International Cancer Genome Consortium Data Portal-a one-stop shop for cancer genomics data

被引：304

作者：

Zhang, Junjun ^{[1
]}

Baran, Joachim ^{[1
]}

Cros, A. ^{[1
]}

Guberman, Jonathan M. ^{[1
]}

Haider, Syed ^{[2
]}

Hsu, Jack ^{[1
]}

Liang, Yong ^{[1
]}

Rivkin, Elena ^{[1
]}

Wang, Jianxin ^{[1
]}

Whitty, Brett ^{[1
]}

Wong-Erasmus, Marie ^{[1
]}

Yao, Long ^{[1
]}

Kasprzyk, Arek ^{[1
]}

机构：

[1] Ontario Inst Canc Res, Toronto, ON M5G 0A3, Canada

[2] Univ Cambridge, Comp Lab, Cambridge CB3 0FD, England

来源：

DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION | 2011年

关键词：

HUMAN BREAST; PATHWAYS; KEGG;

D O I：

10.1093/database/bar026

中图分类号：

Q [生物科学];

学科分类号：

090105 [作物生产系统与生态工程];

摘要：

The International Cancer Genome Consortium (ICGC) is a collaborative effort to characterize genomic abnormalities in 50 different cancer types. To make this data available, the ICGC has created the ICGC Data Portal. Powered by the BioMart software, the Data Portal allows each ICGC member institution to manage and maintain its own databases locally, while seamlessly presenting all the data in a single access point for users. The Data Portal currently contains data from 24 cancer projects, including ICGC, The Cancer Genome Atlas (TCGA), Johns Hopkins University, and the Tumor Sequencing Project. It consists of 3478 genomes and 13 cancer types and subtypes. Available open access data types include simple somatic mutations, copy number alterations, structural rearrangements, gene expression, microRNAs, DNA methylation and exon junctions. Additionally, simple germline variations are available as controlled access data. The Data Portal uses a web-based graphical user interface (GUI) to offer researchers multiple ways to quickly and easily search and analyze the available data. The web interface can assist in constructing complicated queries across multiple data sets. Several application programming interfaces are also available for programmatic access. Here we describe the organization, functionality, and capabilities of the ICGC Data Portal. Database URL: http://dcc.icgc.org

引用

页数：10

共 11 条

[1]

Comprehensive genomic characterization defines human glioblastoma genes and core pathways [J].

Chin, L. ;

Meyerson, M. ;

Aldape, K. ;

Bigner, D. ;

Mikkelsen, T. ;

VandenBerg, S. ;

Kahn, A. ;

Penny, R. ;

Ferguson, M. L. ;

Gerhard, D. S. ;

Getz, G. ;

Brennan, C. ;

Taylor, B. S. ;

Winckler, W. ;

Park, P. ;

Ladanyi, M. ;

Hoadley, K. A. ;

Verhaak, R. G. W. ;

Hayes, D. N. ;

Spellman, Paul T. ;

Absher, D. ;

Weir, B. A. ;

Ding, L. ;

Wheeler, D. ;

Lawrence, M. S. ;

Cibulskis, K. ;

Mardis, E. ;

Zhang, Jinghui ;

Wilson, R. K. ;

Donehower, L. ;

Wheeler, D. A. ;

Purdom, E. ;

Wallis, J. ;

Laird, P. W. ;

Herman, J. G. ;

Schuebel, K. E. ;

Weisenberger, D. J. ;

Baylin, S. B. ;

Schultz, N. ;

Yao, Jun ;

Wiedemeyer, R. ;

Weinstein, J. ;

Sander, C. ;

Gibbs, R. A. ;

Gray, J. ;

Kucherlapati, R. ;

Lander, E. S. ;

Myers, R. M. ;

Perou, C. M. ;

McLendon, Roger .

NATURE, 2008, 455 (7216) :1061-1068

[2]

Somatic mutations affect key pathways in lung adenocarcinoma [J].

Ding, Li ;

Getz, Gad ;

Wheeler, David A. ;

Mardis, Elaine R. ;

McLellan, Michael D. ;

Cibulskis, Kristian ;

Sougnez, Carrie ;

Greulich, Heidi ;

Muzny, Donna M. ;

Morgan, Margaret B. ;

Fulton, Lucinda ;

Fulton, Robert S. ;

Zhang, Qunyuan ;

Wendl, Michael C. ;

Lawrence, Michael S. ;

Larson, David E. ;

Chen, Ken ;

Dooling, David J. ;

Sabo, Aniko ;

Hawes, Alicia C. ;

Shen, Hua ;

Jhangiani, Shalini N. ;

Lewis, Lora R. ;

Hall, Otis ;

Zhu, Yiming ;

Mathew, Tittu ;

Ren, Yanru ;

Yao, Jiqiang ;

Scherer, Steven E. ;

Clerc, Kerstin ;

Metcalf, Ginger A. ;

Ng, Brian ;

Milosavljevic, Aleksandar ;

Gonzalez-Garay, Manuel L. ;

Osborne, John R. ;

Meyer, Rick ;

Shi, Xiaoqi ;

Tang, Yuzhu ;

Koboldt, Daniel C. ;

Lin, Ling ;

Abbott, Rachel ;

Miner, Tracie L. ;

Pohl, Craig ;

Fewell, Ginger ;

Haipek, Carrie ;

Schmidt, Heather ;

Dunford-Shore, Brian H. ;

Kraja, Aldi ;

Crosby, Seth D. ;

Sawyer, Christopher S. .

NATURE, 2008, 455 (7216) :1069-1075

[3]

BioMart Central Portal-unified access to biological data [J].

Haider, Syed ;

Ballester, Benoit ;

Smedley, Damian ;

Zhang, Junjun ;

Rice, Peter ;

Kasprzyk, Arek .

NUCLEIC ACIDS RESEARCH, 2009, 37 :W23-W27

[4]

International network of cancer genome projects [J].

Hudson, Thomas J. ;

Anderson, Warwick ;

Aretz, Axel ;

Barker, Anna D. ;

Bell, Cindy ;

Bernabe, Rosa R. ;

Bhan, M. K. ;

Calvo, Fabien ;

Eerola, Iiro ;

Gerhard, Daniela S. ;

Guttmacher, Alan ;

Guyer, Mark ;

Hemsley, Fiona M. ;

Jennings, Jennifer L. ;

Kerr, David ;

Klatt, Peter ;

Kolar, Patrik ;

Kusuda, Jun ;

Lane, David P. ;

Laplace, Frank ;

Lu, Youyong ;

Nettekoven, Gerd ;

Ozenberger, Brad ;

Peterson, Jane ;

Rao, T. S. ;

Remacle, Jacques ;

Schafer, Alan J. ;

Shibata, Tatsuhiro ;

Stratton, Michael R. ;

Vockley, Joseph G. ;

Watanabe, Koichi ;

Yang, Huanming ;

Yuen, Matthew M. F. ;

Knoppers, M. ;

Bobrow, Martin ;

Cambon-Thomsen, Anne ;

Dressler, Lynn G. ;

Dyke, Stephanie O. M. ;

Joly, Yann ;

Kato, Kazuto ;

Kennedy, Karen L. ;

Nicolas, Pilar ;

Parker, Michael J. ;

Rial-Sebbag, Emmanuelle ;

Romeo-Casabona, Carlos M. ;

Shaw, Kenna M. ;

Wallace, Susan ;

Wiesner, Georgia L. ;

Zeps, Nikolajs ;

Lichter, Peter .

NATURE, 2010, 464 (7291) :993-998

[5]

Core signaling pathways in human pancreatic cancers revealed by global genomic analyses [J].

Jones, Sian ;

Zhang, Xiaosong ;

Parsons, D. Williams ;

Lin, Jimmy Cheng-Ho ;

Leary, Rebecca J. ;

Angenendt, Philipp ;

Mankoo, Parminder ;

Carter, Hannah ;

Kamiyama, Hirohiko ;

Jimeno, Antonio ;

Hong, Seung-Mo ;

Fu, Baojin ;

Lin, Ming-Tseh ;

Calhoun, Eric S. ;

Kamiyama, Mihoko ;

Walter, Kimberly ;

Nikolskaya, Tatiana ;

Nikolsky, Yuri ;

Hartigan, James ;

Smith, Douglas R. ;

Hidalgo, Manuel ;

Leach, Steven D. ;

Klein, Alison P. ;

Jaffee, Elizabeth M. ;

Goggins, Michael ;

Maitra, Anirban ;

Iacobuzio-Donahue, Christine ;

Eshleman, James R. ;

Kern, Scott E. ;

Hruban, Ralph H. ;

Karchin, Rachel ;

Papadopoulos, Nickolas ;

Parmigiani, Giovanni ;

Vogelstein, Bert ;

Velculescu, Victor E. ;

Kinzler, Kenneth W. .

SCIENCE, 2008, 321 (5897) :1801-1806

[6]

KEGG for representation and analysis of molecular networks involving diseases and drugs [J].

Kanehisa, Minoru ;

Goto, Susumu ;

Furumichi, Miho ;

Tanabe, Mao ;

Hirakawa, Mika .

NUCLEIC ACIDS RESEARCH, 2010, 38 :D355-D360

[7]

From genomics to chemical genomics: new developments in KEGG [J].

Kanehisa, Minoru ;

Goto, Susumu ;

Hattori, Masahiro ;

Aoki-Kinoshita, Kiyoko F. ;

Itoh, Masumi ;

Kawashima, Shuichi ;

Katayama, Toshiaki ;

Araki, Michihiro ;

Hirakawa, Mika .

NUCLEIC ACIDS RESEARCH, 2006, 34 :D354-D357

[8]

KEGG: Kyoto Encyclopedia of Genes and Genomes [J].

Ogata, H ;

Goto, S ;

Sato, K ;

Fujibuchi, W ;

Bono, H ;

Kanehisa, M .

NUCLEIC ACIDS RESEARCH, 1999, 27 (01) :29-34

[9]

An integrated genomic analysis of human glioblastoma Multiforme [J].

Parsons, D. Williams ;

Jones, Sian ;

Zhang, Xiaosong ;

Lin, Jimmy Cheng-Ho ;

Leary, Rebecca J. ;

Angenendt, Philipp ;

Mankoo, Parminder ;

Carter, Hannah ;

Siu, I-Mei ;

Gallia, Gary L. ;

Olivi, Alessandro ;

McLendon, Roger ;

Rasheed, B. Ahmed ;

Keir, Stephen ;

Nikolskaya, Tatiana ;

Nikolsky, Yuri ;

Busam, Dana A. ;

Tekleab, Hanna ;

Diaz, Luis A., Jr. ;

Hartigan, James ;

Smith, Doug R. ;

Strausberg, Robert L. ;

Marie, Suely Kazue Nagahashi ;

Shinjo, Sueli Mieko Oba ;

Yan, Hai ;

Riggins, Gregory J. ;

Bigner, Darell D. ;

Karchin, Rachel ;

Papadopoulos, Nick ;

Parmigiani, Giovanni ;

Vogelstein, Bert ;

Velculescu, Victor E. ;

Kinzler, Kenneth W. .

SCIENCE, 2008, 321 (5897) :1807-1812

[10]

The consensus coding sequences of human breast and colorectal cancers [J].

Sjoeblom, Tobias ;

Jones, Sian ;

Wood, Laura D. ;

Parsons, D. Williams ;

Lin, Jimmy ;

Barber, Thomas D. ;

Mandelker, Diana ;

Leary, Rebecca J. ;

Ptak, Janine ;

Silliman, Natalie ;

Szabo, Steve ;

Buckhaults, Phillip ;

Farrell, Christopher ;

Meeh, Paul ;

Markowitz, Sanford D. ;

Willis, Joseph ;

Dawson, Dawn ;

Willson, James K. V. ;

Gazdar, Adi F. ;

Hartigan, James ;

Wu, Leo ;

Liu, Changsheng ;

Parmigiani, Giovanni ;

Park, Ben Ho ;

Bachman, Kurtis E. ;

Papadopoulos, Nickolas ;

Vogelstein, Bert ;

Kinzler, Kenneth W. ;

Velculescu, Victor E. .

SCIENCE, 2006, 314 (5797) :268-274

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