維基百科

ENCODE

DNA元件百科全書（英語：Encyclopedia of DNA Elements，簡稱為ENCODE項目）是一個由美國國家人類基因組研究所(NHGRI)在2003年9月發起的一項公共聯合研究項目[2]，旨在找出人類基因組中所有功能組件[1][3][4][5]。

ENCODE
內容
相關信息
研究中心史丹福大學
實驗室
  • 聖塔克魯茲加利福尼亞大學（2003-2012）
  • 史丹福大學（2007年至今）
創始人Brian J Raney[1]
發佈日期2010年
訪問入口
網站encodeproject.org
工具
其他

這是既完成人類基因組計劃後國家人類基因組研究所開始的最重要的項目之一。

所有在該項目中產生的數據都會被迅速的在公共數據庫中公開。

ENCOD項目

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ENCODE分三個階段實施：試驗階段，技術發展階段，和生產階段。

ENCODE一期項目：試驗項目

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試驗項目測試和比較現有方法進行嚴格分析一個所定義的人類基因組序列的一部分。

ENCODE二期項目：生產階段項目

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ENCODE數據的圖像，在UCSC Genome Browser（英語：UCSC Genome Browser）。 This shows several tracks containing information on gene regulation. The gene on the left (ATP2B4) is transcribed in a wide variety of cells. The gene on the right is only transcribed in a few types of cells, including embryonic stem cells.

2007年9月，國家人類基因組研究所（NHGRI）開始了ENCODE項目生產階段的撥款。在這個階段，目標是分析整個基因組，並進行「額外中試規模研究」[6]。

作為試點項目，生產工作被組織作為一個開放的聯盟。 2007年10月，國家人類基因組研究所（NHGRI）在四年期間獲撥款總額超過$8000萬美元[7]。生產階段還包括一個數據協調中心，數據分析中心，和技術開發工作[8]。當時該項目發展成為一個真正的全球性企業，涉及來自世界各地的32個實驗室的440名科學家。

生產階段結果

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2012年9月5日，該項目的初步結果被整理為30篇論文並同時發表於多個刊物，包括6篇論文在《自然》、6篇論文在《基因組生物學》及18篇論文在《基因組研究》上[9][10]。

最引人注目的發現是，人類DNA有生物活性的分數大於以前估計中即使是最樂觀的估計還要高得多。這些發表的論文顯示人類基因組內的非編碼DNA至少80%是有生物活性的，而非像之前認為的僅僅是「垃圾」。這個結果非常重要，因為人類基因組中98%的DNA是非編碼的，意味着它們並不直接編碼任何蛋白質序列。

參見

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參考文獻

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  1. ^ 1.0 1.1 Raney BJ, Cline MS, Rosenbloom KR, Dreszer TR, Learned K, Barber GP, Meyer LR, Sloan CA, Malladi VS, Roskin KM, Suh BB, Hinrichs AS, Clawson H, Zweig AS, Kirkup V, Fujita PA, Rhead B, Smith KE, Pohl A, Kuhn RM, Karolchik D, Haussler D, Kent, WJ. ENCODE whole-genome data in the UCSC genome browser (2011 update). Nucleic Acids Res. January 2011, 39 (Database issue): D871–5. PMC 3013645  . PMID 21037257. doi:10.1093/nar/gkq1017. 
  2. ^ Maher B. ENCODE: The human encyclopaedia. Nature. 2012, 489 (7414): 46–48. doi:10.1038/489046a. 
  3. ^ The ENCODE Project Consortium. A User's Guide to the Encyclopedia of DNA Elements (ENCODE). PLOS Biology. 2011-04-19, 9 (4): e1001046 [2018-04-02]. ISSN 1545-7885. doi:10.1371/journal.pbio.1001046. （原始內容存檔於2018-03-28） （英語）. 
  4. ^ ENCODE Project Consortium, 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, 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, NISC Comparative Sequencing Program, Baylor College of Medicine Human Genome Sequencing Center, Washington University Genome Sequencing Center, Broad Institute, Children's Hospital Oakland Research Institute, Serafim Batzoglou, Nick Goldman, Ross C. Hardison, David Haussler, Webb Miller, Arend Sidow, Nathan D. Trinklein, Zhengdong D. 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, Atif Shahab, 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, Yijun Ruan, 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. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature. 2007-06-14, 447 (7146): 799–816 [2019-02-12]. ISSN 1476-4687. PMC 2212820  . PMID 17571346. doi:10.1038/nature05874. （原始內容存檔於2019-06-19）. 
  5. ^ Roderic Guigó, Paul Flicek, Josep F. Abril, Alexandre Reymond, Julien Lagarde, France Denoeud, Stylianos Antonarakis, Michael Ashburner, Vladimir B. Bajic, Ewan Birney, Robert Castelo, Eduardo Eyras, Catherine Ucla, Thomas R. Gingeras, Jennifer Harrow, Tim Hubbard, Suzanna E. Lewis, Martin G. Reese. EGASP: the human ENCODE Genome Annotation Assessment Project. Genome Biology. 2006,. 7 Suppl 1: S2.1–31 [2019-02-12]. ISSN 1474-760X. doi:10.1186/gb-2006-7-s1-s2. （原始內容存檔於2016-04-01）. 
  6. ^ Genome.gov | ENCODE and modENCODE Projects. The ENCODE Project: ENCyclopedia Of DNA Elements. United States National Human Genome Research Institute. 2011-08-01 [2011-08-05]. （原始內容存檔於2011-08-07）. 
  7. ^ National Human Genome Research Institute - Organization. The NIH Almanac. United States National Institutes of Health. [2011-08-05]. （原始內容存檔於2015-10-04）. 
  8. ^ Genome.gov | ENCODE Participants and Projects. The ENCODE Project: ENCyclopedia Of DNA Elements. United States National Human Genome Research Institute. 2011-08-01 [2011-08-05]. （原始內容存檔於2011-08-07）. 
  9. ^ ENCODE project at UCSC. ENCODE Consortium. [2012-09-05]. （原始內容存檔於2012-09-10）. 
  10. ^ Walsh, Fergus. Detailed map of genome function. BBC News. 2012-09-05 [2012-09-06]. （原始內容存檔於2012-09-06）. 

外部連結

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取自 "https://zh.wikipedia.org/w/index.php?title=ENCODE&oldid=80031367"