. 42; Wold, Barbara 30,43; Boise State University and University of North Carolina at Chapel Hill Proteomics groups (data production and analysis); Yu, Yanbao 44; Wrobel, John 11; Risk, Brian A. 11; Gunawardena, Harsha P. 44; Kuiper, Heather C. 44; Maier, Christopher W. 44; Xie, Ling 44; Chen, Xian 44; Broad Institute Group (data production and analysis); Mikkelsen, Tarjei S. 7; Gillespie, Shawn 34; Goren, Alon 7,34; Ram, Oren 7,34; Zhang, Xiaolan 7; Wang, Li 7; Issner, Robbyn 7; Coyne, Michael J. 7; Durham, Timothy 7; Ku, Manching 7,34; Truong, Thanh 7; Eaton, Matthew L. 20; Cold Spring Harbor, University of Geneva, Center for Genomic Regulation, Barcelona, RIKEN, Sanger Institute, University of Lausanne, Genome Institute of Singapore group (data production and analysis); Dobin, Alex 5; Tanzer, Andrea 23; Lagarde, Julien 23; Lin, Wei 5; Xue, Chenghai 5; Williams, Brian A. 30; Zaleski, Chris 5; Roder, Maik 23; Kokocinski, Felix 9,82,+; Abdelhamid, Rehab F. 29; Alioto, Tyler 23,45; Antoshechkin, Igor 30; Baer, Michael T. 5; Batut, Philippe 5; Bell, Ian 46; Bell, Kimberly 5; Chakrabortty, Sudipto 5; Chrast, Jacqueline 47; Curado, Joao 23; Derrien, Thomas 23,82,+; Drenkow, Jorg 5; Dumais, Erica 46; Dumais, Jackie 46; Duttagupta, Radha 46; Fastuca, Megan 5; Fejes-Toth, Kata 5,82,+; Ferreira, Pedro 23; Foissac, Sylvain 46; Fullwood, Melissa J. 48,82,+; Gao, Hui 46; Gonzalez, David 23; Gordon, Assaf 5; Howald, Cedric 47; Jha, Sonali 5; Johnson, Rory 23; Kapranov, Philipp 46,82,+; King, Brandon 30; Kingswood, Colin 23,45; Li, Guoliang 49; Luo, Oscar J. 48; Park, Eddie 31; Preall, Jonathan B. 5; Presaud, Kimberly 5; Ribeca, Paolo 23,45; Robyr, Daniel 50; Ruan, Xiaoan 48; Sammeth, Michael 23,45; Singh Sandhu, Kuljeet 48; Schaeffer, Lorain 30; See, Lei-Hoon 5; Shahab, Atif 48; Skancke, Jorgen 23; Maria Suzuki, Ana 29; Takahashi, Hazuki 29; Tilgner, Hagen 23,82,+; Trout, Diane 30; Walters, Nathalie 47; Wang, Huaien 5; Hayashizaki, Yoshihide 29; Reymond, Alexandre 47; Antonarakis, Stylianos E. 50; Hannon, Gregory J. 5; Ruan, Yijun 48; Carninci, Piero 29; Data coordination center at UC Santa Cruz (production data coordination); Sloan, Cricket A. 16; Learned, Katrina 16; Malladi, Venkat S. 16; Wong, Matthew C. 16; Barber, Galt P. 16; Cline, Melissa S. 16; Dreszer, Timothy R. 16; Heitner, Steven G. 16; Karolchik, Donna 16; Kirkup, Vanessa M. 16; Meyer, Laurence R. 16; Long, Jeffrey C. 16; Maddren, Morgan 16; Raney, Brian J. 16; Duke University, EBI, University of Texas, Austin, University of North Carolina-Chapel Hill group (data production and analysis); Grasfeder, Linda L. 19; Giresi, Paul G. 19; Battenhouse, Anna 14; Sheffield, Nathan C. 18; Showers, Kimberly A. 19; London, Darin 18; Bhinge, Akshay A. 14; Shestak, Christopher 19; Schaner, Matthew R. 19; Ki Kim, Seul 19; Zhang, Zhuzhu Z. 19; Mieczkowski, Piotr A. 51; Mieczkowska, Joanna O. 19; Liu, Zheng 14; McDaniell, Ryan M. 14; Ni, Yunyun 14; Rashid, Naim U. 52; Jae Kim, Min 19; Adar, Sheera 19; Zhang, Zhancheng 25; Wang, Tianyuan 18; Winter, Deborah 18; Keefe, Damian 2; Iyer, Vishwanath R. 14; Genome Institute of Singapore group (data production and analysis); Zheng, Meizhen 48; Wang, Ping 48; HudsonAlpha Institute, Caltech, UC Irvine, Stanford group (data production and analysis); Gertz, Jason 15; Vielmetter, Jost 30,43; Christopher Partridge, E. 15; Varley, Katherine E. 15; Gasper, Clarke 30,43; Bansal, Anita 15; Pepke, Shirley 30,53; Jain, Preti 15; Amrhein, Henry 30; Bowling, Kevin M. 15; Anaya, Michael 30,43; Cross, Marie K. 15; Muratet, Michael A. 15; Newberry, Kimberly M. 15; McCue, Kenneth 30; Nesmith, Amy S. 15; Fisher-Aylor, Katherine I. 30,43; Pusey, Barbara 15; DeSalvo, Gilberto 30,43; Parker, Stephanie L. 15,82,+; Balasubramanian, Sreeram 30,43; Davis, Nicholas S. 15; Meadows, Sarah K. 15; Eggleston, Tracy 15; Scott Newberry, J. 15; Levy, Shawn E. 15; Absher, Devin M. 15; Wong, Wing H. 54; Lawrence Berkeley National Laboratory group (targeted experimental validation); Blow, Matthew J. 55; Visel, Axel 55,56; Pennachio, Len A. 55,56; NHGRI groups (data production and analysis); Petrykowska, Hanna M. 38; Sanger Institute, Washington University, Yale University, Center for Genomic Regulation, Barcelona, UCSC, MIT, University of Lausanne, CNIO group (data production and analysis); Abyzov, Alexej 22; Aken, Bronwen 9; Barrell, Daniel 9; Barson, Gemma 9; Berry, Andrew 9; Bignell, Alexandra 9; Boychenko, Veronika 9; Bussotti, Giovanni 23; Davidson, Claire 9; Despacio-Reyes, Gloria 9; Diekhans, Mark 16; Ezkurdia, Iakes 57; Frankish, Adam 9; Gilbert, James 9; Manuel Gonzalez, Jose 9; Griffiths, Ed 9; Harte, Rachel 16; Hendrix, David A. 20; Hunt, Toby 9; Jungreis, Irwin 20; Kay, Mike 9; Khurana, Ekta 22; Leng, Jing 22; Lin, Michael F. 20; Loveland, Jane 9; Lu, Zhi 58; Manthravadi, Deepa 9; Mariotti, Marco 23; Mudge, Jonathan 9; Mukherjee, Gaurab 9; Notredame, Cedric 23; Pei, Baikang 22; Manuel Rodriguez, Jose 57; Saunders, Gary 9; Sboner, Andrea 59; Searle, Stephen 9; Sisu, Cristina 22; Snow, Catherine 9; Steward, Charlie 9; Tapanari, Electra 9; Tress, Michael L. 57; van Baren, Marijke J. 60,82,+; Washietl, Stefan 20; Wilming, Laurens 9; Zadissa, Amonida 9; Zhang, Zhengdong 61; Brent, Michael 60; Haussler, David 62; Valencia, Alfonso 57; Stanford-Yale, Harvard, University of Massachusetts Medical School, University of Southern CaliforniaUC Davis group (data production and analysis) /; Addleman, Nick 13; Alexander, Roger P. 22; Auerbach, Raymond K. 22; Balasubramanian, Suganthi 22; Bettinger, Keith 13; Bhardwaj, Nitin 22; Boyle, Alan P. 13; Cao, Alina R. 63; Cayting, Philip 13; Charos, Alexandra 64; Cheng, Yong 13; Eastman, Catharine 13; Euskirchen, Ghia 13; Fleming, Joseph D. 65; Grubert, Fabian 13; Habegger, Lukas 22; Hariharan, Manoj 13; Harmanci, Arif 22; Iyengar, Sushma 66; Jin, Victor X. 67; Karczewski, Konrad J. 13; Kasowski, Maya 13; Lacroute, Phil 13; Lam, Hugo 13; Lamarre-Vincent, Nathan 65; Lian, Jin 68; Lindahl-Allen, Marianne 65; Min, Renqiang 22,82,+; Miotto, Benoit 65; Monahan, Hannah 64; Moqtaderi, Zarmik 65; Mu, Xinmeng J. 22; O'Geen, Henriette 63; Ouyang, Zhengqing 13; Patacsil, Dorrelyn 13; Raha, Debasish 64; Ramirez, Lucia 13; Reed, Brian 64; Shi, Minyi 13; Slifer, Teri 13; Witt, Heather 8; Wu, Linfeng 13; Xu, Xiaoqin 63; Yan, Koon-Kiu 22; Yang, Xinqiong 13; Struhl, Kevin 65; Weissman, Sherman M. 68; University of Albany SUNY group (data production and analysis); Penalva, Luiz O. 69; University of Chicago, Stanford group (data production and analysis); Karmakar, Subhradip 42; Bhanvadia, Raj R. 42; Choudhury, Alina 42; Domanus, Marc 42; Ma, Lijia 42; Moran, Jennifer 42; Victorsen, Alec 42; University of Heidelberg group (targeted experimental validation); Auer, Thomas 70,82,+; Centanin, Lazaro 70; Eichenlaub, Michael 70; Gruhl, Franziska 70; Heermann, Stephan 70; Hoeckendorf, Burkhard 70; Inoue, Daigo 70; Kellner, Tanja 70; Kirchmaier, Stephan 70; Mueller, Claudia 70; Reinhardt, Robert 70; Schertel, Lea 70; Schneider, Stephanie 70; Sinn, Rebecca 70; Wittbrodt, Beate 70; Wittbrodt, Jochen 70; University of Massachusetts Medical School Bioinformatics group (data production and analysis); Jain, Gaurav 12; University of Washington, University of Massachusetts Medical Center group (data production and analysis); Balasundaram, Gayathri 71; Bates, Daniel L. 17; Byron, Rachel 71; Canfield, Theresa K. 17; Diegel, Morgan J. 17; Dunn, Douglas 17; Ebersol, Abigail K. 72; Frum, Tristan 72; Garg, Kavita 73; Gist, Erica 17; Scott Hansen, R. 72; Boatman, Lisa 72; Haugen, Eric 17; Humbert, Richard 17; Johnson, Audra K. 17; Johnson, Ericka M. 72; Kutyavin, Tattyana V. 17; Lee, Kristen 17; Lotakis, Dimitra 72; Maurano, Matthew T. 17; Neph, Shane J. 17; Neri, Fiedencio V. 17; Nguyen, Eric D. 72; Qu, Hongzhu 17; Reynolds, Alex P. 17; Roach, Vaughn 17; Rynes, Eric 17; Sanchez, Minerva E. 72; Sandstrom, Richard S. 17; Shafer, Anthony O. 17; Stergachis, Andrew B. 17; Thomas, Sean 17; Vernot, Benjamin 17; Vierstra, Jeff 17; Vong, Shinny 17; Wang, Hao 17; Weaver, Molly A. 17; Yan, Yongqi 72; Zhang, Miaohua 71; Akey, Joshua M. 17; Bender, Michael 71; Dorschner, Michael O. 74; Groudine, Mark 71; MacCoss, Michael J. 17; Navas, Patrick 72; Stamatoyannopoulos, George 72; Data Analysis Center (data analysis); Beal, Kathryn 2; Brazma, Alvis 75; Flicek, Paul 2; Johnson, Nathan 2; Lukk, Margus 75,82,+; Luscombe, Nicholas M. 76; Sobral, Daniel 2,82,+; Vaquerizas, Juan M. 76; Batzoglou, Serafim 3,+; Sidow, Arend 77; Hussami, Nadine 3,+; Kyriazopoulou-Panagiotopoulou, Sofia 3,+; Libbrecht, Max W. 3,82,+; Schaub, Marc A. 3,+; Miller, Webb 26; Bickel, Peter J. 21; Banfai, Balazs 21; Boley, Nathan P. 21; Huang, Haiyan 21; Jessica Li, Jingyi 21; Stafford Noble, William 17,78; Bilmes, Jeffrey A. 79; Buske, Orion J. 17; Sahu, Avinash D. 17,82,+; Kharchenko, Peter V. 80; Park, Peter J. 80; Baker, Dannon 81; Taylor, James 81; Lochovsky, Lucas 22
[Article]
Nature.
489(7414):57-74, September 6, 2012.
(Format: HTML, PDF)
: The human genome encodes the blueprint of life, but the function of the vast majority of its nearly three billion bases is unknown. The Encyclopedia of DNA Elements (ENCODE) project has systematically mapped regions of transcription, transcription factor association, chromatin structure and histone modification. These data enabled us to assign biochemical functions for 80% of the genome, in particular outside of the well-studied protein-coding regions. Many discovered candidate regulatory elements are physically associated with one another and with expressed genes, providing new insights into the mechanisms of gene regulation. The newly identified elements also show a statistical correspondence to sequence variants linked to human disease, and can thereby guide interpretation of this variation. Overall, the project provides new insights into the organization and regulation of our genes and genome, and is an expansive resource of functional annotations for biomedical research.
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