Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project

  title={Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project},
  author={Ewan Birney and John A. Stamatoyannopoulos and Anindya Dutta and Roderic Guig{\'o} and Thomas R. Gingeras and Elliott H. Margulies and Zhiping Weng and Michael Snyder and Emmanouil T. Dermitzakis and Robert E. Thurman and Michael S. Kuehn and Christopher M Taylor and Shane J. Neph and Christoph M. Koch and Saurabh Asthana and Ankit Malhotra and Ivan A. Adzhubei and Jason A Greenbaum and Robert Andrews and Paul Flicek and Patrick J. Boyle and Hua Cao and Nigel P. Carter and Gayle K. Clelland and Sean Davis and Nathan Day and Pawandeep Dhami and Shane C. Dillon and Michael Dorschner and Heike Fiegler and Paul G. Giresi and Jeff Goldy and Michael Hawrylycz and Andrew K Haydock and Richard Humbert and Keith D. James and Brett E. Johnson and Ericka M. Johnson and Tristan T. Frum and Elizabeth R Rosenzweig and Neerja Karnani and Kirsten G. Lee and Gregory C. Lefebvre and Patrick A. Navas and Fidencio V. Neri and Stephen C. J. Parker and Peter J. Sabo and Richard S. Sandstrom and Anthony Shafer and David Vetrie and M. B. Weaver and Sarah J. Wilcox and Man Yu and Francis S. Collins and Job Dekker and Jason D. Lieb and Thomas D. Tullius and Gregory E. Crawford and Shamil R. Sunyaev and William Stafford Noble and Ian Dunham and France Denoeud and Alexandre Reymond and Philipp Kapranov and Joel S. Rozowsky and Deyou Zheng and Robert Castelo and Adam Frankish and Jennifer L. Harrow and Srinka Ghosh and Albin Sandelin and Ivo L. Hofacker and Robert Baertsch and Damian Keefe and Sujit Dike and Jill Cheng and Heather A. Hirsch and Edward A. Sekinger and Julien Lagarde and Josep F. Abril and Atif Shahab and Christoph Flamm and Claudia Fried and J{\"o}rg Hackerm{\"u}ller and Jana Hertel and Manja Lindemeyer and Kristin Missal and Andrea Tanzer and Stefan Washietl and Jan Korbel and Olof Emanuelsson and Jakob Skou Pedersen and Nancy Holroyd and Ruth Taylor and David Swarbreck and Nicholas L. Matthews and Mark C. Dickson and Daryl J. Thomas and Matthew T. Weirauch and James Gilbert and Jorg Drenkow and Ian Bell and Xiaodong Zhao and Kandhadayar Gopalan Srinivasan and Wing-Kin Sung and Hong Sain Ooi and Kuo Ping Chiu and Sylvain Foissac and Tyler S Alioto and Michael R. Brent and Lior Pachter and Michael L. Tress and Alfonso Valencia and Siew Woh Choo and Chiou Yu Choo and Catherine Ucla and Caroline Manzano and Carine Wyss and Evelyn Ning Man Cheung and Taane G. Clark and J. Ben Brown and Madhavan Ganesh and Sandeep Patel and Hari Tammana and Jacqueline Chrast and Charlotte N. Henrichsen and Chikatoshi Kai and Jun Kawai and Ugrappa Nagalakshmi and Jiaqian Wu and Zheng Lian and Jin Xian Lian and Peter E Newburger and Xueqing Zhang and Peter Bickel and John S. Mattick and Piero Carninci and Yoshihide Hayashizaki and Sherman Weissman and Tim Hubbard and Richard M. Myers and Jane Rogers and Peter F. Stadler and Todd M. Lowe and Chia-Lin Wei and Yijun Ruan and Kevin Struhl and Mark Gerstein and Stylianos E. Antonarakis and Yutao Fu and Eric D. Green and Ulaş Kara{\"o}z and Adam Siepel and James Taylor and Laura A Liefer and Kris A. Wetterstrand and Peter J. Good and Elise A. Feingold and M. Susan Guyer and Gregory M. Cooper and George Asimenos and Colin N. Dewey and Minmei Hou and Sergey Nikolaev and Juan I Montoya-Burgos and Ari L{\"o}ytynoja and Simon Whelan and Fabio Pardi and Tim Massingham and Haiyan Huang and Nancy R. Zhang and Ian Holmes and James C. Mullikin and Abel Ureta-Vidal and Benedict Paten and Michael R. Seringhaus and Deanna M. Church and Kate R. Rosenbloom and W. James Kent and Eric A. Stone and Serafim Batzoglou and Nick Goldman and Ross C. Hardison and David Haussler and Webb Miller and Arend Sidow and Nathan D. Trinklein and Zhengdong D. Zhang and Leah Barrera and Rhona K. Stuart and D. C. King and Adam Ameur and Stefan Enroth and Mark C. Bieda and Jonghwan Kim and Akshay A. Bhinge and Nan Jiang and Jun Liu and Fei Yao and Vinsensius B. Vega and Charlie Wah Heng Lee and Patrick Ng and Annie Yang and Zarmik Moqtaderi and Zhou Zhu and Xiaoqin Xu and Sharon Squazzo and Matthew J Oberley and David Inman and Michael A. Singer and Todd A. Richmond and Kyle J. Munn and Alvaro Rada-Iglesias and Ola Wallerman and Jan Komorowski and Joanna C. Fowler and Phillippe Couttet and Alexander W Bruce and Oliver M Dovey and Peter F. Ellis and Cordelia Langford and David A. Nix and Ghia M Euskirchen and Stephen Hartman and Alexander E. Urban and Peter Kraus and Sara Van Calcar and Nate Heintzman and Tae Hoon Kim and Kun Wang and Chunxu Qu and Gary Chung Hon and Rosa Luna and Christopher K. Glass and Michael G. Rosenfeld and Shelley J Force Aldred and Sara J. Cooper and Anason S. Halees and Jane Marie Lin and Hennady P. Shulha and Xiaoling Zhang and Mousheng Xu and Jaafar N Sleiman Haidar and Yong Yu and Vishwanath R. Iyer and R. D. Green and Claes Wadelius and Peggy J. Farnham and Bing Ren and Rachel A. Harte and Angie S. Hinrichs and Heather Trumbower and Hiram Clawson and Jennifer Hillman-Jackson and Ann S. Zweig and Kayla Smith and Archana Thakkapallayil and Galt P. Barber and Robert M. Kuhn and Donna Karolchik and Llu{\'i}s Armengol and Christine P. Bird and Paul I W de Bakker and Andrew D. Kern and N{\'u}ria L{\'o}pez-Bigas and Joel D. Martin and Barbara E. Stranger and Abigail Woodroffe and Eugene Davydov and Antigone S. Dimas and Eduardo Eyras and Ingileif B. Hallgr{\'i}msd{\'o}ttir and Julian Leon Huppert and Michael C. Zody and Gonçalo R. Abecasis and Xavier Estivill and Gerard G. Bouffard and Xiaobin Guan and Nancy F. Hansen and Jacquelyn R. Idol and Valerie V. B. Maduro and Baishali Maskeri and Jennifer C. McDowell and Morgan Park and Pamela J. Thomas and Alice C. Young and R. W. Blakesley and Donna M. Muzny and Erica Sodergren and David A. Wheeler and K. C. Worley and Huaiyang Jiang and George Weinstock and Richard A. Gibbs and Tina A. Graves and Robert Fulton and Elaine R. Mardis and Richard K. Wilson and Michele Clamp and James Cuff and Sante Gnerre and David B. Jaffe and Jean L. Chang and Kerstin Lindblad-Toh and Eric S. Lander and Maxim Y. Koriabine and Mikhail Nefedov and Kazutoyo Osoegawa and Yuko Yoshinaga and Baoli Zhu and Pieter J de Jong},
We report the generation and analysis of functional data from multiple, diverse experiments performed on a targeted 1% of the human genome as part of the pilot phase of the ENCODE Project. These data have been further integrated and augmented by a number of evolutionary and computational analyses. Together, our results advance the collective knowledge about human genome function in several major areas. First, our studies provide convincing evidence that the genome is pervasively transcribed… CONTINUE READING
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Integrated analysis of experimental datasets reveals many novel promoters in 1% of the human genome

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Genome Res 2007;17:720–731 • 2007