A user's guide to the Encyclopedia of DNA elements (ENCODE)

Richard M. Myers, John Stamatoyannopoulos, Michael Snyder, Ian Dunham, Ross C. Hardison, Bradley E. Bernstein, Thomas R. Gingeras, W. James Kent, Ewan Birney, Barbara Wold, Gregory E. Crawford, Bradley E. Bernstein, Charles B. Epstein, Noam Shoresh, Jason Ernst, Tarjei S. Mikkelsen, Pouya Kheradpour, Xiaolan Zhang, Li Wang, Robbyn IssnerMichael J. Coyne, Timothy Durham, Manching Ku, Thanh Truong, Lucas D. Ward, Robert C. Altshuler, Michael F. Lin, Manolis Kellis, Thomas R. Gingeras, Carrie A. Davis, Philipp Kapranov, Alexander Dobin, Christopher Zaleski, Felix Schlesinger, Philippe Batut, Sudipto Chakrabortty, Sonali Jha, Wei Lin, Jorg Drenkow, Huaien Wang, Kim Bell, Hui Gao, Ian Bell, Erica Dumais, Jacqueline Dumais, Stylianos E. Antonarakis, Catherine Ucla, Christelle Borel, Roderic Guigo, Sarah Djebali, Julien Lagarde, Colin Kingswood, Paolo Ribeca, Micha Sammeth, Tyler Alioto, Angelika Merkel, Hagen Tilgner, Piero Carninci, Yoshihide Hayashizaki, Timo Lassmann, Hazuki Takahashi, Rehab F. Abdelhamid, Gregory Hannon, Katalin Toth Fejes, Jonathan Preall, Assaf Gordon, Vihra Sotirova, Alexandre Reymond, Cedric Howald, Emilie Aït Yahya Graison, Jacqueline Chrast, Yijun Ruan, Xiaoan Ruan, Atif Shahab, Wan Ting Poh, Chia Lin Wei, Gregory E. Crawford, Terrence S. Furey, Alan P. Boyle, Nathan C. Sheffield, Lingyun Song, Yoichiro Shibata, Teresa Vales, Deborah Winter, Zhancheng Zhang, Darin London, Tianyuan Wang, Ewan Birney, Damian Keefe, Vishwanath R. Iyer, Bum Kyu Lee, Ryan M. McDaniell, Zheng Liu, Anna Battenhouse, Akshay A. Bhinge, Jason D. Lieb, Linda L. Grasfeder, Kimberly A. Showers, Paul G. Giresi, Seul K C Kim, Christopher Shestak, Richard M. Myers, Florencia Pauli, Timothy E. Reddy, Jason Gertz, E. Christopher Partridge, Preti Jain, Rebekka O. Sprouse, Anita Bansal, Barbara Pusey, Michael A. Muratet, Katherine E. Varley, Kevin M. Bowling, Kimberly M. Newberry, Amy S. Nesmith, Jason A. Dilocker, Stephanie L. Parker, Lindsay L. Waite, Krista Thibeault, Kevin Roberts, Devin M. Absher, Barbara Wold, Ali Mortazavi, Brian Williams, Georgi Marinov, Diane Trout, Shirley Pepke, Brandon King, Kenneth McCue, Anthony Kirilusha, Gilberto DeSalvo, Katherine Aylor Fisher, Henry Amrhein, Jost Vielmetter, Gavin Sherlock, Arend Sidow, Serafim Batzoglou, Rami Rauch, Anshul Kundaje, Max Libbrecht, Elliott H. Margulies, Stephen C J Parker, Laura Elnitski, Eric D. Green, Tim Hubbard, Jennifer Harrow, Stephen Searle, Felix Kokocinski, Browen Aken, Adam Frankish, Toby Hunt, Gloria Despacio-Reyes, Mike Kay, Gaurab Mukherjee, Alexandra Bignell, Gary Saunders, Veronika Boychenko, Michael Brent, M. J. van Baren, Randall H. Brown, Mark Gerstein, Ekta Khurana, Suganthi Balasubramanian, Zhengdong Zhang, Hugo Lam, Philip Cayting, Rebecca Robilotto, Zhi Lu, Roderic Guigo, Thomas Derrien, Andrea Tanzer, David G. Knowles, Marco Mariotti, W. James Kent, David Haussler, Rachel Harte, Mark Diekhans, Manolis Kellis, Mike Lin, Pouya Kheradpour, Jason Ernst, Alexandre Reymond, Cedric Howald, Emilie Aït Yahya Graison, Jacqueline Chrast, Alfonso Valencia, Michael Tress, Jose Manuel Rodriguez, Michael Snyder, Stephen G. Landt, Debasish Raha, Minyi Shi, Ghia Euskirchen, Fabian Grubert, Maya Kasowski, Jin Lian, Philip Cayting, Phil Lacroute, Youhan Xu, Hannah Monahan, Dorrelyn Patacsil, Teri Slifer, Xinqiong Yang, Alexandra Charos, Brian Reed, Linfeng Wu, Raymond K. Auerbach, Lukas Habegger, Manoj Hariharan, Joel Rozowsky, Alexej Abyzov, Sherman M. Weissman, Mark Gerstein, Kevin Struhl, Nathan Vincent Lamarre, Marianne Allen Lindahl, Benoit Miotto, Zarmik Moqtaderi, Joseph D. Fleming, Peter Newburger, Peggy J. Farnham, Seth Frietze, Henriette O'Geen, Xiaoqin Xu, Kim R. Blahnik, Alina R. Cao, Sushma Iyengar, John A. Stamatoyannopoulos, Rajinder Kaul, Robert E. Thurman, Hao Wang, Patrick A. Navas, Richard Sandstrom, Peter J. Sabo, Molly Weaver, Theresa Canfield, Kristen Lee, Shane Neph, Vaughan Roach, Alex Reynolds, Audra Johnson, Eric Rynes, Erika Giste, Shinny Vong, Jun Neri, Tristan Frum, Ericka M. Johnson, Eric D. Nguyen, Abigail K. Ebersol, Minerva E. Sanchez, Hadar H. Sheffer, Dimitra Lotakis, Eric Haugen, Richard Humbert, Tanya Kutyavin, Tony Shafer, Job Dekker, Bryan R. Lajoie, Amartya Sanyal, W. James Kent, Kate R. Rosenbloom, Timothy R. Dreszer, Brian J. Raney, Galt P. Barber, Laurence R. Meyer, Cricket A. Sloan, Venkat S. Malladi, Melissa S. Cline, Katrina Learned, Vanessa K. Swing, Ann S. Zweig, Brooke Rhead, Pauline A. Fujita, Krishna Roskin, Donna Karolchik, Robert M. Kuhn, David Haussler, Ewan Birney, Ian Dunham, Steven P. Wilder, Damian Keefe, Daniel Sobral, Javier Herrero, Kathryn Beal, Margus Lukk, Alvis Brazma, Juan M. Vaquerizas, Nicholas M. Luscombe, Peter J. Bickel, Nathan Boley, James B. Brown, Qunhua Li, Haiyan Huang, Mark Gerstein, Lukas Habegger, Andrea Sboner, Joel Rozowsky, Raymond K. Auerbach, Kevin Y. Yip, Chao Cheng, Koon Kiu Yan, Nitin Bhardwaj, Jing Wang, Lucas Lochovsky, Justin Jee, Theodore Gibson, Jing Leng, Jiang Du, Ross C. Hardison, Robert S. Harris, Giltae Song, Webb Miller, David Haussler, Krishna Roskin, Bernard Suh, Ting Wang, Benedict Paten, William S. Noble, Michael M. Hoffman, Orion J. Buske, Zhiping Weng, Xianjun Dong, Jie Wang, Hualin Xi, Scott A. Tenenbaum, Frank Doyle, Luiz O. Penalva, Sridar Chittur, Thomas D. Tullius, Stephen C J Parker, Kevin P. White, Subhradip Karmakar, Alec Victorsen, Nader Jameel, Nick Bild, Robert L. Grossman, Michael Snyder, Stephen G. Landt, Xinqiong Yang, Dorrelyn Patacsil, Teri Slifer, Job Dekker, Bryan R. Lajoie, Amartya Sanyal, Zhiping Weng, Troy W. Whitfield, Jie Wang, Patrick J. Collins, Nathan D. Trinklein, E. Christopher Partridge, Richard M. Myers, Morgan C. Giddings, Xian Chen, Jainab Khatun, Chris Maier, Yanbao Yu, Harsha Gunawardena, Brian Risk, Elise A. Feingold, Rebecca F. Lowdon, Laura A L Dillon, Peter J. Good

Research output: Contribution to journalArticle

968 Scopus citations

Abstract

The mission of the Encyclopedia of DNA Elements (ENCODE) Project is to enable the scientific and medical communities to interpret the human genome sequence and apply it to understand human biology and improve health. The ENCODE Consortium is integrating multiple technologies and approaches in a collective effort to discover and define the functional elements encoded in the human genome, including genes, transcripts, and transcriptional regulatory regions, together with their attendant chromatin states and DNA methylation patterns. In the process, standards to ensure high-quality data have been implemented, and novel algorithms have been developed to facilitate analysis. Data and derived results are made available through a freely accessible database. Here we provide an overview of the project and the resources it is generating and illustrate the application of ENCODE data to interpret the human genome.

Original languageEnglish (US)
Article numbere1001046
JournalPLoS Biology
Volume9
Issue number4
DOIs
StatePublished - Apr 2011

ASJC Scopus subject areas

  • Agricultural and Biological Sciences(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Immunology and Microbiology(all)
  • Neuroscience(all)

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    Myers, R. M., Stamatoyannopoulos, J., Snyder, M., Dunham, I., Hardison, R. C., Bernstein, B. E., Gingeras, T. R., Kent, W. J., Birney, E., Wold, B., Crawford, G. E., Bernstein, B. E., Epstein, C. B., Shoresh, N., Ernst, J., Mikkelsen, T. S., Kheradpour, P., Zhang, X., Wang, L., ... Good, P. J. (2011). A user's guide to the Encyclopedia of DNA elements (ENCODE). PLoS Biology, 9(4), [e1001046]. https://doi.org/10.1371/journal.pbio.1001046