An integrated encyclopedia of DNA elements in the human genome

James Taylor, Peter J. Park, Axel Visel, M Snyder, Konrad J. Karczewski, Bryan R. Lajoie, Michael O. Dorschner, Timo Lassmann, B Bernstein, Philipp Kapranov, T Gingeras, Xianjun Dong, Alexandre Reymond, Yanbao Yu, Robert E. Thurman, Eric Rynes, Richard Humbert, Matthew T. Maurano, Nathan C. Sheffield, Andrew B. Stergachis, Benjamin Vernot, Richard Sandstrom, Daniel Bates, Lisa Boatman, Douglas Dunn, Abigail K. Ebersol, Audra Johnson, Ericka M. Johnson, Kristen Lee, Darin London, Shane Neph, Éric Nguyen, Hongzhu Qu, Alex Reynolds, Vaughn Roach, Alexias Safi, Minerva E. Sanchez, Amartya Sanyal, Lingyun Song, Shinny Vong, Yongqi Yan, Zhancheng Zhang, R. Scott Hansen, Vishwanath R. Iyer, Joshua M. Akey, Terrence S. Furey, J Stamatoyannopoulos, Oren Ram, Timothy E. Reddy, Peggy Farnham, Sylvain Foissac, Ewan Birney, Stefan Washietl, Zhengqing Ouyang, Adam Frankish, Piero Carninci, Akshay Bhinge, Jason Ernst, Pouya Kheradpour, Lucas D. Ward, Matthew L. Eaton, Noam Shoresh, José M. González, Electra Tapanari, Felix Kokocinski, Amonida Zadissa, Veronika Boychenko, Gaurab Mukherjee, Gloria Despacio-Reyes, Cédric Howald, Andrea Tanzer, Thomas Derrien, Jacqueline Chrast, Nathalie Walters, Suganthi Balasubramanian, Baikang Pei, José Manuel Rodrı́guez, Iakes Ezkurdia, Gemma Barson, Alan P. Boyle, Claire Davidson, Gilberto DeSalvo, Sarah Djebali, Jörg Drenkow, Elise A. Feingold, Katherine Fisher-Aylor, Peter J. Good, Alon Goren, Ed Griffiths, Fabian Grubert, Manoj Hariharan, Robbyn Issner, Julien Lagarde, Deepa Manthravadi, Georgi K. Marinov, Kimberly M. Newberry, William Stafford Noble, Michael J. Pazin, Cristina Sisu, Teri Slifer, Alec Victorsen, Jost Vielmetter, Xinqiong Yang, Chris Zaleski, Michael J. MacCoss, Ian Dunham, Balázs Bánfai, Dannon Baker, Erica Dumais, Sonali Jha, Giovanni Bussotti, Cédric Notredame, Subhradip Karmakar, Huaien Wang, Michael F. Lin, Gayathri Balasundaram, Stephen G. Landt, Gaurav Jain, Henry Amrhein, Chenghai Xue, Melissa Cline, Vanessa M. Kirkup, Katrina Learned, Kate R. Rosenbloom, Leslie B. Adams, Angelika Merkel, Xiaoan Ruan, David A. Hendrix, Jainab Khatun, Maik Röder, Michael T. Baer, João Curado, Radha Duttagupta, Assaf Gordon, Harsha P. Gunawardena, Brandon King, Colin Kingswood, Eddie Park, Jonathan Preall, Paolo Ribeca, Brian A. Risk, Michael Sammeth, Atif Shahab, Jørgen Skancke, Stylianos E. Antonarakis, Morgan C. Giddings, Guoliang Li, Troy W. Whitfield, Javier Herrero, Michael M. Hoffman, Alvis Brāzma, Peter V. Kharchenko, Robert C. Altshuler, Phil Lacroute, Lukas Habegger, Chris Gunter, Kevin M. Bowling, Andrea Sboner, Robert S. Harris, Stephen C.J. Parker, Henriette O’Geen, Roger P. Alexander, Brian J. Raney, Damian Keefe, Nathan D. Trinklein, Zarmik Moqtaderi, Xiaoqin Xu, Galt P Barber, Renqiang Min, Nick Addleman, Nitin Bhardwaj, Jason Gertz, Jing Leng, Hannah Monahan, Dorrelyn Patacsil, Debasish Raha, Linfeng Wu, Miaohua Zhang, Raymond K. Auerbach, Kuljeet Singh Sandhu, Meizhen Zheng, Ping Wang, Mark Gerstein, Victor X. Jin, Sofia Kyriazopoulou-Panagiotopoulou, Marc A. Schaub, Donna Karolchik, Patrick Collins, Orion J. Buske, Steven P. Wilder, Daniel Sobral, Margus Lukk, Shawn Levy, Marijke J. van Baren, Jingyi Jessica Li, Naim U. Rashid, Nicholas M. Luscombe, Linda L. Grasfeder, Ryan M. McDaniell, Kimberly A. Showers, Jeffrey A. Bilmes, Sheera Adar, Laurence Meyer, Judith R. Wexler, Timothy R. Dreszer, Devin M. Absher, Catherine Snow, Scott A. Tenenbaum, Shirley Pepke, Jiali Zhuang, Pedro Ferreira, Matthew C. Wong, Marco Mariotti, Ian Bell, Michael Muratet, Lucas Lochovsky, Weisheng Wu, Jeffrey C. Long, Amy S. Nesmith, Jackie Dumais, Kathryn Beal, Paul Flicek, Nathan Johnson, Anshul Kundaje, Serafim Batzoglou, Nadine Hussami, Max W. Libbrecht, Shelley F. Aldred, Carrie A. Davis, Felix Schlesinger, Alex Dobin, Wei Lin, Philippe Batut, Kimberly Bell, Sudipto Chakrabortty, Megan Fastuca, Kata Fejes-Toth, Kimberly Presaud, Lei-Hoon See, Gregory J. Hannon, Francis Doyle, Charles B. Epstein, Tarjei S. Mikkelsen, Xiaolan Zhang, Li Wang, Michael J. Coyne, Timothy Durham, Manching Ku, Thanh Truong, Seth Frietze, Heather Witt, Jennifer Harrow, Timothy J. Hubbard, Bronwen Aken, Daniel Barrell, Andrew Berry, Alexandra Bignell, James Gilbert, Toby Hunt, Mike Kay, Jane Loveland, Jonathan Mudge, Gary Saunders, Stephen Searle, Charlie Steward, Laurens Wilming, Rajinder Kaul, John Wrobel, Job Dekker, Keith Bettinger, Philip Cayting, Yong Cheng, Catharine Eastman, G. Euskirchen, Maya Kasowski, Hugo Lam, Lucia Ramirez, Minyi Shi, Bum-Kyu Lee, Anna Battenhouse, Zheng Liu, 倪芸芸, Florencia Pauli, Richard M. Myers, E. Partridge, Katherine E. Varley, Anita Bansal, Preti Jain, Marie K. Cross, Barbara Pusey, Stephanie Parker, Nicholas S. Davis, Sarah K. Meadows, Tracy Eggleston, J. Scott Newberry, W. James Kent, Cricket A. Sloan, Venkat S. Malladi, Steven G. Heitner, Morgan Maddren, Mark Diekhans, Rachel Harte, Peter Sabo, Theresa K. Canfield, Morgan J. Diegel, Erica Gist, Eric Haugen, Tattyana V. Kutyavin, Fiedencio V. Neri, Anthony O. Shafer, Sean Thomas, Jeff Vierstra, Hao Wang, Molly A. Weaver, Avinash D. Sahu, Gregory E. Crawford, Tianyuan Wang, Deborah Winter, Jeremy M. Simon, Jason D. Lieb, Paul G. Giresi, Christopher Shestak, Matthew R. Schaner, Seul Ki Kim, Zhuzhu Z. Zhang, Joanna O Mieczkowska, Min Jae Kim, Manolis Kellis, Irwin Jungreis, James B. Brown, Qunhua Li, Peter J. Bickel, Nathan P. Boley, Haiyan Huang, Chao Cheng, Joel Rozowsky, Kevin Y. Yip, Alexej Abyzov, E Khurana, Arif Harmanci, Xinmeng J. Mu, Koon-Kiu Yan, Roderic Guigó, Tyler Alioto, David Gonzalez, Rory Johnson, Hagen Tilgner, Melissa Greven, Xinying Lin, Jie Wang, Zhiping Weng, Belinda Giardine, R Hardison, Webb Miller, Sowmya Iyer, Rehab F. Abdelhamid, Ana Maria Suzuki, Hazuki Takahashi, Yoshihide Hayashizaki, Barbara Wold, Brian A. Williams, Igor Antoshechkin, Lorain Schaeffer, Diane Trout, Clarke Gasper, Michael Anaya, Kenneth McCue, Sreeram Balasubramanian, Ali Mortazavi, Elliott H. Margulies, Hualin S. Xi, Shawn Gillespie, Eric D. Green, Rebecca F. Lowdon, Laura A. L. Dillon, Caroline J. Kelly, Julia Zhang, Laura Elnitski, Hanna M. Petrykowska, Kevin P. White, Raj R. Bhanvadia, Alina Choudhury, Marc Domanus, Lijia Ma, Jennifer Moran, Heather Kuiper, Christopher W. Maier, Ling Xie, Xian Chen, Hui Gao, Melissa J. Fullwood, Oscar J. Luo, Yijun Ruan, Daniel Robyr, Piotr A. Mieczkowski, Wing H. Wong, Matthew J. Blow, Len A. Pennachio, Michael L. Tress, Alfonso Valencia, Zhi Lu, Michael Brent, Zhengdong Zhang, David Haussler, Alina R. Cao, Alexandra Charos, Brian Reed, Joseph D. Fleming, Nathan Lamarre-Vincent, Marianne Lindahl-Allen, Benoît Miotto, Kevin Struhl, Sushma Iyengar, Jin Lian, Sherman M. Weissman, Luiz O. Penalva, Thomas Auer, Lázaro Centanin, Michael Eichenlaub, Franziska Gruhl, Stephan Heermann, Burkhard Hoeckendorf, Daigo Inoue, Tanja Kellner, Stephan Kirchmaier, Claudia Mueller, Robert Reinhardt, Lea Schertel, Stephanie Schneider, R. Sinn, Beate Wittbrodt, Jochen Wittbrodt, Rachel Byron, Michael Bender, Mark Groudine, T Frum, Dimitra Lotakis, Patrick Navas, George Stamatoyannopoulos, Kavita Garg, Juan M. Vaquerizas, Arend Sidow
2012-09-01
SCID:  54.1/zxgsbq9n
Abstract (AI)
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. This overview of the ENCODE project outlines the data accumulated so far, revealing that 80% of the human genome now has at least one biochemical function assigned to it; the newly identified functional elements should aid the interpretation of results of genome-wide association studies, as many correspond to sites of association with human disease. The Encyclopedia of DNA Elements (ENCODE) project has systematically mapped regions of transcription, transcription-factor association, chromatin structure and histone modification. In this overview, the Consortium guides the readers through the project itself, the data and their integrated analyses. Eighty per cent of the human genome now has at least one biochemical function assigned to it. In addition to expanding our understanding of how gene expression is regulated on a genome-wide scale, the newly identified functional elements should help researchers to interpret the results of genome-wide associated studies because many correspond to sites associated with human disease.
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2012-09-01
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Authors
James Taylor
Peter J. Park
Axel Visel
M Snyder
Konrad J. Karczewski
Bryan R. Lajoie
Michael O. Dorschner
Timo Lassmann
B Bernstein
Philipp Kapranov
T Gingeras
Xianjun Dong
Alexandre Reymond
Yanbao Yu
Robert E. Thurman
Eric Rynes
Richard Humbert
Matthew T. Maurano
Nathan C. Sheffield
Andrew B. Stergachis
Benjamin Vernot
Richard Sandstrom
Daniel Bates
Lisa Boatman
Douglas Dunn
Abigail K. Ebersol
Audra Johnson
Ericka M. Johnson
Kristen Lee
Darin London
Shane Neph
Éric Nguyen
Hongzhu Qu
Alex Reynolds
Vaughn Roach
Alexias Safi
Minerva E. Sanchez
Amartya Sanyal
Lingyun Song
Shinny Vong
Yongqi Yan
Zhancheng Zhang
R. Scott Hansen
Vishwanath R. Iyer
Joshua M. Akey
Terrence S. Furey
J Stamatoyannopoulos
Oren Ram
Timothy E. Reddy
Peggy Farnham
Sylvain Foissac
Ewan Birney
Stefan Washietl
Zhengqing Ouyang
Adam Frankish
Piero Carninci
Akshay Bhinge
Jason Ernst
Pouya Kheradpour
Lucas D. Ward
Matthew L. Eaton
Noam Shoresh
José M. González
Electra Tapanari
Felix Kokocinski
Amonida Zadissa
Veronika Boychenko
Gaurab Mukherjee
Gloria Despacio-Reyes
Cédric Howald
Andrea Tanzer
Thomas Derrien
Jacqueline Chrast
Nathalie Walters
Suganthi Balasubramanian
Baikang Pei
José Manuel Rodrı́guez
Iakes Ezkurdia
Gemma Barson
Alan P. Boyle
Claire Davidson
Gilberto DeSalvo
Sarah Djebali
Jörg Drenkow
Elise A. Feingold
Katherine Fisher-Aylor
Peter J. Good
Alon Goren
Ed Griffiths
Fabian Grubert
Manoj Hariharan
Robbyn Issner
Julien Lagarde
Deepa Manthravadi
Georgi K. Marinov
Kimberly M. Newberry
William Stafford Noble
Michael J. Pazin
Cristina Sisu
Teri Slifer
Alec Victorsen
Jost Vielmetter
Xinqiong Yang
Chris Zaleski
Michael J. MacCoss
Ian Dunham
Balázs Bánfai
Dannon Baker
Erica Dumais
Sonali Jha
Giovanni Bussotti
Cédric Notredame
Subhradip Karmakar
Huaien Wang
Michael F. Lin
Gayathri Balasundaram
Stephen G. Landt
Gaurav Jain
Henry Amrhein
Chenghai Xue
Melissa Cline
Vanessa M. Kirkup
Katrina Learned
Kate R. Rosenbloom
Leslie B. Adams
Angelika Merkel
Xiaoan Ruan
David A. Hendrix
Jainab Khatun
Maik Röder
Michael T. Baer
João Curado
Radha Duttagupta
Assaf Gordon
Harsha P. Gunawardena
Brandon King
Colin Kingswood
Eddie Park
Jonathan Preall
Paolo Ribeca
Brian A. Risk
Michael Sammeth
Atif Shahab
Jørgen Skancke
Stylianos E. Antonarakis
Morgan C. Giddings
Guoliang Li
Troy W. Whitfield
Javier Herrero
Michael M. Hoffman
Alvis Brāzma
Peter V. Kharchenko
Robert C. Altshuler
Phil Lacroute
Lukas Habegger
Chris Gunter
Kevin M. Bowling
Andrea Sboner
Robert S. Harris
Stephen C.J. Parker
Henriette O’Geen
Roger P. Alexander
Brian J. Raney
Damian Keefe
Nathan D. Trinklein
Zarmik Moqtaderi
Xiaoqin Xu
Galt P Barber
Renqiang Min
Nick Addleman
Nitin Bhardwaj
Jason Gertz
Jing Leng
Hannah Monahan
Dorrelyn Patacsil
Debasish Raha
Linfeng Wu
Miaohua Zhang
Raymond K. Auerbach
Kuljeet Singh Sandhu
Meizhen Zheng
Ping Wang
Mark Gerstein
Victor X. Jin
Sofia Kyriazopoulou-Panagiotopoulou
Marc A. Schaub
Donna Karolchik
Patrick Collins
Orion J. Buske
Steven P. Wilder
Daniel Sobral
Margus Lukk
Shawn Levy
Marijke J. van Baren
Jingyi Jessica Li
Naim U. Rashid
Nicholas M. Luscombe
Linda L. Grasfeder
Ryan M. McDaniell
Kimberly A. Showers
Jeffrey A. Bilmes
Sheera Adar
Laurence Meyer
Judith R. Wexler
Timothy R. Dreszer
Devin M. Absher
Catherine Snow
Scott A. Tenenbaum
Shirley Pepke
Jiali Zhuang
Pedro Ferreira
Matthew C. Wong
Marco Mariotti
Ian Bell
Michael Muratet
Lucas Lochovsky
Weisheng Wu
Jeffrey C. Long
Amy S. Nesmith
Jackie Dumais
Kathryn Beal
Paul Flicek
Nathan Johnson
Anshul Kundaje
Serafim Batzoglou
Nadine Hussami
Max W. Libbrecht
Shelley F. Aldred
Carrie A. Davis
Felix Schlesinger
Alex Dobin
Wei Lin
Philippe Batut
Kimberly Bell
Sudipto Chakrabortty
Megan Fastuca
Kata Fejes-Toth
Kimberly Presaud
Lei-Hoon See
Gregory J. Hannon
Francis Doyle
Charles B. Epstein
Tarjei S. Mikkelsen
Xiaolan Zhang
Li Wang
Michael J. Coyne
Timothy Durham
Manching Ku
Thanh Truong
Seth Frietze
Heather Witt
Jennifer Harrow
Timothy J. Hubbard
Bronwen Aken
Daniel Barrell
Andrew Berry
Alexandra Bignell
James Gilbert
Toby Hunt
Mike Kay
Jane Loveland
Jonathan Mudge
Gary Saunders
Stephen Searle
Charlie Steward
Laurens Wilming
Rajinder Kaul
John Wrobel
Job Dekker
Keith Bettinger
Philip Cayting
Yong Cheng
Catharine Eastman
G. Euskirchen
Maya Kasowski
Hugo Lam
Lucia Ramirez
Minyi Shi
Bum-Kyu Lee
Anna Battenhouse
Zheng Liu
倪芸芸
Florencia Pauli
Richard M. Myers
E. Partridge
Katherine E. Varley
Anita Bansal
Preti Jain
Marie K. Cross
Barbara Pusey
Stephanie Parker
Nicholas S. Davis
Sarah K. Meadows
Tracy Eggleston
J. Scott Newberry
W. James Kent
Cricket A. Sloan
Venkat S. Malladi
Steven G. Heitner
Morgan Maddren
Mark Diekhans
Rachel Harte
Peter Sabo
Theresa K. Canfield
Morgan J. Diegel
Erica Gist
Eric Haugen
Tattyana V. Kutyavin
Fiedencio V. Neri
Anthony O. Shafer
Sean Thomas
Jeff Vierstra
Hao Wang
Molly A. Weaver
Avinash D. Sahu
Gregory E. Crawford
Tianyuan Wang
Deborah Winter
Jeremy M. Simon
Jason D. Lieb
Paul G. Giresi
Christopher Shestak
Matthew R. Schaner
Seul Ki Kim
Zhuzhu Z. Zhang
Joanna O Mieczkowska
Min Jae Kim
Manolis Kellis
Irwin Jungreis
James B. Brown
Qunhua Li
Peter J. Bickel
Nathan P. Boley
Haiyan Huang
Chao Cheng
Joel Rozowsky
Kevin Y. Yip
Alexej Abyzov
E Khurana
Arif Harmanci
Xinmeng J. Mu
Koon-Kiu Yan
Roderic Guigó
Tyler Alioto
David Gonzalez
Rory Johnson
Hagen Tilgner
Melissa Greven
Xinying Lin
Jie Wang
Zhiping Weng
Belinda Giardine
R Hardison
Webb Miller
Sowmya Iyer
Rehab F. Abdelhamid
Ana Maria Suzuki
Hazuki Takahashi
Yoshihide Hayashizaki
Barbara Wold
Brian A. Williams
Igor Antoshechkin
Lorain Schaeffer
Diane Trout
Clarke Gasper
Michael Anaya
Kenneth McCue
Sreeram Balasubramanian
Ali Mortazavi
Elliott H. Margulies
Hualin S. Xi
Shawn Gillespie
Eric D. Green
Rebecca F. Lowdon
Laura A. L. Dillon
Caroline J. Kelly
Julia Zhang
Laura Elnitski
Hanna M. Petrykowska
Kevin P. White
Raj R. Bhanvadia
Alina Choudhury
Marc Domanus
Lijia Ma
Jennifer Moran
Heather Kuiper
Christopher W. Maier
Ling Xie
Xian Chen
Hui Gao
Melissa J. Fullwood
Oscar J. Luo
Yijun Ruan
Daniel Robyr
Piotr A. Mieczkowski
Wing H. Wong
Matthew J. Blow
Len A. Pennachio
Michael L. Tress
Alfonso Valencia
Zhi Lu
Michael Brent
Zhengdong Zhang
David Haussler
Alina R. Cao
Alexandra Charos
Brian Reed
Joseph D. Fleming
Nathan Lamarre-Vincent
Marianne Lindahl-Allen
Benoît Miotto
Kevin Struhl
Sushma Iyengar
Jin Lian
Sherman M. Weissman
Luiz O. Penalva
Thomas Auer
Lázaro Centanin
Michael Eichenlaub
Franziska Gruhl
Stephan Heermann
Burkhard Hoeckendorf
Daigo Inoue
Tanja Kellner
Stephan Kirchmaier
Claudia Mueller
Robert Reinhardt
Lea Schertel
Stephanie Schneider
R. Sinn
Beate Wittbrodt
Jochen Wittbrodt
Rachel Byron
Michael Bender
Mark Groudine
T Frum
Dimitra Lotakis
Patrick Navas
George Stamatoyannopoulos
Kavita Garg
Juan M. Vaquerizas
Arend Sidow
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