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

Ewan Birney, John A. Stamatoyannopoulos, Anindya Dutta, Roderic Guigó, Thomas R. Gingeras, Elliott H. Margulies, Zhiping Weng, Michael Snyder, Emmanouil T. Dermitzakis, Robert E. Thurman, Michael S. Kuehn, Christopher M. Taylor, Shane Neph, Christoph M. Koch, Saurabh Asthana, Ankit Malhotra, Ivan Adzhubei, Jason A. Greenbaum, Robert M. Andrews, Paul Flicek & 291 others Patrick J. Boyle, Hua Cao, Nigel P. Carter, Gayle K. Clelland, Sean Davis, Nathan Day, Pawandeep Dhami, Shane C. Dillon, Michael O. Dorschner, Heike Fiegler, Paul G. Giresi, Jeff Goldy, Michael Hawrylycz, Andrew Haydock, Richard Humbert, Keith D. James, Brett E. Johnson, Ericka M. Johnson, Tristan T. Frum, Elizabeth R. Rosenzweig, Neerja Karnani, Kirsten Lee, Gregory C. Lefebvre, Patrick A. Navas, Fidencio Neri, Stephen C J Parker, Peter J. Sabo, Richard Sandstrom, Anthony Shafer, David Vetrie, Molly Weaver, Sarah Wilcox, Man Yu, Francis S. Collins, Job Dekker, Jason D. Lieb, Thomas D. Tullius, Gregory E. Crawford, Shamil Sunyaev, William S. Noble, Ian Dunham, France Denoeud, Alexandre Reymond, Philipp Kapranov, Joel Rozowsky, Deyou Zheng, Robert Castelo, Adam Frankish, Jennifer Harrow, Srinka Ghosh, Albin Sandelin, Ivo L. Hofacker, Robert Baertsch, Damian Keefe, Sujit Dike, Jill Cheng, Heather A. Hirsch, Edward A. Sekinger, Julien Lagarde, Josep F. Abril, Atif Shahab, Christoph Flamm, Claudia Fried, Jörg Hackermüller, Jana Hertel, Manja Lindemeyer, Kristin Missal, Andrea Tanzer, Stefan Washietl, Jan Korbel, Olof Emanuelsson, Jakob S. Pedersen, Nancy Holroyd, Ruth Taylor, David Swarbreck, Nicholas Matthews, Mark C. Dickson, Daryl J. Thomas, Matthew T. Weirauch, James Gilbert, Jorg Drenkow, Ian Bell, Xiaodong Zhao, K. G. Srinivasan, Wing Kin Sung, Hong Sain Ooi, Kuo Ping Chiu, Sylvain Foissac, Tyler Alioto, Michael Brent, Lior Pachter, Michael L. Tress, Alfonso Valencia, Siew Woh Choo, Chiou Yu Choo, Catherine Ucla, Caroline Manzano, Carine Wyss, Evelyn Cheung, Taane G. Clark, James B. Brown, Madhavan Ganesh, Sandeep Patel, Hari Tammana, Jacqueline Chrast, Charlotte N. Henrichsen, Chikatoshi Kai, Jun Kawai, Ugrappa Nagalakshmi, Jiaqian Wu, Zheng Lian, Jin Lian, Peter Newburger, Xueqing Zhang, Peter Bickel, John S. Mattick, Piero Carninci, Yoshihide Hayashizaki, Sherman Weissman, Tim Hubbard, Richard M. Myers, Jane Rogers, Peter F. Stadler, Todd M. Lowe, Chia Lin Wei, Yijun Ruan, Kevin Struhl, Mark Gerstein, Stylianos E. Antonarakis, Yutao Fu, Eric D. Green, Ulaş Karaöz, Adam Siepel, James Taylor, Laura A. Liefer, Kris A. Wetterstrand, Peter J. Good, Elise A. Feingold, Mark S. Guyer, Gregory M. Cooper, George Asimenos, Colin N. Dewey, Minmei Hou, Sergey Nikolaev, Juan I. Montoya-Burgos, Ari Löytynoja, Simon Whelan, Fabio Pardi, Tim Massingham, Haiyan Huang, Nancy R. Zhang, Ian Holmes, James C. Mullikin, Abel Ureta-Vidal, Benedict Paten, Michael Seringhaus, Deanna Church, Kate Rosenbloom, W. James Kent, Eric A. Stone, Serafim Batzoglou, Nick Goldman, Ross C. Hardison, David Haussler, Webb Miller, Arend Sidow, Nathan D. Trinklein, Zhengdong Zhang, Leah Barrera, Rhona Stuart, David C. King, Adam Ameur, Stefan Enroth, Mark C. Bieda, Jonghwan Kim, Akshay A. Bhinge, Nan Jiang, Jun Liu, Fei Yao, Vinsensius B. Vega, Charlie W H Lee, Patrick Ng, Annie Yang, Zarmik Moqtaderi, Zhou Zhu, Xiaoqin Xu, Sharon Squazzo, Matthew J. Oberley, David Inman, Michael A. Singer, Todd A. Richmond, Kyle J. Munn, Alvaro Rada-Iglesias, Ola Wallerman, Jan Komorowski, Joanna C. Fowler, Phillippe Couttet, Alexander W. Bruce, Oliver M. Dovey, Peter D. Ellis, Cordelia F. Langford, David A. Nix, Ghia Euskirchen, Stephen Hartman, Alexander E. Urban, Peter Kraus, Sara Van Calcar, Nate Heintzman, Tae Hoon Kim, Kun Wang, Chunxu Qu, Gary Hon, Rosa Luna, Christopher K. Glass, M. Geoff Rosenfeld, Shelley Force Aldred, Sara J. Cooper, Anason Halees, Jane M. Lin, Hennady P. Shulha, Xiaoling Zhang, Mousheng Xu, Jaafar N S Haidar, Yong Yu, Vishwanath R. Iyer, Roland D. Green, Claes Wadelius, Peggy J. Farnham, Bing Ren, Rachel A. Harte, Angie S. Hinrichs, Heather Trumbower, Hiram Clawson, Jennifer Hillman-Jackson, Ann S. Zweig, Kayla Smith, Archana Thakkapallayil, Galt Barber, Robert M. Kuhn, Donna Karolchik, Lluis Armengol, Christine P. Bird, Paul I W De Bakker, Andrew D. Kern, Nuria Lopez-Bigas, Joel D. Martin, Barbara E. Stranger, Abigail Woodroffe, Eugene Davydov, Antigone Dimas, Eduardo Eyras, Ingileif B. Hallgrímsdóttir, Julian Huppert, Michael C. Zody, Gonçalo R. Abecasis, Xavier Estivill, Gerard G. Bouffard, Xiaobin Guan, Nancy F. Hansen, Jacquelyn R. Idol, Valerie V B Maduro, Baishali Maskeri, Jennifer C. McDowell, Morgan Park, Pamela J. Thomas, Alice C. Young, Robert W. Blakesley, Donna M. Muzny, Erica Sodergren, David A. Wheeler, Kim C. Worley, Huaiyang Jiang, George M. Weinstock, Richard A. Gibbs, Tina Graves, Robert Fulton, Elaine R. Mardis, Richard K. Wilson, Michele Clamp, James Cuff, Sante Gnerre, David B. Jaffe, Jean L. Chang, Kerstin Lindblad-Toh, Eric S. Lander, Maxim Koriabine, Mikhail Nefedov, Kazutoyo Osoegawa, Yuko Yoshinaga, Baoli Zhu, Pieter J. De Jong

Research output: Contribution to journalArticle

3502 Citations (Scopus)

Abstract

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, such that the majority of its bases can be found in primary transcripts, including non-protein-coding transcripts, and those that extensively overlap one another. Second, systematic examination of transcriptional regulation has yielded new understanding about transcription start sites, including their relationship to specific regulatory sequences and features of chromatin accessibility and histone modification. Third, a more sophisticated view of chromatin structure has emerged, including its inter-relationship with DNA replication and transcriptional regulation. Finally, integration of these new sources of information, in particular with respect to mammalian evolution based on inter- and intra-species sequence comparisons, has yielded new mechanistic and evolutionary insights concerning the functional landscape of the human genome. Together, these studies are defining a path for pursuit of a more comprehensive characterization of human genome function.

Original languageEnglish (US)
Pages (from-to)799-816
Number of pages18
JournalNature
Volume447
Issue number7146
DOIs
StatePublished - Jun 14 2007
Externally publishedYes

Fingerprint

Human Genome
Chromatin
Histone Code
Transcription Initiation Site
DNA Replication
Genome

ASJC Scopus subject areas

  • General

Cite this

Birney, E., Stamatoyannopoulos, J. A., Dutta, A., Guigó, R., Gingeras, T. R., Margulies, E. H., ... De Jong, P. J. (2007). Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature, 447(7146), 799-816. https://doi.org/10.1038/nature05874

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. / Birney, Ewan; Stamatoyannopoulos, John A.; Dutta, Anindya; Guigó, Roderic; Gingeras, Thomas R.; Margulies, Elliott H.; Weng, Zhiping; Snyder, Michael; Dermitzakis, Emmanouil T.; Thurman, Robert E.; Kuehn, Michael S.; Taylor, Christopher M.; Neph, Shane; Koch, Christoph M.; Asthana, Saurabh; Malhotra, Ankit; Adzhubei, Ivan; Greenbaum, Jason A.; Andrews, Robert M.; Flicek, Paul; Boyle, Patrick J.; Cao, Hua; Carter, Nigel P.; Clelland, Gayle K.; Davis, Sean; Day, Nathan; Dhami, Pawandeep; Dillon, Shane C.; Dorschner, Michael O.; Fiegler, Heike; Giresi, Paul G.; Goldy, Jeff; Hawrylycz, Michael; Haydock, Andrew; Humbert, Richard; James, Keith D.; Johnson, Brett E.; Johnson, Ericka M.; Frum, Tristan T.; Rosenzweig, Elizabeth R.; Karnani, Neerja; Lee, Kirsten; Lefebvre, Gregory C.; Navas, Patrick A.; Neri, Fidencio; Parker, Stephen C J; Sabo, Peter J.; Sandstrom, Richard; Shafer, Anthony; Vetrie, David; Weaver, Molly; Wilcox, Sarah; Yu, Man; Collins, Francis S.; Dekker, Job; Lieb, Jason D.; Tullius, Thomas D.; Crawford, Gregory E.; Sunyaev, Shamil; Noble, William S.; Dunham, Ian; Denoeud, France; Reymond, Alexandre; Kapranov, Philipp; Rozowsky, Joel; Zheng, Deyou; Castelo, Robert; Frankish, Adam; Harrow, Jennifer; Ghosh, Srinka; Sandelin, Albin; Hofacker, Ivo L.; Baertsch, Robert; Keefe, Damian; Dike, Sujit; Cheng, Jill; Hirsch, Heather A.; Sekinger, Edward A.; Lagarde, Julien; Abril, Josep F.; Shahab, Atif; Flamm, Christoph; Fried, Claudia; Hackermüller, Jörg; Hertel, Jana; Lindemeyer, Manja; Missal, Kristin; Tanzer, Andrea; Washietl, Stefan; Korbel, Jan; Emanuelsson, Olof; Pedersen, Jakob S.; Holroyd, Nancy; Taylor, Ruth; Swarbreck, David; Matthews, Nicholas; Dickson, Mark C.; Thomas, Daryl J.; Weirauch, Matthew T.; Gilbert, James; Drenkow, Jorg; Bell, Ian; Zhao, Xiaodong; Srinivasan, K. G.; Sung, Wing Kin; Ooi, Hong Sain; Chiu, Kuo Ping; Foissac, Sylvain; Alioto, Tyler; Brent, Michael; Pachter, Lior; Tress, Michael L.; Valencia, Alfonso; Choo, Siew Woh; Choo, Chiou Yu; Ucla, Catherine; Manzano, Caroline; Wyss, Carine; Cheung, Evelyn; Clark, Taane G.; Brown, James B.; Ganesh, Madhavan; Patel, Sandeep; Tammana, Hari; Chrast, Jacqueline; Henrichsen, Charlotte N.; Kai, Chikatoshi; Kawai, Jun; Nagalakshmi, Ugrappa; Wu, Jiaqian; Lian, Zheng; Lian, Jin; Newburger, Peter; Zhang, Xueqing; Bickel, Peter; Mattick, John S.; Carninci, Piero; Hayashizaki, Yoshihide; Weissman, Sherman; Hubbard, Tim; Myers, Richard M.; Rogers, Jane; Stadler, Peter F.; Lowe, Todd M.; Wei, Chia Lin; Ruan, Yijun; Struhl, Kevin; Gerstein, Mark; Antonarakis, Stylianos E.; Fu, Yutao; Green, Eric D.; Karaöz, Ulaş; Siepel, Adam; Taylor, James; Liefer, Laura A.; Wetterstrand, Kris A.; Good, Peter J.; Feingold, Elise A.; Guyer, Mark S.; Cooper, Gregory M.; Asimenos, George; Dewey, Colin N.; Hou, Minmei; Nikolaev, Sergey; Montoya-Burgos, Juan I.; Löytynoja, Ari; Whelan, Simon; Pardi, Fabio; Massingham, Tim; Huang, Haiyan; Zhang, Nancy R.; Holmes, Ian; Mullikin, James C.; Ureta-Vidal, Abel; Paten, Benedict; Seringhaus, Michael; Church, Deanna; Rosenbloom, Kate; Kent, W. James; Stone, Eric A.; Batzoglou, Serafim; Goldman, Nick; Hardison, Ross C.; Haussler, David; Miller, Webb; Sidow, Arend; Trinklein, Nathan D.; Zhang, Zhengdong; Barrera, Leah; Stuart, Rhona; King, David C.; Ameur, Adam; Enroth, Stefan; Bieda, Mark C.; Kim, Jonghwan; Bhinge, Akshay A.; Jiang, Nan; Liu, Jun; Yao, Fei; Vega, Vinsensius B.; Lee, Charlie W H; Ng, Patrick; Yang, Annie; Moqtaderi, Zarmik; Zhu, Zhou; Xu, Xiaoqin; Squazzo, Sharon; Oberley, Matthew J.; Inman, David; Singer, Michael A.; Richmond, Todd A.; Munn, Kyle J.; Rada-Iglesias, Alvaro; Wallerman, Ola; Komorowski, Jan; Fowler, Joanna C.; Couttet, Phillippe; Bruce, Alexander W.; Dovey, Oliver M.; Ellis, Peter D.; Langford, Cordelia F.; Nix, David A.; Euskirchen, Ghia; Hartman, Stephen; Urban, Alexander E.; Kraus, Peter; Van Calcar, Sara; Heintzman, Nate; Hoon Kim, Tae; Wang, Kun; Qu, Chunxu; Hon, Gary; Luna, Rosa; Glass, Christopher K.; Rosenfeld, M. Geoff; Aldred, Shelley Force; Cooper, Sara J.; Halees, Anason; Lin, Jane M.; Shulha, Hennady P.; Zhang, Xiaoling; Xu, Mousheng; Haidar, Jaafar N S; Yu, Yong; Iyer, Vishwanath R.; Green, Roland D.; Wadelius, Claes; Farnham, Peggy J.; Ren, Bing; Harte, Rachel A.; Hinrichs, Angie S.; Trumbower, Heather; Clawson, Hiram; Hillman-Jackson, Jennifer; Zweig, Ann S.; Smith, Kayla; Thakkapallayil, Archana; Barber, Galt; Kuhn, Robert M.; Karolchik, Donna; Armengol, Lluis; Bird, Christine P.; De Bakker, Paul I W; Kern, Andrew D.; Lopez-Bigas, Nuria; Martin, Joel D.; Stranger, Barbara E.; Woodroffe, Abigail; Davydov, Eugene; Dimas, Antigone; Eyras, Eduardo; Hallgrímsdóttir, Ingileif B.; Huppert, Julian; Zody, Michael C.; Abecasis, Gonçalo R.; Estivill, Xavier; Bouffard, Gerard G.; Guan, Xiaobin; Hansen, Nancy F.; Idol, Jacquelyn R.; Maduro, Valerie V B; Maskeri, Baishali; McDowell, Jennifer C.; Park, Morgan; Thomas, Pamela J.; Young, Alice C.; Blakesley, Robert W.; Muzny, Donna M.; Sodergren, Erica; Wheeler, David A.; Worley, Kim C.; Jiang, Huaiyang; Weinstock, George M.; Gibbs, Richard A.; Graves, Tina; Fulton, Robert; Mardis, Elaine R.; Wilson, Richard K.; Clamp, Michele; Cuff, James; Gnerre, Sante; Jaffe, David B.; Chang, Jean L.; Lindblad-Toh, Kerstin; Lander, Eric S.; Koriabine, Maxim; Nefedov, Mikhail; Osoegawa, Kazutoyo; Yoshinaga, Yuko; Zhu, Baoli; De Jong, Pieter J.

In: Nature, Vol. 447, No. 7146, 14.06.2007, p. 799-816.

Research output: Contribution to journalArticle

Birney, E, Stamatoyannopoulos, JA, Dutta, A, Guigó, R, Gingeras, TR, Margulies, EH, Weng, Z, Snyder, M, Dermitzakis, ET, Thurman, RE, Kuehn, MS, Taylor, CM, Neph, S, Koch, CM, Asthana, S, Malhotra, A, Adzhubei, I, Greenbaum, JA, Andrews, RM, Flicek, P, Boyle, PJ, Cao, H, Carter, NP, Clelland, GK, Davis, S, Day, N, Dhami, P, Dillon, SC, Dorschner, MO, Fiegler, H, Giresi, PG, Goldy, J, Hawrylycz, M, Haydock, A, Humbert, R, James, KD, Johnson, BE, Johnson, EM, Frum, TT, Rosenzweig, ER, Karnani, N, Lee, K, Lefebvre, GC, Navas, PA, Neri, F, Parker, SCJ, Sabo, PJ, Sandstrom, R, Shafer, A, Vetrie, D, Weaver, M, Wilcox, S, Yu, M, Collins, FS, Dekker, J, Lieb, JD, Tullius, TD, Crawford, GE, Sunyaev, S, Noble, WS, Dunham, I, Denoeud, F, Reymond, A, Kapranov, P, Rozowsky, J, Zheng, D, Castelo, R, Frankish, A, Harrow, J, Ghosh, S, Sandelin, A, Hofacker, IL, Baertsch, R, Keefe, D, Dike, S, Cheng, J, Hirsch, HA, Sekinger, EA, Lagarde, J, Abril, JF, Shahab, A, Flamm, C, Fried, C, Hackermüller, J, Hertel, J, Lindemeyer, M, Missal, K, Tanzer, A, Washietl, S, Korbel, J, Emanuelsson, O, Pedersen, JS, Holroyd, N, Taylor, R, Swarbreck, D, Matthews, N, Dickson, MC, Thomas, DJ, Weirauch, MT, Gilbert, J, Drenkow, J, Bell, I, Zhao, X, Srinivasan, KG, Sung, WK, Ooi, HS, Chiu, KP, Foissac, S, Alioto, T, Brent, M, Pachter, L, Tress, ML, Valencia, A, Choo, SW, Choo, CY, Ucla, C, Manzano, C, Wyss, C, Cheung, E, Clark, TG, Brown, JB, Ganesh, M, Patel, S, Tammana, H, Chrast, J, Henrichsen, CN, Kai, C, Kawai, J, Nagalakshmi, U, Wu, J, Lian, Z, Lian, J, Newburger, P, Zhang, X, Bickel, P, Mattick, JS, Carninci, P, Hayashizaki, Y, Weissman, S, Hubbard, T, Myers, RM, Rogers, J, Stadler, PF, Lowe, TM, Wei, CL, Ruan, Y, Struhl, K, Gerstein, M, Antonarakis, SE, Fu, Y, Green, ED, Karaöz, U, Siepel, A, Taylor, J, Liefer, LA, Wetterstrand, KA, Good, PJ, Feingold, EA, Guyer, MS, Cooper, GM, Asimenos, G, Dewey, CN, Hou, M, Nikolaev, S, Montoya-Burgos, JI, Löytynoja, A, Whelan, S, Pardi, F, Massingham, T, Huang, H, Zhang, NR, Holmes, I, Mullikin, JC, Ureta-Vidal, A, Paten, B, Seringhaus, M, Church, D, Rosenbloom, K, Kent, WJ, Stone, EA, Batzoglou, S, Goldman, N, Hardison, RC, Haussler, D, Miller, W, Sidow, A, Trinklein, ND, Zhang, Z, Barrera, L, Stuart, R, King, DC, Ameur, A, Enroth, S, Bieda, MC, Kim, J, Bhinge, AA, Jiang, N, Liu, J, Yao, F, Vega, VB, Lee, CWH, Ng, P, Yang, A, Moqtaderi, Z, Zhu, Z, Xu, X, Squazzo, S, Oberley, MJ, Inman, D, Singer, MA, Richmond, TA, Munn, KJ, Rada-Iglesias, A, Wallerman, O, Komorowski, J, Fowler, JC, Couttet, P, Bruce, AW, Dovey, OM, Ellis, PD, Langford, CF, Nix, DA, Euskirchen, G, Hartman, S, Urban, AE, Kraus, P, Van Calcar, S, Heintzman, N, Hoon Kim, T, Wang, K, Qu, C, Hon, G, Luna, R, Glass, CK, Rosenfeld, MG, Aldred, SF, Cooper, SJ, Halees, A, Lin, JM, Shulha, HP, Zhang, X, Xu, M, Haidar, JNS, Yu, Y, Iyer, VR, Green, RD, Wadelius, C, Farnham, PJ, Ren, B, Harte, RA, Hinrichs, AS, Trumbower, H, Clawson, H, Hillman-Jackson, J, Zweig, AS, Smith, K, Thakkapallayil, A, Barber, G, Kuhn, RM, Karolchik, D, Armengol, L, Bird, CP, De Bakker, PIW, Kern, AD, Lopez-Bigas, N, Martin, JD, Stranger, BE, Woodroffe, A, Davydov, E, Dimas, A, Eyras, E, Hallgrímsdóttir, IB, Huppert, J, Zody, MC, Abecasis, GR, Estivill, X, Bouffard, GG, Guan, X, Hansen, NF, Idol, JR, Maduro, VVB, Maskeri, B, McDowell, JC, Park, M, Thomas, PJ, Young, AC, Blakesley, RW, Muzny, DM, Sodergren, E, Wheeler, DA, Worley, KC, Jiang, H, Weinstock, GM, Gibbs, RA, Graves, T, Fulton, R, Mardis, ER, Wilson, RK, Clamp, M, Cuff, J, Gnerre, S, Jaffe, DB, Chang, JL, Lindblad-Toh, K, Lander, ES, Koriabine, M, Nefedov, M, Osoegawa, K, Yoshinaga, Y, Zhu, B & De Jong, PJ 2007, 'Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project', Nature, vol. 447, no. 7146, pp. 799-816. https://doi.org/10.1038/nature05874
Birney E, Stamatoyannopoulos JA, Dutta A, Guigó R, Gingeras TR, Margulies EH et al. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature. 2007 Jun 14;447(7146):799-816. https://doi.org/10.1038/nature05874
Birney, Ewan ; Stamatoyannopoulos, John A. ; Dutta, Anindya ; Guigó, Roderic ; Gingeras, Thomas R. ; Margulies, Elliott H. ; Weng, Zhiping ; Snyder, Michael ; Dermitzakis, Emmanouil T. ; Thurman, Robert E. ; Kuehn, Michael S. ; Taylor, Christopher M. ; Neph, Shane ; Koch, Christoph M. ; Asthana, Saurabh ; Malhotra, Ankit ; Adzhubei, Ivan ; Greenbaum, Jason A. ; Andrews, Robert M. ; Flicek, Paul ; Boyle, Patrick J. ; Cao, Hua ; Carter, Nigel P. ; Clelland, Gayle K. ; Davis, Sean ; Day, Nathan ; Dhami, Pawandeep ; Dillon, Shane C. ; Dorschner, Michael O. ; Fiegler, Heike ; Giresi, Paul G. ; Goldy, Jeff ; Hawrylycz, Michael ; Haydock, Andrew ; Humbert, Richard ; James, Keith D. ; Johnson, Brett E. ; Johnson, Ericka M. ; Frum, Tristan T. ; Rosenzweig, Elizabeth R. ; Karnani, Neerja ; Lee, Kirsten ; Lefebvre, Gregory C. ; Navas, Patrick A. ; Neri, Fidencio ; Parker, Stephen C J ; Sabo, Peter J. ; Sandstrom, Richard ; Shafer, Anthony ; Vetrie, David ; Weaver, Molly ; Wilcox, Sarah ; Yu, Man ; Collins, Francis S. ; Dekker, Job ; Lieb, Jason D. ; Tullius, Thomas D. ; Crawford, Gregory E. ; Sunyaev, Shamil ; Noble, William S. ; Dunham, Ian ; Denoeud, France ; Reymond, Alexandre ; Kapranov, Philipp ; Rozowsky, Joel ; Zheng, Deyou ; Castelo, Robert ; Frankish, Adam ; Harrow, Jennifer ; Ghosh, Srinka ; Sandelin, Albin ; Hofacker, Ivo L. ; Baertsch, Robert ; Keefe, Damian ; Dike, Sujit ; Cheng, Jill ; Hirsch, Heather A. ; Sekinger, Edward A. ; Lagarde, Julien ; Abril, Josep F. ; Shahab, Atif ; Flamm, Christoph ; Fried, Claudia ; Hackermüller, Jörg ; Hertel, Jana ; Lindemeyer, Manja ; Missal, Kristin ; Tanzer, Andrea ; Washietl, Stefan ; Korbel, Jan ; Emanuelsson, Olof ; Pedersen, Jakob S. ; Holroyd, Nancy ; Taylor, Ruth ; Swarbreck, David ; Matthews, Nicholas ; Dickson, Mark C. ; Thomas, Daryl J. ; Weirauch, Matthew T. ; Gilbert, James ; Drenkow, Jorg ; Bell, Ian ; Zhao, Xiaodong ; Srinivasan, K. G. ; Sung, Wing Kin ; Ooi, Hong Sain ; Chiu, Kuo Ping ; Foissac, Sylvain ; Alioto, Tyler ; Brent, Michael ; Pachter, Lior ; Tress, Michael L. ; Valencia, Alfonso ; Choo, Siew Woh ; Choo, Chiou Yu ; Ucla, Catherine ; Manzano, Caroline ; Wyss, Carine ; Cheung, Evelyn ; Clark, Taane G. ; Brown, James B. ; Ganesh, Madhavan ; Patel, Sandeep ; Tammana, Hari ; Chrast, Jacqueline ; Henrichsen, Charlotte N. ; Kai, Chikatoshi ; Kawai, Jun ; Nagalakshmi, Ugrappa ; Wu, Jiaqian ; Lian, Zheng ; Lian, Jin ; Newburger, Peter ; Zhang, Xueqing ; Bickel, Peter ; Mattick, John S. ; Carninci, Piero ; Hayashizaki, Yoshihide ; Weissman, Sherman ; Hubbard, Tim ; Myers, Richard M. ; Rogers, Jane ; Stadler, Peter F. ; Lowe, Todd M. ; Wei, Chia Lin ; Ruan, Yijun ; Struhl, Kevin ; Gerstein, Mark ; Antonarakis, Stylianos E. ; Fu, Yutao ; Green, Eric D. ; Karaöz, Ulaş ; Siepel, Adam ; Taylor, James ; Liefer, Laura A. ; Wetterstrand, Kris A. ; Good, Peter J. ; Feingold, Elise A. ; Guyer, Mark S. ; Cooper, Gregory M. ; Asimenos, George ; Dewey, Colin N. ; Hou, Minmei ; Nikolaev, Sergey ; Montoya-Burgos, Juan I. ; Löytynoja, Ari ; Whelan, Simon ; Pardi, Fabio ; Massingham, Tim ; Huang, Haiyan ; Zhang, Nancy R. ; Holmes, Ian ; Mullikin, James C. ; Ureta-Vidal, Abel ; Paten, Benedict ; Seringhaus, Michael ; Church, Deanna ; Rosenbloom, Kate ; Kent, W. James ; Stone, Eric A. ; Batzoglou, Serafim ; Goldman, Nick ; Hardison, Ross C. ; Haussler, David ; Miller, Webb ; Sidow, Arend ; Trinklein, Nathan D. ; Zhang, Zhengdong ; Barrera, Leah ; Stuart, Rhona ; King, David C. ; Ameur, Adam ; Enroth, Stefan ; Bieda, Mark C. ; Kim, Jonghwan ; Bhinge, Akshay A. ; Jiang, Nan ; Liu, Jun ; Yao, Fei ; Vega, Vinsensius B. ; Lee, Charlie W H ; Ng, Patrick ; Yang, Annie ; Moqtaderi, Zarmik ; Zhu, Zhou ; Xu, Xiaoqin ; Squazzo, Sharon ; Oberley, Matthew J. ; Inman, David ; Singer, Michael A. ; Richmond, Todd A. ; Munn, Kyle J. ; Rada-Iglesias, Alvaro ; Wallerman, Ola ; Komorowski, Jan ; Fowler, Joanna C. ; Couttet, Phillippe ; Bruce, Alexander W. ; Dovey, Oliver M. ; Ellis, Peter D. ; Langford, Cordelia F. ; Nix, David A. ; Euskirchen, Ghia ; Hartman, Stephen ; Urban, Alexander E. ; Kraus, Peter ; Van Calcar, Sara ; Heintzman, Nate ; Hoon Kim, Tae ; Wang, Kun ; Qu, Chunxu ; Hon, Gary ; Luna, Rosa ; Glass, Christopher K. ; Rosenfeld, M. Geoff ; Aldred, Shelley Force ; Cooper, Sara J. ; Halees, Anason ; Lin, Jane M. ; Shulha, Hennady P. ; Zhang, Xiaoling ; Xu, Mousheng ; Haidar, Jaafar N S ; Yu, Yong ; Iyer, Vishwanath R. ; Green, Roland D. ; Wadelius, Claes ; Farnham, Peggy J. ; Ren, Bing ; Harte, Rachel A. ; Hinrichs, Angie S. ; Trumbower, Heather ; Clawson, Hiram ; Hillman-Jackson, Jennifer ; Zweig, Ann S. ; Smith, Kayla ; Thakkapallayil, Archana ; Barber, Galt ; Kuhn, Robert M. ; Karolchik, Donna ; Armengol, Lluis ; Bird, Christine P. ; De Bakker, Paul I W ; Kern, Andrew D. ; Lopez-Bigas, Nuria ; Martin, Joel D. ; Stranger, Barbara E. ; Woodroffe, Abigail ; Davydov, Eugene ; Dimas, Antigone ; Eyras, Eduardo ; Hallgrímsdóttir, Ingileif B. ; Huppert, Julian ; Zody, Michael C. ; Abecasis, Gonçalo R. ; Estivill, Xavier ; Bouffard, Gerard G. ; Guan, Xiaobin ; Hansen, Nancy F. ; Idol, Jacquelyn R. ; Maduro, Valerie V B ; Maskeri, Baishali ; McDowell, Jennifer C. ; Park, Morgan ; Thomas, Pamela J. ; Young, Alice C. ; Blakesley, Robert W. ; Muzny, Donna M. ; Sodergren, Erica ; Wheeler, David A. ; Worley, Kim C. ; Jiang, Huaiyang ; Weinstock, George M. ; Gibbs, Richard A. ; Graves, Tina ; Fulton, Robert ; Mardis, Elaine R. ; Wilson, Richard K. ; Clamp, Michele ; Cuff, James ; Gnerre, Sante ; Jaffe, David B. ; Chang, Jean L. ; Lindblad-Toh, Kerstin ; Lander, Eric S. ; Koriabine, Maxim ; Nefedov, Mikhail ; Osoegawa, Kazutoyo ; Yoshinaga, Yuko ; Zhu, Baoli ; De Jong, Pieter J. / Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. In: Nature. 2007 ; Vol. 447, No. 7146. pp. 799-816.
@article{b8cd820b712c4e6f9edac67c6e134288,
title = "Identification and analysis of functional elements in 1{\%} of the human genome by the ENCODE pilot project",
abstract = "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, such that the majority of its bases can be found in primary transcripts, including non-protein-coding transcripts, and those that extensively overlap one another. Second, systematic examination of transcriptional regulation has yielded new understanding about transcription start sites, including their relationship to specific regulatory sequences and features of chromatin accessibility and histone modification. Third, a more sophisticated view of chromatin structure has emerged, including its inter-relationship with DNA replication and transcriptional regulation. Finally, integration of these new sources of information, in particular with respect to mammalian evolution based on inter- and intra-species sequence comparisons, has yielded new mechanistic and evolutionary insights concerning the functional landscape of the human genome. Together, these studies are defining a path for pursuit of a more comprehensive characterization of human genome function.",
author = "Ewan Birney and Stamatoyannopoulos, {John A.} and Anindya Dutta and Roderic Guig{\'o} and Gingeras, {Thomas R.} and Margulies, {Elliott H.} and Zhiping Weng and Michael Snyder and Dermitzakis, {Emmanouil T.} and Thurman, {Robert E.} and Kuehn, {Michael S.} and Taylor, {Christopher M.} and Shane Neph and Koch, {Christoph M.} and Saurabh Asthana and Ankit Malhotra and Ivan Adzhubei and Greenbaum, {Jason A.} and Andrews, {Robert M.} and Paul Flicek and Boyle, {Patrick J.} and Hua Cao and Carter, {Nigel P.} and Clelland, {Gayle K.} and Sean Davis and Nathan Day and Pawandeep Dhami and Dillon, {Shane C.} and Dorschner, {Michael O.} and Heike Fiegler and Giresi, {Paul G.} and Jeff Goldy and Michael Hawrylycz and Andrew Haydock and Richard Humbert and James, {Keith D.} and Johnson, {Brett E.} and Johnson, {Ericka M.} and Frum, {Tristan T.} and Rosenzweig, {Elizabeth R.} and Neerja Karnani and Kirsten Lee and Lefebvre, {Gregory C.} and Navas, {Patrick A.} and Fidencio Neri and Parker, {Stephen C J} and Sabo, {Peter J.} and Richard Sandstrom and Anthony Shafer and David Vetrie and Molly Weaver and Sarah Wilcox and Man Yu and Collins, {Francis S.} and Job Dekker and Lieb, {Jason D.} and Tullius, {Thomas D.} and Crawford, {Gregory E.} and Shamil Sunyaev and Noble, {William S.} and Ian Dunham and France Denoeud and Alexandre Reymond and Philipp Kapranov and Joel Rozowsky and Deyou Zheng and Robert Castelo and Adam Frankish and Jennifer Harrow and Srinka Ghosh and Albin Sandelin and Hofacker, {Ivo L.} and Robert Baertsch and Damian Keefe and Sujit Dike and Jill Cheng and Hirsch, {Heather A.} and Sekinger, {Edward A.} and Julien Lagarde and Abril, {Josep F.} 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 Pedersen, {Jakob S.} and Nancy Holroyd and Ruth Taylor and David Swarbreck and Nicholas Matthews and Dickson, {Mark C.} and Thomas, {Daryl J.} and Weirauch, {Matthew T.} and James Gilbert and Jorg Drenkow and Ian Bell and Xiaodong Zhao and Srinivasan, {K. G.} and Sung, {Wing Kin} and Ooi, {Hong Sain} and Chiu, {Kuo Ping} and Sylvain Foissac and Tyler Alioto and Michael Brent and Lior Pachter and Tress, {Michael L.} and Alfonso Valencia and Choo, {Siew Woh} and Choo, {Chiou Yu} and Catherine Ucla and Caroline Manzano and Carine Wyss and Evelyn Cheung and Clark, {Taane G.} and Brown, {James B.} and Madhavan Ganesh and Sandeep Patel and Hari Tammana and Jacqueline Chrast and Henrichsen, {Charlotte N.} and Chikatoshi Kai and Jun Kawai and Ugrappa Nagalakshmi and Jiaqian Wu and Zheng Lian and Jin Lian and Peter Newburger and Xueqing Zhang and Peter Bickel and Mattick, {John S.} and Piero Carninci and Yoshihide Hayashizaki and Sherman Weissman and Tim Hubbard and Myers, {Richard M.} and Jane Rogers and Stadler, {Peter F.} and Lowe, {Todd M.} and Wei, {Chia Lin} and Yijun Ruan and Kevin Struhl and Mark Gerstein and Antonarakis, {Stylianos E.} and Yutao Fu and Green, {Eric D.} and Ulaş Kara{\"o}z and Adam Siepel and James Taylor and Liefer, {Laura A.} and Wetterstrand, {Kris A.} and Good, {Peter J.} and Feingold, {Elise A.} and Guyer, {Mark S.} and Cooper, {Gregory M.} and George Asimenos and Dewey, {Colin N.} and Minmei Hou and Sergey Nikolaev and Montoya-Burgos, {Juan I.} and Ari L{\"o}ytynoja and Simon Whelan and Fabio Pardi and Tim Massingham and Haiyan Huang and Zhang, {Nancy R.} and Ian Holmes and Mullikin, {James C.} and Abel Ureta-Vidal and Benedict Paten and Michael Seringhaus and Deanna Church and Kate Rosenbloom and Kent, {W. James} and Stone, {Eric A.} and Serafim Batzoglou and Nick Goldman and Hardison, {Ross C.} and David Haussler and Webb Miller and Arend Sidow and Trinklein, {Nathan D.} and Zhengdong Zhang and Leah Barrera and Rhona Stuart and King, {David C.} and Adam Ameur and Stefan Enroth and Bieda, {Mark C.} and Jonghwan Kim and Bhinge, {Akshay A.} and Nan Jiang and Jun Liu and Fei Yao and Vega, {Vinsensius B.} and Lee, {Charlie W H} and Patrick Ng and Annie Yang and Zarmik Moqtaderi and Zhou Zhu and Xiaoqin Xu and Sharon Squazzo and Oberley, {Matthew J.} and David Inman and Singer, {Michael A.} and Richmond, {Todd A.} and Munn, {Kyle J.} and Alvaro Rada-Iglesias and Ola Wallerman and Jan Komorowski and Fowler, {Joanna C.} and Phillippe Couttet and Bruce, {Alexander W.} and Dovey, {Oliver M.} and Ellis, {Peter D.} and Langford, {Cordelia F.} and Nix, {David A.} and Ghia Euskirchen and Stephen Hartman and Urban, {Alexander E.} and Peter Kraus and {Van Calcar}, Sara and Nate Heintzman and {Hoon Kim}, Tae and Kun Wang and Chunxu Qu and Gary Hon and Rosa Luna and Glass, {Christopher K.} and Rosenfeld, {M. Geoff} and Aldred, {Shelley Force} and Cooper, {Sara J.} and Anason Halees and Lin, {Jane M.} and Shulha, {Hennady P.} and Xiaoling Zhang and Mousheng Xu and Haidar, {Jaafar N S} and Yong Yu and Iyer, {Vishwanath R.} and Green, {Roland D.} and Claes Wadelius and Farnham, {Peggy J.} and Bing Ren and Harte, {Rachel A.} and Hinrichs, {Angie S.} and Heather Trumbower and Hiram Clawson and Jennifer Hillman-Jackson and Zweig, {Ann S.} and Kayla Smith and Archana Thakkapallayil and Galt Barber and Kuhn, {Robert M.} and Donna Karolchik and Lluis Armengol and Bird, {Christine P.} and {De Bakker}, {Paul I W} and Kern, {Andrew D.} and Nuria Lopez-Bigas and Martin, {Joel D.} and Stranger, {Barbara E.} and Abigail Woodroffe and Eugene Davydov and Antigone Dimas and Eduardo Eyras and Hallgr{\'i}msd{\'o}ttir, {Ingileif B.} and Julian Huppert and Zody, {Michael C.} and Abecasis, {Gon{\cc}alo R.} and Xavier Estivill and Bouffard, {Gerard G.} and Xiaobin Guan and Hansen, {Nancy F.} and Idol, {Jacquelyn R.} and Maduro, {Valerie V B} and Baishali Maskeri and McDowell, {Jennifer C.} and Morgan Park and Thomas, {Pamela J.} and Young, {Alice C.} and Blakesley, {Robert W.} and Muzny, {Donna M.} and Erica Sodergren and Wheeler, {David A.} and Worley, {Kim C.} and Huaiyang Jiang and Weinstock, {George M.} and Gibbs, {Richard A.} and Tina Graves and Robert Fulton and Mardis, {Elaine R.} and Wilson, {Richard K.} and Michele Clamp and James Cuff and Sante Gnerre and Jaffe, {David B.} and Chang, {Jean L.} and Kerstin Lindblad-Toh and Lander, {Eric S.} and Maxim Koriabine and Mikhail Nefedov and Kazutoyo Osoegawa and Yuko Yoshinaga and Baoli Zhu and {De Jong}, {Pieter J.}",
year = "2007",
month = "6",
day = "14",
doi = "10.1038/nature05874",
language = "English (US)",
volume = "447",
pages = "799--816",
journal = "Nature",
issn = "0028-0836",
publisher = "Nature Publishing Group",
number = "7146",

}

TY - JOUR

T1 - Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project

AU - Birney, Ewan

AU - Stamatoyannopoulos, John A.

AU - Dutta, Anindya

AU - Guigó, Roderic

AU - Gingeras, Thomas R.

AU - Margulies, Elliott H.

AU - Weng, Zhiping

AU - Snyder, Michael

AU - Dermitzakis, Emmanouil T.

AU - Thurman, Robert E.

AU - Kuehn, Michael S.

AU - Taylor, Christopher M.

AU - Neph, Shane

AU - Koch, Christoph M.

AU - Asthana, Saurabh

AU - Malhotra, Ankit

AU - Adzhubei, Ivan

AU - Greenbaum, Jason A.

AU - Andrews, Robert M.

AU - Flicek, Paul

AU - Boyle, Patrick J.

AU - Cao, Hua

AU - Carter, Nigel P.

AU - Clelland, Gayle K.

AU - Davis, Sean

AU - Day, Nathan

AU - Dhami, Pawandeep

AU - Dillon, Shane C.

AU - Dorschner, Michael O.

AU - Fiegler, Heike

AU - Giresi, Paul G.

AU - Goldy, Jeff

AU - Hawrylycz, Michael

AU - Haydock, Andrew

AU - Humbert, Richard

AU - James, Keith D.

AU - Johnson, Brett E.

AU - Johnson, Ericka M.

AU - Frum, Tristan T.

AU - Rosenzweig, Elizabeth R.

AU - Karnani, Neerja

AU - Lee, Kirsten

AU - Lefebvre, Gregory C.

AU - Navas, Patrick A.

AU - Neri, Fidencio

AU - Parker, Stephen C J

AU - Sabo, Peter J.

AU - Sandstrom, Richard

AU - Shafer, Anthony

AU - Vetrie, David

AU - Weaver, Molly

AU - Wilcox, Sarah

AU - Yu, Man

AU - Collins, Francis S.

AU - Dekker, Job

AU - Lieb, Jason D.

AU - Tullius, Thomas D.

AU - Crawford, Gregory E.

AU - Sunyaev, Shamil

AU - Noble, William S.

AU - Dunham, Ian

AU - Denoeud, France

AU - Reymond, Alexandre

AU - Kapranov, Philipp

AU - Rozowsky, Joel

AU - Zheng, Deyou

AU - Castelo, Robert

AU - Frankish, Adam

AU - Harrow, Jennifer

AU - Ghosh, Srinka

AU - Sandelin, Albin

AU - Hofacker, Ivo L.

AU - Baertsch, Robert

AU - Keefe, Damian

AU - Dike, Sujit

AU - Cheng, Jill

AU - Hirsch, Heather A.

AU - Sekinger, Edward A.

AU - Lagarde, Julien

AU - Abril, Josep F.

AU - Shahab, Atif

AU - Flamm, Christoph

AU - Fried, Claudia

AU - Hackermüller, Jörg

AU - Hertel, Jana

AU - Lindemeyer, Manja

AU - Missal, Kristin

AU - Tanzer, Andrea

AU - Washietl, Stefan

AU - Korbel, Jan

AU - Emanuelsson, Olof

AU - Pedersen, Jakob S.

AU - Holroyd, Nancy

AU - Taylor, Ruth

AU - Swarbreck, David

AU - Matthews, Nicholas

AU - Dickson, Mark C.

AU - Thomas, Daryl J.

AU - Weirauch, Matthew T.

AU - Gilbert, James

AU - Drenkow, Jorg

AU - Bell, Ian

AU - Zhao, Xiaodong

AU - Srinivasan, K. G.

AU - Sung, Wing Kin

AU - Ooi, Hong Sain

AU - Chiu, Kuo Ping

AU - Foissac, Sylvain

AU - Alioto, Tyler

AU - Brent, Michael

AU - Pachter, Lior

AU - Tress, Michael L.

AU - Valencia, Alfonso

AU - Choo, Siew Woh

AU - Choo, Chiou Yu

AU - Ucla, Catherine

AU - Manzano, Caroline

AU - Wyss, Carine

AU - Cheung, Evelyn

AU - Clark, Taane G.

AU - Brown, James B.

AU - Ganesh, Madhavan

AU - Patel, Sandeep

AU - Tammana, Hari

AU - Chrast, Jacqueline

AU - Henrichsen, Charlotte N.

AU - Kai, Chikatoshi

AU - Kawai, Jun

AU - Nagalakshmi, Ugrappa

AU - Wu, Jiaqian

AU - Lian, Zheng

AU - Lian, Jin

AU - Newburger, Peter

AU - Zhang, Xueqing

AU - Bickel, Peter

AU - Mattick, John S.

AU - Carninci, Piero

AU - Hayashizaki, Yoshihide

AU - Weissman, Sherman

AU - Hubbard, Tim

AU - Myers, Richard M.

AU - Rogers, Jane

AU - Stadler, Peter F.

AU - Lowe, Todd M.

AU - Wei, Chia Lin

AU - Ruan, Yijun

AU - Struhl, Kevin

AU - Gerstein, Mark

AU - Antonarakis, Stylianos E.

AU - Fu, Yutao

AU - Green, Eric D.

AU - Karaöz, Ulaş

AU - Siepel, Adam

AU - Taylor, James

AU - Liefer, Laura A.

AU - Wetterstrand, Kris A.

AU - Good, Peter J.

AU - Feingold, Elise A.

AU - Guyer, Mark S.

AU - Cooper, Gregory M.

AU - Asimenos, George

AU - Dewey, Colin N.

AU - Hou, Minmei

AU - Nikolaev, Sergey

AU - Montoya-Burgos, Juan I.

AU - Löytynoja, Ari

AU - Whelan, Simon

AU - Pardi, Fabio

AU - Massingham, Tim

AU - Huang, Haiyan

AU - Zhang, Nancy R.

AU - Holmes, Ian

AU - Mullikin, James C.

AU - Ureta-Vidal, Abel

AU - Paten, Benedict

AU - Seringhaus, Michael

AU - Church, Deanna

AU - Rosenbloom, Kate

AU - Kent, W. James

AU - Stone, Eric A.

AU - Batzoglou, Serafim

AU - Goldman, Nick

AU - Hardison, Ross C.

AU - Haussler, David

AU - Miller, Webb

AU - Sidow, Arend

AU - Trinklein, Nathan D.

AU - Zhang, Zhengdong

AU - Barrera, Leah

AU - Stuart, Rhona

AU - King, David C.

AU - Ameur, Adam

AU - Enroth, Stefan

AU - Bieda, Mark C.

AU - Kim, Jonghwan

AU - Bhinge, Akshay A.

AU - Jiang, Nan

AU - Liu, Jun

AU - Yao, Fei

AU - Vega, Vinsensius B.

AU - Lee, Charlie W H

AU - Ng, Patrick

AU - Yang, Annie

AU - Moqtaderi, Zarmik

AU - Zhu, Zhou

AU - Xu, Xiaoqin

AU - Squazzo, Sharon

AU - Oberley, Matthew J.

AU - Inman, David

AU - Singer, Michael A.

AU - Richmond, Todd A.

AU - Munn, Kyle J.

AU - Rada-Iglesias, Alvaro

AU - Wallerman, Ola

AU - Komorowski, Jan

AU - Fowler, Joanna C.

AU - Couttet, Phillippe

AU - Bruce, Alexander W.

AU - Dovey, Oliver M.

AU - Ellis, Peter D.

AU - Langford, Cordelia F.

AU - Nix, David A.

AU - Euskirchen, Ghia

AU - Hartman, Stephen

AU - Urban, Alexander E.

AU - Kraus, Peter

AU - Van Calcar, Sara

AU - Heintzman, Nate

AU - Hoon Kim, Tae

AU - Wang, Kun

AU - Qu, Chunxu

AU - Hon, Gary

AU - Luna, Rosa

AU - Glass, Christopher K.

AU - Rosenfeld, M. Geoff

AU - Aldred, Shelley Force

AU - Cooper, Sara J.

AU - Halees, Anason

AU - Lin, Jane M.

AU - Shulha, Hennady P.

AU - Zhang, Xiaoling

AU - Xu, Mousheng

AU - Haidar, Jaafar N S

AU - Yu, Yong

AU - Iyer, Vishwanath R.

AU - Green, Roland D.

AU - Wadelius, Claes

AU - Farnham, Peggy J.

AU - Ren, Bing

AU - Harte, Rachel A.

AU - Hinrichs, Angie S.

AU - Trumbower, Heather

AU - Clawson, Hiram

AU - Hillman-Jackson, Jennifer

AU - Zweig, Ann S.

AU - Smith, Kayla

AU - Thakkapallayil, Archana

AU - Barber, Galt

AU - Kuhn, Robert M.

AU - Karolchik, Donna

AU - Armengol, Lluis

AU - Bird, Christine P.

AU - De Bakker, Paul I W

AU - Kern, Andrew D.

AU - Lopez-Bigas, Nuria

AU - Martin, Joel D.

AU - Stranger, Barbara E.

AU - Woodroffe, Abigail

AU - Davydov, Eugene

AU - Dimas, Antigone

AU - Eyras, Eduardo

AU - Hallgrímsdóttir, Ingileif B.

AU - Huppert, Julian

AU - Zody, Michael C.

AU - Abecasis, Gonçalo R.

AU - Estivill, Xavier

AU - Bouffard, Gerard G.

AU - Guan, Xiaobin

AU - Hansen, Nancy F.

AU - Idol, Jacquelyn R.

AU - Maduro, Valerie V B

AU - Maskeri, Baishali

AU - McDowell, Jennifer C.

AU - Park, Morgan

AU - Thomas, Pamela J.

AU - Young, Alice C.

AU - Blakesley, Robert W.

AU - Muzny, Donna M.

AU - Sodergren, Erica

AU - Wheeler, David A.

AU - Worley, Kim C.

AU - Jiang, Huaiyang

AU - Weinstock, George M.

AU - Gibbs, Richard A.

AU - Graves, Tina

AU - Fulton, Robert

AU - Mardis, Elaine R.

AU - Wilson, Richard K.

AU - Clamp, Michele

AU - Cuff, James

AU - Gnerre, Sante

AU - Jaffe, David B.

AU - Chang, Jean L.

AU - Lindblad-Toh, Kerstin

AU - Lander, Eric S.

AU - Koriabine, Maxim

AU - Nefedov, Mikhail

AU - Osoegawa, Kazutoyo

AU - Yoshinaga, Yuko

AU - Zhu, Baoli

AU - De Jong, Pieter J.

PY - 2007/6/14

Y1 - 2007/6/14

N2 - 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, such that the majority of its bases can be found in primary transcripts, including non-protein-coding transcripts, and those that extensively overlap one another. Second, systematic examination of transcriptional regulation has yielded new understanding about transcription start sites, including their relationship to specific regulatory sequences and features of chromatin accessibility and histone modification. Third, a more sophisticated view of chromatin structure has emerged, including its inter-relationship with DNA replication and transcriptional regulation. Finally, integration of these new sources of information, in particular with respect to mammalian evolution based on inter- and intra-species sequence comparisons, has yielded new mechanistic and evolutionary insights concerning the functional landscape of the human genome. Together, these studies are defining a path for pursuit of a more comprehensive characterization of human genome function.

AB - 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, such that the majority of its bases can be found in primary transcripts, including non-protein-coding transcripts, and those that extensively overlap one another. Second, systematic examination of transcriptional regulation has yielded new understanding about transcription start sites, including their relationship to specific regulatory sequences and features of chromatin accessibility and histone modification. Third, a more sophisticated view of chromatin structure has emerged, including its inter-relationship with DNA replication and transcriptional regulation. Finally, integration of these new sources of information, in particular with respect to mammalian evolution based on inter- and intra-species sequence comparisons, has yielded new mechanistic and evolutionary insights concerning the functional landscape of the human genome. Together, these studies are defining a path for pursuit of a more comprehensive characterization of human genome function.

UR - http://www.scopus.com/inward/record.url?scp=34250305146&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=34250305146&partnerID=8YFLogxK

U2 - 10.1038/nature05874

DO - 10.1038/nature05874

M3 - Article

VL - 447

SP - 799

EP - 816

JO - Nature

JF - Nature

SN - 0028-0836

IS - 7146

ER -