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An integrated encyclopedia of DNA elements in the human genome
Authors :
Dunham, Ian Kundaje, Anshul Aldred, Shelley F. Collins, Patrick J. Davis, Carrie A. Doyle, Francis Epstein, Charles B. Frietze, Seth Harrow, Jennifer Kaul, Rajinder Khatun, Jainab Lajoie, Bryan R. Landt, Stephen G. Lee, Bum-Kyu Pauli, Florencia Rosenbloom, Kate R. Sabo, Peter Safi, Alexias Sanyal, Amartya Shoresh, Noam Simon, Jeremy M. Song, Lingyun Trinklein, Nathan D. Altshuler, Robert C. Birney, Ewan Brown, James B. Cheng, Chao Djebali, Sarah Dong, Xianjun Ernst, Jason Furey, Terrence S. Gerstein, Mark Giardine, Belinda Greven, Melissa Hardison, Ross C. Harris, Robert S. Herrero, Javier Hoffman, Michael M. Iyer, Sowmya Kellis, Manolis Kheradpour, Pouya Lassmann, Timo Li, Qunhua Lin, Xinying Marinov, Georgi K. Merkel, Angelika Mortazavi, Ali Parker, Stephen C. J. Reddy, Timothy E. Rozowsky, Joel Schlesinger, Felix Thurman, Robert E. Wang, Jie Ward, Lucas D. Whitfield, Troy W. Wilder, Steven P. Wu, Weisheng Xi, Hualin S. Yip, Kevin Y. Zhuang, Jiali Bernstein, Bradley E. Green, Eric D. Gunter, Chris Snyder, Michael Pazin, Michael J. Lowdon, Rebecca F. Dillon, Laura A. L. Adams, Leslie B. Kelly, Caroline J. Zhang, Julia Wexler, Judith R. Good, Peter J. Feingold, Elise A. Crawford, Gregory E. Dekker, Job Elnitski, Laura Farnham, Peggy J. Giddings, Morgan C. Gingeras, Thomas R. Guigo, Roderic Hubbard, Timothy J. Kent, W. James Lieb, Jason D. Margulies, Elliott H. Myers, Richard M. Stamatoyannopoulos, John A. Tenenbaum, Scott A. Weng, Zhiping White, Kevin P. Wold, Barbara Yu, Yanbao Wrobel, John Risk, Brian A. Gunawardena, Harsha P. Kuiper, Heather C. Maier, Christopher W. Xie, Ling Chen, Xian Mikkelsen, Tarjei S. Gillespie, Shawn Goren, Alon Ram, Oren Zhang, Xiaolan Wang, Li Issner, Robbyn Coyne, Michael J. Durham, Timothy Ku, Manching Truong, Thanh Eaton, Matthew L. Dobin, Alex Tanzer, Andrea Lagarde, Julien Lin, Wei Xue, Chenghai Williams, Brian A. Zaleski, Chris Roder, Maik Kokocinski, Felix Abdelhamid, Rehab F. Alioto, Tyler Antoshechkin, Igor Baer, Michael T. Batut, Philippe Bell, Ian Bell, Kimberly Chakrabortty, Sudipto Chrast, Jacqueline Curado, Joao Derrien, Thomas Drenkow, Jorg Dumais, Erica Dumais, Jackie Duttagupta, Radha Fastuca, Megan Fejes-Toth, Kata Ferreira, Pedro Foissac, Sylvain Fullwood, Melissa J. Gao, Hui Gonzalez, David Gordon, Assaf Howald, Cedric Jha, Sonali Johnson, Rory Kapranov, Philipp King, Brandon Kingswood, Colin Li, Guoliang Luo, Oscar J. Park, Eddie Preall, Jonathan B. Presaud, Kimberly Ribeca, Paolo Robyr, Daniel Ruan, Xiaoan Sammeth, Michael Sandhu, Kuljeet Singh Schaeffer, Lorain See, Lei-Hoon Shahab, Atif Skancke, Jorgen Suzuki, Ana Maria Takahashi, Hazuki Tilgner, Hagen Trout, Diane Walters, Nathalie Wang, Huaien Hayashizaki, Yoshihide Reymond, Alexandre Antonarakis, Stylianos E. Hannon, Gregory J. Ruan, Yijun Carninci, Piero Sloan, Cricket A. Learned, Katrina Malladi, Venkat S. Wong, Matthew C. Barber, Galt P. Cline, Melissa S. Dreszer, Timothy R. Heitner, Steven G. Karolchik, Donna Kirkup, Vanessa M. Meyer, Laurence R. Long, Jeffrey C. Maddren, Morgan Raney, Brian J. Grasfeder, Linda L. Giresi, Paul G. Battenhouse, Anna Sheffield, Nathan C. Showers, Kimberly A. London, Darin Bhinge, Akshay A. Shestak, Christopher Schaner, Matthew R. Ki Kim, Seul Zhang, Zhuzhu Z. Mieczkowski, Piotr A. Mieczkowska, Joanna O. Liu, Zheng McDaniell, Ryan M. Ni, Yunyun Rashid, Naim U. Kim, Min Jae Adar, Sheera Zhang, Zhancheng Wang, Tianyuan Winter, Deborah Keefe, Damian Iyer, Vishwanath R. Zheng, Meizhen Wang, Ping Gertz, Jason Vielmetter, Jost Partridge, E. Varley, Katherine E. Gasper, Clarke Bansal, Anita Pepke, Shirley Jain, Preti Amrhein, Henry Bowling, Kevin M. Anaya, Michael Cross, Marie K. Muratet, Michael A. Newberry, Kimberly M. McCue, Kenneth Nesmith, Amy S. Fisher-Aylor, Katherine I. Pusey, Barbara DeSalvo, Gilberto Parker, Stephanie L. Balasubramanian, Sreeram Davis, Nicholas S. Meadows, Sarah K. Eggleston, Tracy Newberry, J. Scott Levy, Shawn E. Absher, Devin M. Wong, Wing H. Blow, Matthew J. Visel, Axel Pennachio, Len A. Petrykowska, Hanna M. Abyzov, Alexej Aken, Bronwen Barrell, Daniel Barson, Gemma Berry, Andrew Bignell, Alexandra Boychenko, Veronika Bussotti, Giovanni Davidson, Claire Despacio-Reyes, Gloria Diekhans, Mark Ezkurdia, Iakes Frankish, Adam Gilbert, James Gonzalez, Jose Manuel Griffiths, Ed Harte, Rachel Hendrix, David A. Hunt, Toby Jungreis, Irwin Kay, Mike Khurana, Ekta Leng, Jing Lin, Michael F. Loveland, Jane Lu, Zhi Manthravadi, Deepa Mariotti, Marco Mudge, Jonathan Mukherjee, Gaurab Notredame, Cedric Pei, Baikang Rodriguez, Jose Manuel Saunders, Gary Sboner, Andrea Searle, Stephen Sisu, Cristina Snow, Catherine Steward, Charlie Tapanari, Electra Tress, Michael L. van Baren, Marijke J. Washietl, Stefan Wilming, Laurens Zadissa, Amonida Zhang, Zhengdong Brent, Michael Haussler, David Valencia, Alfonso Addleman, Nick Alexander, Roger P. Auerbach, Raymond K. Balasubramanian, Suganthi Bettinger, Keith Bhardwaj, Nitin Boyle, Alan P. Cao, Alina R. Cayting, Philip Charos, Alexandra Cheng, Yong Eastman, Catharine Euskirchen, Ghia Fleming, Joseph D. Grubert, Fabian Habegger, Lukas Hariharan, Manoj Harmanci, Arif Iyengar, Sushma Jin, Victor X. Karczewski, Konrad J. Kasowski, Maya Lacroute, Phil Lam, Hugo Lamarre-Vincent, Nathan Lian, Jin Lindahl-Allen, Marianne Min, Renqiang Miotto, Benoit Monahan, Hannah Moqtaderi, Zarmik Mu, Xinmeng J. Ouyang, Zhengqing Patacsil, Dorrelyn Raha, Debasish Ramirez, Lucia Reed, Brian Shi, Minyi Slifer, Teri Witt, Heather Wu, Linfeng Xu, Xiaoqin Yan, Koon-Kiu Yang, Xinqiong Struhl, Kevin Weissman, Sherman M. Penalva, Luiz O. Karmakar, Subhradip Bhanvadia, Raj R. Choudhury, Alina Domanus, Marc Ma, Lijia Moran, Jennifer Victorsen, Alec Auer, Thomas Centanin, Lazaro Eichenlaub, Michael Gruhl, Franziska Heermann, Stephan Hoeckendorf, Burkhard Inoue, Daigo Kellner, Tanja Kirchmaier, Stephan Mueller, Claudia Reinhardt, Robert Schertel, Lea Schneider, Stephanie Sinn, Rebecca Wittbrodt, Beate Wittbrodt, Jochen Partridge, E. Christopher Jain, Gaurav Balasundaram, Gayathri Bates, Daniel L. Byron, Rachel Canfield, Theresa K. Diegel, Morgan J. Dunn, Douglas Ebersol, Abigail K. Frum, Tristan Garg, Kavita Gist, Erica Hansen, R. Scott Boatman, Lisa Haugen, Eric Humbert, Richard Johnson, Audra K. Johnson, Ericka M. Kutyavin, Tattyana V. Lee, Kristen Lotakis, Dimitra Maurano, Matthew T. Neph, Shane J. Neri, Fiedencio V. Nguyen, Eric D. Qu, Hongzhu Reynolds, Alex P. Roach, Vaughn Rynes, Eric Sanchez, Minerva E. Sandstrom, Richard S. Shafer, Anthony O. Stergachis, Andrew B. Thomas, Sean Vernot, Benjamin Vierstra, Jeff Vong, Shinny Weaver, Molly A. Yan, Yongqi Zhang, Miaohua Akey, Joshua M. Bender, Michael Dorschner, Michael O. Groudine, Mark MacCoss, Michael J. Navas, Patrick Stamatoyannopoulos, George Beal, Kathryn Brazma, Alvis Flicek, Paul Johnson, Nathan Lukk, Margus Luscombe, Nicholas M. Sobral, Daniel Vaquerizas, Juan M. Batzoglou, Serafim Sidow, Arend Hussami, Nadine Kyriazopoulou-Panagiotopoulou, Sofia Libbrecht, Max W. Schaub, Marc A. Miller, Webb Bickel, Peter J. Banfai, Balazs Boley, Nathan P. Huang, Haiyan Li, Jingyi Jessica Noble, William Stafford Bilmes, Jeffrey A. Buske, Orion J. Sahu, Avinash D. Kharchenko, Peter V. Park, Peter J. Baker, Dannon Taylor, James Lochovsky, Lucas
Source :
Nature. September 6, 2012, Vol. 489 Issue 7414, p57, 18 p.
Publication Year :
2012
Abstract
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.<br />Author(s): The ENCODE Project Consortium; Overall coordination (data analysis coordination); Ian Dunham [2]; Anshul Kundaje [3, 82]; Data production leads (data production); Shelley F. Aldred [4]; Patrick J. Collins [4]; [...]
Details
Language :
English
ISSN :
00280836
Volume :
489
Issue :
7414
Database :
Gale General OneFile
Journal :
Nature
Publication Type :
Academic Journal
Accession number :
edsgcl.488649463
Full Text :
https://doi.org/10.1038/nature11247