The Encyclopedia of DNA elements (ENCODE): data portal update

被引：1203

作者：

Davis, Carrie A. ^{[1
]}

Hitz, Benjamin C. ^{[1
]}

Sloan, Cricket A. ^{[1
]}

Chan, Esther T. ^{[1
]}

Davidson, Jean M. ^{[1
]}

Gabdank, Idan ^{[1
]}

Hilton, Jason A. ^{[1
]}

Jain, Kriti ^{[1
]}

Baymuradov, Ulugbek K. ^{[1
]}

Narayanan, Aditi K. ^{[1
]}

Onate, Kathrina C. ^{[1
]}

Graham, Keenan ^{[1
]}

Miyasato, Stuart R. ^{[1
]}

Dreszer, Timothy R. ^{[1
]}

Strattan, J. Seth ^{[1
]}

Jolanki, Otto ^{[1
]}

Tanaka, Forrest Y. ^{[1
]}

Cherry, J. Michael ^{[1
]}

机构：

[1] Stanford Univ, Dept Genet, Stanford, CA 94305 USA

来源：

NUCLEIC ACIDS RESEARCH | 2018年 / 46卷 / D1期

基金：

美国国家卫生研究院;

关键词：

UCSC GENOME BROWSER; INTEGRATIVE ANALYSIS; FUNCTIONAL ELEMENTS; PROJECT; IDENTIFICATION; ANTIBODIES; MODENCODE;

D O I：

10.1093/nar/gkx1081

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

070307 [化学生物学]; 071010 [生物化学与分子生物学];

摘要：

The Encyclopedia of DNA Elements (ENCODE) Data Coordinating Center has developed the ENCODE Portal database and website as the source for the data and metadata generated by the ENCODE Consortium. Two principles have motivated the design. First, experimental protocols, analytical procedures and the data themselves should be made publicly accessible through a coherent, web-based search and download interface. Second, the same interface should serve carefully curated metadata that record the provenance of the data and justify its interpretation in biological terms. Since its initial release in 2013 and in response to recommendations from consortium members and the wider community of scientists who use the Portal to access ENCODE data, the Portal has been regularly updated to better reflect these design principles. Here we report on these updates, including results from new experiments, uniformly-processed data from other projects, new visualization tools and more comprehensive metadata to describe experiments and analyses. Additionally, the Portal is now home to meta(data) from related projects including Genomics of Gene Regulation, Roadmap Epigenome Project, Model organism ENCODE (modENCODE) and modERN.

引用

页码：D794 / D801

页数：8

共 19 条

[1]

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Aken, Bronwen L. ;

Achuthan, Premanand ;

Akanni, Wasiu ;

Amode, M. Ridwan ;

Bernsdorff, Friederike ;

Bhai, Jyothish ;

Billis, Konstantinos ;

Carvalho-Silva, Denise ;

Cummins, Carla ;

Clapham, Peter ;

Gil, Laurent ;

Giron, Carlos Garcia ;

Gordon, Leo ;

Hourlier, Thibaut ;

Hunt, Sarah E. ;

Janacek, Sophie H. ;

Juettemann, Thomas ;

Keenan, Stephen ;

Laird, Matthew R. ;

Lavidas, Ilias ;

Maurel, Thomas ;

McLaren, William ;

Moore, Benjamin ;

Murphy, Daniel N. ;

Nag, Rishi ;

Newman, Victoria ;

Nuhn, Michael ;

Ong, Chuang Kee ;

Parker, Anne ;

Patricio, Mateus ;

Riat, Harpreet Singh ;

Sheppard, Daniel ;

Sparrow, Helen ;

Taylor, Kieron ;

Thormann, Anja ;

Vullo, Alessandro ;

Walts, Brandon ;

Wilder, Steven P. ;

Zadissa, Amonida ;

Kostadima, Myrto ;

Martin, Fergal J. ;

Muffato, Matthieu ;

Perry, Emily ;

Ruffier, Magali ;

Staines, Daniel M. ;

Trevanion, Stephen J. ;

Cunningham, Fiona ;

Yates, Andrew ;

Zerbino, Daniel R. ;

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Margulies, Elliott H. ;

Weng, Zhiping ;

Snyder, Michael ;

Dermitzakis, Emmanouil T. ;

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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. ;

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Morais, David Anderson de Lima ;

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Chen, Kuang Chung ;

Laperle, Jonathan ;

Markovits, Alexei Nordell ;

Pastinen, Tomi ;

Caron, Bryan ;

Veilleux, Alain ;

Jacques, Pierre-Etienne ;

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Dekker, Job ;

Belmont, Andrew S. ;

Guttman, Mitchell ;

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Mirny, Leonid A. ;

O'Shea, Clodagh C. ;

Park, Peter J. ;

Ren, Bing ;

Politz, Joan C. Ritland ;

Shendure, Jay ;

Zhong, Sheng ;

van den Berg, Aafke ;

Heckert, Alec Basil ;

Bertero, Alessandro ;

Bortnick, Alex ;

Kukalev, Alexander ;

Moore, Amanda ;

Pombo, Ana ;

Hansen, Anders Sejr ;

Chiariello, Andrea Maria ;

Sali, Andrej ;

Belmont, Andrew ;

Stephens, Andrew ;

Nand, Ankita ;

Valton, Anne-Laure ;

Goloborodko, Anton ;

He, Arthur ;

van Steensel, Bas ;

Webb, Ben ;

Roscoe, Benjamin ;

Li, Bin ;

Ren, Bing ;

Chait, Brian ;

Blau, C. Anthony ;

Annunziatella, Carlo ;

Ware, Carol ;

Wei, Chia Lin ;

Leemans, Christ ;

Disteche, Christine ;

Jarjour, Christine ;

Thieme, Christoph ;

Murry, Chuck ;

Barcia, Claudia Trevilla ;

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Piipari, Matias ;

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Dunham, Ian ;

Kundaje, Anshul ;

Aldred, Shelley F. ;

Collins, Patrick J. ;

Davis, CarrieA. ;

Doyle, Francis ;

Epstein, Charles B. ;

Frietze, Seth ;

Harrow, Jennifer ;

Kaul, Rajinder ;

Khatun, Jainab ;

Lajoie, Bryan R. ;

Landt, Stephen G. ;

Lee, Bum-Kyu ;

Pauli, Florencia ;

Rosenbloom, Kate R. ;

Sabo, Peter ;

Safi, Alexias ;

Sanyal, Amartya ;

Shoresh, Noam ;

Simon, Jeremy M. ;

Song, Lingyun ;

Trinklein, Nathan D. ;

Altshuler, Robert C. ;

Birney, Ewan ;

Brown, James B. ;

Cheng, Chao ;

Djebali, Sarah ;

Dong, Xianjun ;

Dunham, Ian ;

Ernst, Jason ;

Furey, Terrence S. ;

Gerstein, Mark ;

Giardine, Belinda ;

Greven, Melissa ;

Hardison, Ross C. ;

Harris, Robert S. ;

Herrero, Javier ;

Hoffman, Michael M. ;

Iyer, Sowmya ;

Kellis, Manolis ;

Khatun, Jainab ;

Kheradpour, Pouya ;

Kundaje, Anshul ;

Lassmann, Timo ;

Li, Qunhua ;

Lin, Xinying ;

Marinov, Georgi K. ;

Merkel, Angelika ;

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Integrative Analysis of the Caenorhabditis elegans Genome by the modENCODE Project [J].

Gerstein, Mark B. ;

Lu, Zhi John ;

Van Nostrand, Eric L. ;

Cheng, Chao ;

Arshinoff, Bradley I. ;

Liu, Tao ;

Yip, Kevin Y. ;

Robilotto, Rebecca ;

Rechtsteiner, Andreas ;

Ikegami, Kohta ;

Alves, Pedro ;

Chateigner, Aurelien ;

Perry, Marc ;

Morris, Mitzi ;

Auerbach, Raymond K. ;

Feng, Xin ;

Leng, Jing ;

Vielle, Anne ;

Niu, Wei ;

Rhrissorrakrai, Kahn ;

Agarwal, Ashish ;

Alexander, Roger P. ;

Barber, Galt ;

Brdlik, Cathleen M. ;

Brennan, Jennifer ;

Brouillet, Jeremy Jean ;

Carr, Adrian ;

Cheung, Ming-Sin ;

Clawson, Hiram ;

Contrino, Sergio ;

Dannenberg, Luke O. ;

Dernburg, Abby F. ;

Desai, Arshad ;

Dick, Lindsay ;

Dose, Andrea C. ;

Du, Jiang ;

Egelhofer, Thea ;

Ercan, Sevinc ;

Euskirchen, Ghia ;

Ewing, Brent ;

Feingold, Elise A. ;

Gassmann, Reto ;

Good, Peter J. ;

Green, Phil ;

Gullier, Francois ;

Gutwein, Michelle ;

Guyer, Mark S. ;

Habegger, Lukas ;

Han, Ting ;

Henikoff, Jorja G. .

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[9]

GENCODE: The reference human genome annotation for The ENCODE Project [J].

Harrow, Jennifer ;

Frankish, Adam ;

Gonzalez, Jose M. ;

Tapanari, Electra ;

Diekhans, Mark ;

Kokocinski, Felix ;

Aken, Bronwen L. ;

Barrell, Daniel ;

Zadissa, Amonida ;

Searle, Stephen ;

Barnes, If ;

Bignell, Alexandra ;

Boychenko, Veronika ;

Hunt, Toby ;

Kay, Mike ;

Mukherjee, Gaurab ;

Rajan, Jeena ;

Despacio-Reyes, Gloria ;

Saunders, Gary ;

Steward, Charles ;

Harte, Rachel ;

Lin, Michael ;

Howald, Cedric ;

Tanzer, Andrea ;

Derrien, Thomas ;

Chrast, Jacqueline ;

Walters, Nathalie ;

Balasubramanian, Suganthi ;

Pei, Baikang ;

Tress, Michael ;

Manuel Rodriguez, Jose ;

Ezkurdia, Iakes ;

van Baren, Jeltje ;

Brent, Michael ;

Haussler, David ;

Kellis, Manolis ;

Valencia, Alfonso ;

Reymond, Alexandre ;

Gerstein, Mark ;

Guigo, Roderic ;

Hubbard, Tim J. .

GENOME RESEARCH, 2012, 22 (09) :1760-1774

[10]

SnoVault and encodeD: A novel object-based storage system and applications to ENCODE metadata [J].

Hitz, Benjamin C. ;

Rowe, Laurence D. ;

Podduturi, Nikhil R. ;

Glick, David I. ;

Baymuradov, Ulugbek K. ;

Malladi, Venkat S. ;

Chan, Esther T. ;

Davidson, Jean M. ;

Gabdank, Idan ;

Narayana, Aditi K. ;

Onate, Kathrina C. ;

Hilton, Jason ;

Ho, Marcus C. ;

Lee, Brian T. ;

Miyasato, Stuart R. ;

Dreszer, Timothy R. ;

Sloan, Cricket A. ;

Strattan, J. Seth ;

Tanaka, Forrest Y. ;

Hong, Eurie L. ;

Cherry, J. Michael .

PLOS ONE, 2017, 12 (04)

← 1 2 →

共 19 条

[1]

Ensembl 2017 [J].

Aken, Bronwen L. ;

Achuthan, Premanand ;

Akanni, Wasiu ;

Amode, M. Ridwan ;

Bernsdorff, Friederike ;

Bhai, Jyothish ;

Billis, Konstantinos ;

Carvalho-Silva, Denise ;

Cummins, Carla ;

Clapham, Peter ;

Gil, Laurent ;

Giron, Carlos Garcia ;

Gordon, Leo ;

Hourlier, Thibaut ;

Hunt, Sarah E. ;

Janacek, Sophie H. ;

Juettemann, Thomas ;

Keenan, Stephen ;

Laird, Matthew R. ;

Lavidas, Ilias ;

Maurel, Thomas ;

McLaren, William ;

Moore, Benjamin ;

Murphy, Daniel N. ;

Nag, Rishi ;

Newman, Victoria ;

Nuhn, Michael ;

Ong, Chuang Kee ;

Parker, Anne ;

Patricio, Mateus ;

Riat, Harpreet Singh ;

Sheppard, Daniel ;

Sparrow, Helen ;

Taylor, Kieron ;

Thormann, Anja ;

Vullo, Alessandro ;

Walts, Brandon ;

Wilder, Steven P. ;

Zadissa, Amonida ;

Kostadima, Myrto ;

Martin, Fergal J. ;

Muffato, Matthieu ;

Perry, Emily ;

Ruffier, Magali ;

Staines, Daniel M. ;

Trevanion, Stephen J. ;

Cunningham, Fiona ;

Yates, Andrew ;

Zerbino, Daniel R. ;

Flicek, Paul .

NUCLEIC ACIDS RESEARCH, 2017, 45 (D1) :D635-D642

[2]

BLAME IT ON THE ANTIBODIES [J].

Baker, Monya .

NATURE, 2015, 521 (7552) :274-276

[3]

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

Birney, Ewan ;

Stamatoyannopoulos, John A. ;

Dutta, Anindya ;

Guigo, Roderic ;

Gingeras, Thomas R. ;

Margulies, Elliott H. ;

Weng, Zhiping ;

Snyder, Michael ;

Dermitzakis, Emmanouil T. ;

Stamatoyannopoulos, John A. ;

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 .

NATURE, 2007, 447 (7146) :799-816

[4]

The International Human Epigenome Consortium Data Portal [J].

Bujold, David ;

Morais, David Anderson de Lima ;

Gauthier, Carol ;

Cote, Catherine ;

Caron, Maxime ;

Kwan, Tony ;

Chen, Kuang Chung ;

Laperle, Jonathan ;

Markovits, Alexei Nordell ;

Pastinen, Tomi ;

Caron, Bryan ;

Veilleux, Alain ;

Jacques, Pierre-Etienne ;

Bourque, Guillaume .

CELL SYSTEMS, 2016, 3 (05) :496-+

[5]

The 4D nucleome project [J].

Dekker, Job ;

Belmont, Andrew S. ;

Guttman, Mitchell ;

Leshyk, Victor O. ;

Lis, John T. ;

Lomvardas, Stavros ;

Mirny, Leonid A. ;

O'Shea, Clodagh C. ;

Park, Peter J. ;

Ren, Bing ;

Politz, Joan C. Ritland ;

Shendure, Jay ;

Zhong, Sheng ;

van den Berg, Aafke ;

Heckert, Alec Basil ;

Bertero, Alessandro ;

Bortnick, Alex ;

Kukalev, Alexander ;

Moore, Amanda ;

Pombo, Ana ;

Hansen, Anders Sejr ;

Chiariello, Andrea Maria ;

Sali, Andrej ;

Belmont, Andrew ;

Stephens, Andrew ;

Nand, Ankita ;

Valton, Anne-Laure ;

Goloborodko, Anton ;

He, Arthur ;

van Steensel, Bas ;

Webb, Ben ;

Roscoe, Benjamin ;

Li, Bin ;

Ren, Bing ;

Chait, Brian ;

Blau, C. Anthony ;

Annunziatella, Carlo ;

Ware, Carol ;

Wei, Chia Lin ;

Leemans, Christ ;

Disteche, Christine ;

Jarjour, Christine ;

Thieme, Christoph ;

Murry, Chuck ;

Barcia, Claudia Trevilla ;

Trapnell, Cole ;

Murre, Cornelis ;

Peric-Hupkes, Daan ;

Simon, Dan ;

Bartlett, Daniel .

NATURE, 2017, 549 (7671) :219-226

[6]

Dalliance: interactive genome viewing on the web [J].

Down, Thomas A. ;

Piipari, Matias ;

Hubbard, Tim J. P. .

BIOINFORMATICS, 2011, 27 (06) :889-890

[7]

An integrated encyclopedia of DNA elements in the human genome [J].

Dunham, Ian ;

Kundaje, Anshul ;

Aldred, Shelley F. ;

Collins, Patrick J. ;

Davis, CarrieA. ;

Doyle, Francis ;

Epstein, Charles B. ;

Frietze, Seth ;

Harrow, Jennifer ;

Kaul, Rajinder ;

Khatun, Jainab ;

Lajoie, Bryan R. ;

Landt, Stephen G. ;

Lee, Bum-Kyu ;

Pauli, Florencia ;

Rosenbloom, Kate R. ;

Sabo, Peter ;

Safi, Alexias ;

Sanyal, Amartya ;

Shoresh, Noam ;

Simon, Jeremy M. ;

Song, Lingyun ;

Trinklein, Nathan D. ;

Altshuler, Robert C. ;

Birney, Ewan ;

Brown, James B. ;

Cheng, Chao ;

Djebali, Sarah ;

Dong, Xianjun ;

Dunham, Ian ;

Ernst, Jason ;

Furey, Terrence S. ;

Gerstein, Mark ;

Giardine, Belinda ;

Greven, Melissa ;

Hardison, Ross C. ;

Harris, Robert S. ;

Herrero, Javier ;

Hoffman, Michael M. ;

Iyer, Sowmya ;

Kellis, Manolis ;

Khatun, Jainab ;

Kheradpour, Pouya ;

Kundaje, Anshul ;

Lassmann, Timo ;

Li, Qunhua ;

Lin, Xinying ;

Marinov, Georgi K. ;

Merkel, Angelika ;

Mortazavi, Ali .

NATURE, 2012, 489 (7414) :57-74

[8]

Integrative Analysis of the Caenorhabditis elegans Genome by the modENCODE Project [J].

Gerstein, Mark B. ;

Lu, Zhi John ;

Van Nostrand, Eric L. ;

Cheng, Chao ;

Arshinoff, Bradley I. ;

Liu, Tao ;

Yip, Kevin Y. ;

Robilotto, Rebecca ;

Rechtsteiner, Andreas ;

Ikegami, Kohta ;

Alves, Pedro ;

Chateigner, Aurelien ;

Perry, Marc ;

Morris, Mitzi ;

Auerbach, Raymond K. ;

Feng, Xin ;

Leng, Jing ;

Vielle, Anne ;

Niu, Wei ;

Rhrissorrakrai, Kahn ;

Agarwal, Ashish ;

Alexander, Roger P. ;

Barber, Galt ;

Brdlik, Cathleen M. ;

Brennan, Jennifer ;

Brouillet, Jeremy Jean ;

Carr, Adrian ;

Cheung, Ming-Sin ;

Clawson, Hiram ;

Contrino, Sergio ;

Dannenberg, Luke O. ;

Dernburg, Abby F. ;

Desai, Arshad ;

Dick, Lindsay ;

Dose, Andrea C. ;

Du, Jiang ;

Egelhofer, Thea ;

Ercan, Sevinc ;

Euskirchen, Ghia ;

Ewing, Brent ;

Feingold, Elise A. ;

Gassmann, Reto ;

Good, Peter J. ;

Green, Phil ;

Gullier, Francois ;

Gutwein, Michelle ;

Guyer, Mark S. ;

Habegger, Lukas ;

Han, Ting ;

Henikoff, Jorja G. .

SCIENCE, 2010, 330 (6012) :1775-1787

[9]

GENCODE: The reference human genome annotation for The ENCODE Project [J].

Harrow, Jennifer ;

Frankish, Adam ;

Gonzalez, Jose M. ;

Tapanari, Electra ;

Diekhans, Mark ;

Kokocinski, Felix ;

Aken, Bronwen L. ;

Barrell, Daniel ;

Zadissa, Amonida ;

Searle, Stephen ;

Barnes, If ;

Bignell, Alexandra ;

Boychenko, Veronika ;

Hunt, Toby ;

Kay, Mike ;

Mukherjee, Gaurab ;

Rajan, Jeena ;

Despacio-Reyes, Gloria ;

Saunders, Gary ;

Steward, Charles ;

Harte, Rachel ;

Lin, Michael ;

Howald, Cedric ;

Tanzer, Andrea ;

Derrien, Thomas ;

Chrast, Jacqueline ;

Walters, Nathalie ;

Balasubramanian, Suganthi ;

Pei, Baikang ;

Tress, Michael ;

Manuel Rodriguez, Jose ;

Ezkurdia, Iakes ;

van Baren, Jeltje ;

Brent, Michael ;

Haussler, David ;

Kellis, Manolis ;

Valencia, Alfonso ;

Reymond, Alexandre ;

Gerstein, Mark ;

Guigo, Roderic ;

Hubbard, Tim J. .

GENOME RESEARCH, 2012, 22 (09) :1760-1774

[10]

SnoVault and encodeD: A novel object-based storage system and applications to ENCODE metadata [J].

Hitz, Benjamin C. ;

Rowe, Laurence D. ;

Podduturi, Nikhil R. ;

Glick, David I. ;

Baymuradov, Ulugbek K. ;

Malladi, Venkat S. ;

Chan, Esther T. ;

Davidson, Jean M. ;

Gabdank, Idan ;

Narayana, Aditi K. ;

Onate, Kathrina C. ;

Hilton, Jason ;

Ho, Marcus C. ;

Lee, Brian T. ;

Miyasato, Stuart R. ;

Dreszer, Timothy R. ;

Sloan, Cricket A. ;

Strattan, J. Seth ;

Tanaka, Forrest Y. ;

Hong, Eurie L. ;

Cherry, J. Michael .

PLOS ONE, 2017, 12 (04)

← 1 2 →