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

@article{citeulike:1394766, 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 = {{ENCODE Project Consortium} and Birney, Ewan and Stamatoyannopoulos, John A. and Dutta, Anindya and Guig\'{o}, Roderic and Gingeras, Thomas R. and Margulies, Elliott H. and Weng, Zhiping and Snyder, Michael and Dermitzakis, Emmanouil T. and Thurman, Robert E. and Kuehn, Michael S. and Taylor, Christopher M. and Neph, Shane and Koch, Christoph M. and Asthana, Saurabh and Malhotra, Ankit and Adzhubei, Ivan and Greenbaum, Jason A. and Andrews, Robert M. and Flicek, Paul and Boyle, Patrick J. and Cao, Hua and Carter, Nigel P. and Clelland, Gayle K. and Davis, Sean and Day, Nathan and Dhami, Pawandeep and Dillon, Shane C. and Dorschner, Michael O. and Fiegler, Heike and Giresi, Paul G. and Goldy, Jeff and Hawrylycz, Michael and Haydock, Andrew and Humbert, Richard and James, Keith D. and Johnson, Brett E. and Johnson, Ericka M. and Frum, Tristan T. and Rosenzweig, Elizabeth R. and Karnani, Neerja and Lee, Kirsten and Lefebvre, Gregory C. and Navas, Patrick A. and Neri, Fidencio and Parker, Stephen C. and Sabo, Peter J. and Sandstrom, Richard and Shafer, Anthony and Vetrie, David and Weaver, Molly and Wilcox, Sarah and Yu, Man and Collins, Francis S. and Dekker, Job and Lieb, Jason D. and Tullius, Thomas D. and Crawford, Gregory E. and Sunyaev, Shamil and Noble, William S. and Dunham, Ian and Denoeud, France and Reymond, Alexandre and Kapranov, Philipp and Rozowsky, Joel and Zheng, Deyou and Castelo, Robert and Frankish, Adam and Harrow, Jennifer and Ghosh, Srinka and Sandelin, Albin and Hofacker, Ivo L. and Baertsch, Robert and Keefe, Damian and Dike, Sujit and Cheng, Jill and Hirsch, Heather A. and Sekinger, Edward A. and Lagarde, Julien and Abril, Josep F. and Shahab, Atif and Flamm, Christoph and Fried, Claudia and Hackerm\"{u}ller, J\"{o}rg and Hertel, Jana and Lindemeyer, Manja and Missal, Kristin and Tanzer, Andrea and Washietl, Stefan and Korbel, Jan and Emanuelsson, Olof and Pedersen, Jakob S. and Holroyd, Nancy and Taylor, Ruth and Swarbreck, David and Matthews, Nicholas and Dickson, Mark C. and Thomas, Daryl J. and Weirauch, Matthew T. and Gilbert, James and Drenkow, Jorg and Bell, Ian and Zhao, XiaoDong and Srinivasan, K. G. and Sung, Wing-Kin K. and Ooi, Hong Sain S. and Chiu, Kuo Ping P. and Foissac, Sylvain and Alioto, Tyler and Brent, Michael and Pachter, Lior and Tress, Michael L. and Valencia, Alfonso and Choo, Siew Woh W. and Choo, Chiou Yu Y. and Ucla, Catherine and Manzano, Caroline and Wyss, Carine and Cheung, Evelyn and Clark, Taane G. and Brown, James B. and Ganesh, Madhavan and Patel, Sandeep and Tammana, Hari and Chrast, Jacqueline and Henrichsen, Charlotte N. and Kai, Chikatoshi and Kawai, Jun and Nagalakshmi, Ugrappa and Wu, Jiaqian and Lian, Zheng and Lian, Jin and Newburger, Peter and Zhang, Xueqing and Bickel, Peter and Mattick, John S. and Carninci, Piero and Hayashizaki, Yoshihide and Weissman, Sherman and Hubbard, Tim and Myers, Richard M. and Rogers, Jane and Stadler, Peter F. and Lowe, Todd M. and Wei, Chia-Lin L. and Ruan, Yijun and Struhl, Kevin and Gerstein, Mark and Antonarakis, Stylianos E. and Fu, Yutao and Green, Eric D. and Kara\"{o}z, Ula\c{s} and Siepel, Adam and Taylor, James 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 Asimenos, George and Dewey, Colin N. and Hou, Minmei and Nikolaev, Sergey and Montoya-Burgos, Juan I. and L\"{o}ytynoja, Ari and Whelan, Simon and Pardi, Fabio and Massingham, Tim and Huang, Haiyan and Zhang, Nancy R. and Holmes, Ian and Mullikin, James C. and Ureta-Vidal, Abel and Paten, Benedict and Seringhaus, Michael and Church, Deanna and Rosenbloom, Kate and Kent, W. James and Stone, Eric A. and {NISC Comparative Sequencing Program} and {Baylor College of Medicine Human Genome Sequencing Center} and {Washington University Genome Sequencing Center} and {Broad Institute} and {Children's Hospital Oakland Research Institute} and Batzoglou, Serafim and Goldman, Nick and Hardison, Ross C. and Haussler, David and Miller, Webb and Sidow, Arend and Trinklein, Nathan D. and Zhang, Zhengdong D. and Barrera, Leah and Stuart, Rhona and King, David C. and Ameur, Adam and Enroth, Stefan and Bieda, Mark C. and Kim, Jonghwan and Bhinge, Akshay A. and Jiang, Nan and Liu, Jun and Yao, Fei and Vega, Vinsensius B. and Lee, Charlie W. and Ng, Patrick and Shahab, Atif and Yang, Annie and Moqtaderi, Zarmik and Zhu, Zhou and Xu, Xiaoqin and Squazzo, Sharon and Oberley, Matthew J. and Inman, David and Singer, Michael A. and Richmond, Todd A. and Munn, Kyle J. and Rada-Iglesias, Alvaro and Wallerman, Ola and Komorowski, Jan and Fowler, Joanna C. and Couttet, Phillippe and Bruce, Alexander W. and Dovey, Oliver M. and Ellis, Peter D. and Langford, Cordelia F. and Nix, David A. and Euskirchen, Ghia and Hartman, Stephen and Urban, Alexander E. and Kraus, Peter and Van Calcar, Sara and Heintzman, Nate and Kim, Tae Hoon H. and Wang, Kun and Qu, Chunxu and Hon, Gary and Luna, Rosa and Glass, Christopher K. and Rosenfeld, M. Geoff and Aldred, Shelley Force F. and Cooper, Sara J. and Halees, Anason and Lin, Jane M. and Shulha, Hennady P. and Zhang, Xiaoling and Xu, Mousheng and Haidar, Jaafar N. and Yu, Yong and Ruan, Yijun and Iyer, Vishwanath R. and Green, Roland D. and Wadelius, Claes and Farnham, Peggy J. and Ren, Bing and Harte, Rachel A. and Hinrichs, Angie S. and Trumbower, Heather and Clawson, Hiram and Hillman-Jackson, Jennifer and Zweig, Ann S. and Smith, Kayla and Thakkapallayil, Archana and Barber, Galt and Kuhn, Robert M. and Karolchik, Donna and Armengol, Lluis and Bird, Christine P. and de Bakker, Paul I. and Kern, Andrew D. and Lopez-Bigas, Nuria and Martin, Joel D. and Stranger, Barbara E. and Woodroffe, Abigail and Davydov, Eugene and Dimas, Antigone and Eyras, Eduardo and Hallgr\'{\i}msd\'{o}ttir, Ingileif B. and Huppert, Julian and Zody, Michael C. and Abecasis, Gon\c{c}alo R. and Estivill, Xavier and Bouffard, Gerard G. and Guan, Xiaobin and Hansen, Nancy F. and Idol, Jacquelyn R. and Maduro, Valerie V. and Maskeri, Baishali and McDowell, Jennifer C. and Park, Morgan and Thomas, Pamela J. and Young, Alice C. and Blakesley, Robert W. and Muzny, Donna M. and Sodergren, Erica and Wheeler, David A. and Worley, Kim C. and Jiang, Huaiyang and Weinstock, George M. and Gibbs, Richard A. and Graves, Tina and Fulton, Robert and Mardis, Elaine R. and Wilson, Richard K. and Clamp, Michele and Cuff, James and Gnerre, Sante and Jaffe, David B. and Chang, Jean L. and Lindblad-Toh, Kerstin and Lander, Eric S. and Koriabine, Maxim and Nefedov, Mikhail and Osoegawa, Kazutoyo and Yoshinaga, Yuko and Zhu, Baoli and de Jong, Pieter J.}, citeulike-article-id = {1394766}, citeulike-linkout-0 = {http://dx.doi.org/10.1038/nature05874}, citeulike-linkout-1 = {http://www.ebi.ac.uk/citexplore/citationDetails.do?externalId=17571346&dataSource=MED}, citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/17571346}, citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=17571346}, day = {14}, doi = {10.1038/nature05874}, issn = {1476-4687}, journal = {Nature}, keywords = {encode, hnf4, motif, myc, taf1, tss}, month = {June}, number = {7146}, pages = {799--816}, posted-at = {2008-01-11 00:36:27}, priority = {5}, title = {Identification and analysis of functional elements in 1\% of the human genome by the ENCODE pilot project.}, url = {http://dx.doi.org/10.1038/nature05874}, volume = {447}, year = {2007} }

TY - JOUR ID - citeulike:1394766 L3 - citeulike-article-id:1394766 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. IS - 7146 JF - Nature SN - 1476-4687 EP - 816 TI - Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. VL - 447 SP - 799 KW - encode KW - hnf4 KW - motif KW - myc KW - taf1 KW - tss AU - Birney, Ewan AU - Stamatoyannopoulos, John AU - Dutta, Anindya AU - Guigó, Roderic AU - Gingeras, Thomas AU - Margulies, Elliott AU - Weng, Zhiping AU - Snyder, Michael AU - Dermitzakis, Emmanouil AU - Thurman, Robert AU - Kuehn, Michael AU - Taylor, Christopher AU - Neph, Shane AU - Koch, Christoph AU - Asthana, Saurabh AU - Malhotra, Ankit AU - Adzhubei, Ivan AU - Greenbaum, Jason AU - Andrews, Robert AU - Flicek, Paul AU - Boyle, Patrick AU - Cao, Hua AU - Carter, Nigel AU - Clelland, Gayle AU - Davis, Sean AU - Day, Nathan AU - Dhami, Pawandeep AU - Dillon, Shane AU - Dorschner, Michael AU - Fiegler, Heike AU - Giresi, Paul AU - Goldy, Jeff AU - Hawrylycz, Michael AU - Haydock, Andrew AU - Humbert, Richard AU - James, Keith AU - Johnson, Brett AU - Johnson, Ericka AU - Frum, Tristan AU - Rosenzweig, Elizabeth AU - Karnani, Neerja AU - Lee, Kirsten AU - Lefebvre, Gregory AU - Navas, Patrick AU - Neri, Fidencio AU - Parker, Stephen AU - Sabo, Peter AU - Sandstrom, Richard AU - Shafer, Anthony AU - Vetrie, David AU - Weaver, Molly AU - Wilcox, Sarah AU - Yu, Man AU - Collins, Francis AU - Dekker, Job AU - Lieb, Jason AU - Tullius, Thomas AU - Crawford, Gregory AU - Sunyaev, Shamil AU - Noble, William 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 AU - Baertsch, Robert AU - Keefe, Damian AU - Dike, Sujit AU - Cheng, Jill AU - Hirsch, Heather AU - Sekinger, Edward AU - Lagarde, Julien AU - Abril, Josep 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 AU - Holroyd, Nancy AU - Taylor, Ruth AU - Swarbreck, David AU - Matthews, Nicholas AU - Dickson, Mark AU - Thomas, Daryl AU - Weirauch, Matthew AU - Gilbert, James AU - Drenkow, Jorg AU - Bell, Ian AU - Zhao, XiaoDong AU - Srinivasan, KG 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 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 AU - Brown, James AU - Ganesh, Madhavan AU - Patel, Sandeep AU - Tammana, Hari AU - Chrast, Jacqueline AU - Henrichsen, Charlotte 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 AU - Carninci, Piero AU - Hayashizaki, Yoshihide AU - Weissman, Sherman AU - Hubbard, Tim AU - Myers, Richard AU - Rogers, Jane AU - Stadler, Peter AU - Lowe, Todd AU - Wei, Chia-Lin AU - Ruan, Yijun AU - Struhl, Kevin AU - Gerstein, Mark AU - Antonarakis, Stylianos AU - Fu, Yutao AU - Green, Eric AU - Karaöz, Ulaş AU - Siepel, Adam AU - Taylor, James AU - Liefer, Laura AU - Wetterstrand, Kris AU - Good, Peter AU - Feingold, Elise AU - Guyer, Mark AU - Cooper, Gregory AU - Asimenos, George AU - Dewey, Colin AU - Hou, Minmei AU - Nikolaev, Sergey AU - Montoya-Burgos, Juan AU - Löytynoja, Ari AU - Whelan, Simon AU - Pardi, Fabio AU - Massingham, Tim AU - Huang, Haiyan AU - Zhang, Nancy AU - Holmes, Ian AU - Mullikin, James AU - Ureta-Vidal, Abel AU - Paten, Benedict AU - Seringhaus, Michael AU - Church, Deanna AU - Rosenbloom, Kate AU - Kent, James AU - Stone, Eric AU - Batzoglou, Serafim AU - Goldman, Nick AU - Hardison, Ross AU - Haussler, David AU - Miller, Webb AU - Sidow, Arend AU - Trinklein, Nathan AU - Zhang, Zhengdong AU - Barrera, Leah AU - Stuart, Rhona AU - King, David AU - Ameur, Adam AU - Enroth, Stefan AU - Bieda, Mark AU - Kim, Jonghwan AU - Bhinge, Akshay AU - Jiang, Nan AU - Liu, Jun AU - Yao, Fei AU - Vega, Vinsensius AU - Lee, Charlie AU - Ng, Patrick AU - Shahab, Atif AU - Yang, Annie AU - Moqtaderi, Zarmik AU - Zhu, Zhou AU - Xu, Xiaoqin AU - Squazzo, Sharon AU - Oberley, Matthew AU - Inman, David AU - Singer, Michael AU - Richmond, Todd AU - Munn, Kyle AU - Rada-Iglesias, Alvaro AU - Wallerman, Ola AU - Komorowski, Jan AU - Fowler, Joanna AU - Couttet, Phillippe AU - Bruce, Alexander AU - Dovey, Oliver AU - Ellis, Peter AU - Langford, Cordelia AU - Nix, David AU - Euskirchen, Ghia AU - Hartman, Stephen AU - Urban, Alexander AU - Kraus, Peter AU - Van Calcar, Sara AU - Heintzman, Nate AU - Kim, Tae Hoon AU - Wang, Kun AU - Qu, Chunxu AU - Hon, Gary AU - Luna, Rosa AU - Glass, Christopher AU - Rosenfeld, Geoff AU - Aldred, Shelley Force AU - Cooper, Sara AU - Halees, Anason AU - Lin, Jane AU - Shulha, Hennady AU - Zhang, Xiaoling AU - Xu, Mousheng AU - Haidar, Jaafar AU - Yu, Yong AU - Ruan, Yijun AU - Iyer, Vishwanath AU - Green, Roland AU - Wadelius, Claes AU - Farnham, Peggy AU - Ren, Bing AU - Harte, Rachel AU - Hinrichs, Angie AU - Trumbower, Heather AU - Clawson, Hiram AU - Hillman-Jackson, Jennifer AU - Zweig, Ann AU - Smith, Kayla AU - Thakkapallayil, Archana AU - Barber, Galt AU - Kuhn, Robert AU - Karolchik, Donna AU - Armengol, Lluis AU - Bird, Christine AU - de Bakker, Paul AU - Kern, Andrew AU - Lopez-Bigas, Nuria AU - Martin, Joel AU - Stranger, Barbara AU - Woodroffe, Abigail AU - Davydov, Eugene AU - Dimas, Antigone AU - Eyras, Eduardo AU - Hallgrímsdóttir, Ingileif AU - Huppert, Julian AU - Zody, Michael AU - Abecasis, Gonçalo AU - Estivill, Xavier AU - Bouffard, Gerard AU - Guan, Xiaobin AU - Hansen, Nancy AU - Idol, Jacquelyn AU - Maduro, Valerie AU - Maskeri, Baishali AU - McDowell, Jennifer AU - Park, Morgan AU - Thomas, Pamela AU - Young, Alice AU - Blakesley, Robert AU - Muzny, Donna AU - Sodergren, Erica AU - Wheeler, David AU - Worley, Kim AU - Jiang, Huaiyang AU - Weinstock, George AU - Gibbs, Richard AU - Graves, Tina AU - Fulton, Robert AU - Mardis, Elaine AU - Wilson, Richard AU - Clamp, Michele AU - Cuff, James AU - Gnerre, Sante AU - Jaffe, David AU - Chang, Jean AU - Lindblad-Toh, Kerstin AU - Lander, Eric AU - Koriabine, Maxim AU - Nefedov, Mikhail AU - Osoegawa, Kazutoyo AU - Yoshinaga, Yuko AU - Zhu, Baoli AU - de Jong, Pieter PY - 2007/06/14/ UR - http://dx.doi.org/10.1038/nature05874 ER -