Exploring TCGA Pan-Cancer Data at the UCSC Cancer Genomics Browser

被引：231

作者：

Cline, Melissa S. ^{[1
]}

Craft, Brian ^{[1
]}

Swatloski, Teresa ^{[1
]}

Goldman, Mary ^{[1
]}

Ma, Singer ^{[1
]}

Haussler, David ^{[1
]}

Zhu, Jingchun ^{[1
]}

机构：

[1] Univ Calif Santa Cruz, Ctr Biomol Sci & Engn, Santa Cruz, CA 95064 USA

来源：

SCIENTIFIC REPORTS | 2013年 / 3卷

关键词：

SUBTYPE; BREAST;

D O I：

10.1038/srep02652

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

070301 [无机化学]; 070403 [天体物理学]; 070507 [自然资源与国土空间规划学]; 090105 [作物生产系统与生态工程];

摘要：

The UCSC Cancer Genomics Browser (https://genome-cancer.ucsc.edu) offers interactive visualization and exploration of TCGA genomic, phenotypic, and clinical data, as produced by the Cancer Genome Atlas Research Network. Researchers can explore the impact of genomic alterations on phenotypes by visualizing gene and protein expression, copy number, DNA methylation, somatic mutation and pathway inference data alongside clinical features, Pan-Cancer subtype classifications and genomic biomarkers. Integrated Kaplan-Meier survival analysis helps investigators to assess survival stratification by any of the information.

引用

页数：6

共 13 条

[1]

The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity [J].

Barretina, Jordi ;

Caponigro, Giordano ;

Stransky, Nicolas ;

Venkatesan, Kavitha ;

Margolin, Adam A. ;

Kim, Sungjoon ;

Wilson, Christopher J. ;

Lehar, Joseph ;

Kryukov, Gregory V. ;

Sonkin, Dmitriy ;

Reddy, Anupama ;

Liu, Manway ;

Murray, Lauren ;

Berger, Michael F. ;

Monahan, John E. ;

Morais, Paula ;

Meltzer, Jodi ;

Korejwa, Adam ;

Jane-Valbuena, Judit ;

Mapa, Felipa A. ;

Thibault, Joseph ;

Bric-Furlong, Eva ;

Raman, Pichai ;

Shipway, Aaron ;

Engels, Ingo H. ;

Cheng, Jill ;

Yu, Guoying K. ;

Yu, Jianjun ;

Aspesi, Peter, Jr. ;

de Silva, Melanie ;

Jagtap, Kalpana ;

Jones, Michael D. ;

Wang, Li ;

Hatton, Charles ;

Palescandolo, Emanuele ;

Gupta, Supriya ;

Mahan, Scott ;

Sougnez, Carrie ;

Onofrio, Robert C. ;

Liefeld, Ted ;

MacConaill, Laura ;

Winckler, Wendy ;

Reich, Michael ;

Li, Nanxin ;

Mesirov, Jill P. ;

Gabriel, Stacey B. ;

Getz, Gad ;

Ardlie, Kristin ;

Chan, Vivien ;

Myer, Vic E. .

NATURE, 2012, 483 (7391) :603-607

[2]

The guanine nucleotide exchange factor (GEF) Ect2 is an oncogene in human cancer [J].

Fields, Alan P. ;

Justilien, Verline .

ADVANCES IN ENZYME REGULATION, VOL 50, 2010, 50 :190-200

[3]

The UCSC Cancer Genomics Browser: update 2013 [J].

Goldman, Mary ;

Craft, Brian ;

Swatloski, Teresa ;

Ellrott, Kyle ;

Cline, Melissa ;

Diekhans, Mark ;

Ma, Singer ;

Wilks, Chris ;

Stuart, Josh ;

Haussler, David ;

Zhu, Jingchun .

NUCLEIC ACIDS RESEARCH, 2013, 41 (D1) :D949-D954

[4]

Subtype and pathway specific responses to anticancer compounds in breast cancer [J].

Heiser, Laura M. ;

Sadanandam, Anguraj ;

Kuo, Wen-Lin ;

Benz, Stephen C. ;

Goldstein, Theodore C. ;

Ng, Sam ;

Gibb, William J. ;

Wang, Nicholas J. ;

Ziyad, Safiyyah ;

Tong, Frances ;

Bayani, Nora ;

Hu, Zhi ;

Billig, Jessica I. ;

Dueregger, Andrea ;

Lewis, Sophia ;

Jakkula, Lakshmi ;

Korkola, James E. ;

Durinck, Steffen ;

Pepin, Francois ;

Guan, Yinghui ;

Purdom, Elizabeth ;

Neuvial, Pierre ;

Bengtsson, Henrik ;

Wood, Kenneth W. ;

Smith, Peter G. ;

Vassilev, Lyubomir T. ;

Hennessy, Bryan T. ;

Greshock, Joel ;

Bachman, Kurtis E. ;

Hardwicke, Mary Ann ;

Park, John W. ;

Marton, Laurence J. ;

Wolf, Denise M. ;

Collisson, Eric A. ;

Neve, Richard M. ;

Mills, Gordon B. ;

Speed, Terence P. ;

Feiler, Heidi S. ;

Wooster, Richard F. ;

Haussler, David ;

Stuart, Joshua M. ;

Gray, Joe W. ;

Spellman, Paul T. .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2012, 109 (08) :2724-2729

[5]

Genomic and Epigenomic Landscapes of Adult De Novo Acute Myeloid Leukemia [J].

Ley, Timothy J. ;

Miller, Christopher ;

Ding, Li ;

Raphael, Benjamin J. ;

Mungall, Andrew J. ;

Robertson, A. Gordon ;

Hoadley, Katherine ;

Triche, Timothy J., Jr. ;

Laird, Peter W. ;

Baty, Jack D. ;

Fulton, Lucinda L. ;

Fulton, Robert ;

Heath, Sharon E. ;

Kalicki-Veizer, Joelle ;

Kandoth, Cyriac ;

Klco, Jeffery M. ;

Koboldt, Daniel C. ;

Kanchi, Krishna-Latha ;

Kulkarni, Shashikant ;

Lamprecht, Tamara L. ;

Larson, David E. ;

Lin, Ling ;

Lu, Charles ;

McLellan, Michael D. ;

McMichael, Joshua F. ;

Payton, Jacqueline ;

Schmidt, Heather ;

Spencer, David H. ;

Tomasson, Michael H. ;

Wallis, John W. ;

Wartman, Lukas D. ;

Watson, Mark A. ;

Welch, John ;

Wendl, Michael C. ;

Ally, Adrian ;

Balasundaram, Miruna ;

Birol, Inanc ;

Butterfield, Yaron ;

Chiu, Readman ;

Chu, Andy ;

Chuah, Eric ;

Chun, Hye-Jung ;

Corbett, Richard ;

Dhalla, Noreen ;

Guin, Ranabir ;

He, An ;

Hirst, Carrie ;

Hirst, Martin ;

Holt, Robert A. ;

Jones, Steven .

NEW ENGLAND JOURNAL OF MEDICINE, 2013, 368 (22) :2059-2074

[6]

Visualizing multidimensional cancer genomics data [J].

Schroeder, Michael P. ;

Gonzalez-Perez, Abel ;

Lopez-Bigas, Nuria .

GENOME MEDICINE, 2013, 5

[7]

Gene expression-based survival prediction in lung adenocarcinoma: a multi-site, blinded validation study [J].

Shedden, Kerby ;

Taylor, Jeremy M. G. ;

Enkemann, Steven A. ;

Tsao, Ming-Sound ;

Yeatman, Timothy J. ;

Gerald, William L. ;

Eschrich, Steven ;

Jurisica, Igor ;

Giordano, Thomas J. ;

Misek, David E. ;

Chang, Andrew C. ;

Zhu, Chang Qi ;

Strumpf, Daniel ;

Hanash, Samir ;

Shepherd, Frances A. ;

Ding, Keyue ;

Seymour, Lesley ;

Naoki, Katsuhiko ;

Pennell, Nathan ;

Weir, Barbara ;

Verhaak, Roel ;

Ladd-Acosta, Christine ;

Golub, Todd ;

Gruidl, Michael ;

Sharma, Anupama ;

Szoke, Janos ;

Zakowski, Maureen ;

Rusch, Valerie ;

Kris, Mark ;

Viale, Agnes ;

Motoi, Noriko ;

Travis, William ;

Conley, Barbara ;

Seshan, Venkatraman E. ;

Meyerson, Matthew ;

Kuick, Rork ;

Dobbin, Kevin K. ;

Lively, Tracy ;

Jacobson, James W. ;

Beer, David G. .

NATURE MEDICINE, 2008, 14 (08) :822-827

[8]

Integrative clustering of multiple genomic data types using a joint latent variable model with application to breast and lung cancer subtype analysis [J].

Shen, Ronglai ;

Olshen, Adam B. ;

Ladanyi, Marc .

BIOINFORMATICS, 2009, 25 (22) :2906-2912

[9]

Diagnostic agreement in the histopathological evaluation of lung cancer tissue in a population-based case-control study [J].

Stang, A ;

Pohlabeln, H ;

Müller, KM ;

Jahn, I ;

Giersiepen, K ;

Jöckel, KH .

LUNG CANCER, 2006, 52 (01) :29-36

[10]

Stinchcombe Thomas E, 2009, Proc Am Thorac Soc, V6, P233, DOI 10.1513/pats.200809-110LC

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