Classification of human lung carcinomas by mRNA expression profiling reveals distinct adenocarcinoma subclasses
Arindam Bhattacharjee,William G. Richards,Jane Staunton,Cheng Li,Stefano Monti,Priya Vasa,Christine Ladd,Javad Beheshti,Raphael Bueno,Michael A. Gillette,Massimo Loda,Griffin M. Weber,Eugene J. Mark,Eric S. Lander,Wing Hung Wong,Bruce E. Johnson,Todd R. Golub,Todd R. Golub,David J. Sugarbaker,Matthew Meyerson +19 more
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TLDR
A molecular taxonomy of lung carcinoma is generated and results suggest that integration of expression profile data with clinical parameters could aid in diagnosis of lung cancer patients.Abstract:
We have generated a molecular taxonomy of lung carcinoma, the leading cause of cancer death in the United States and worldwide. Using oligonucleotide microarrays, we analyzed mRNA expression levels corresponding to 12,600 transcript sequences in 186 lung tumor samples, including 139 adenocarcinomas resected from the lung. Hierarchical and probabilistic clustering of expression data defined distinct subclasses of lung adenocarcinoma. Among these were tumors with high relative expression of neuroendocrine genes and of type II pneumocyte genes, respectively. Retrospective analysis revealed a less favorable outcome for the adenocarcinomas with neuroendocrine gene expression. The diagnostic potential of expression profiling is emphasized by its ability to discriminate primary lung adenocarcinomas from metastases of extra-pulmonary origin. These results suggest that integration of expression profile data with clinical parameters could aid in diagnosis of lung cancer patients.read more
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Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles
Aravind Subramanian,Pablo Tamayo,Vamsi K. Mootha,Sayan Mukherjee,Benjamin L. Ebert,Michael A. Gillette,Amanda G. Paulovich,Scott L. Pomeroy,Todd R. Golub,Eric S. Lander,Jill P. Mesirov +10 more
TL;DR: The Gene Set Enrichment Analysis (GSEA) method as discussed by the authors focuses on gene sets, that is, groups of genes that share common biological function, chromosomal location, or regulation.
Journal ArticleDOI
Comprehensive molecular profiling of lung adenocarcinoma: The cancer genome atlas research network
Eric A. Collisson,Joshua D. Campbell,Angela N. Brooks,Angela N. Brooks,Alice H. Berger,William Lee,Juliann Chmielecki,David G. Beer,Leslie Cope,Chad J. Creighton,Ludmila Danilova,Li Ding,Gad Getz,Gad Getz,Peter S. Hammerman,D. Neil Hayes,Bryan Hernandez,James G. Herman,John V. Heymach,Igor Jurisica,Raju Kucherlapati,David J. Kwiatkowski,Marc Ladanyi,Gordon Robertson,Nikolaus Schultz,Ronglai Shen,Rileen Sinha,Carrie Sougnez,Ming-Sound Tsao,William D. Travis,John N. Weinstein,Dennis A. Wigle,Matthew D. Wilkerson,Andy Chu,Andrew D. Cherniack,Angela Hadjipanayis,Mara Rosenberg,Daniel J. Weisenberger,Peter W. Laird,Amie Radenbaugh,Singer Ma,Joshua M. Stuart,Lauren Averett Byers,Stephen B. Baylin,Ramaswamy Govindan,Matthew Meyerson,Matthew Meyerson,Stacey Gabriel,Kristian Cibulskis,Jaegil Kim,Chip Stewart,Lee Lichtenstein,Eric S. Lander,Eric S. Lander,Michael S. Lawrence,E. Getz,E. Getz,Robert S. Fulton,Lucinda Fulton,Michael D. McLellan,Richard K. Wilson,Kai Ye,Catrina Fronick,Christopher G. Maher,Christopher A. Miller,Michael C. Wendl,Christopher R. Cabanski,Elaine R. Mardis,David A. Wheeler,Miruna Balasundaram,Yaron S.N. Butterfield,Rebecca Carlsen,Eric Chuah,Noreen Dhalla,Ranabir Guin,Carrie Hirst,Darlene Lee,Haiyan I. Li,Michael Mayo,Richard A. Moore,Andrew J. Mungall,Jacqueline E. Schein,Payal Sipahimalani,Angela Tam,Richard Varhol,A. Gordon Robertson,Natasja Wye,Nina Thiessen,Robert A. Holt,Steven J.M. Jones,Marco A. Marra,Marcin Imielinski,Marcin Imielinski,Robert C. Onofrio,Eran Hodis,Travis I. Zack,Elena Helman,Chandra Sekhar Pedamallu,Jill P. Mesirov,Gordon Saksena,Steven E. Schumacher,Scott L. Carter,Levi A. Garraway,Levi A. Garraway,Rameen Beroukhim,Rameen Beroukhim,Semin Lee,Harshad S. Mahadeshwar,Angeliki Pantazi,Angeliki Pantazi,Alexei Protopopov,Xiaojia Ren,Sahil Seth,Xingzhi Song,Jiabin Tang,Lixing Yang,Jianhua Zhang,Peng Chieh Chen,Michael Parfenov,Andrew Wei Xu,Netty Santoso,Lynda Chin,Peter J. Park,Katherine A. Hoadley,J. Todd Auman,Shaowu Meng,Yan Shi,Elizabeth Buda,Scot Waring,Umadevi Veluvolu,Donghui Tan,Piotr A. Mieczkowski,Corbin D. Jones,Janae V. Simons,Matthew G. Soloway,Tom Bodenheimer,Stuart R. Jefferys,Jeffrey Roach,Alan P. Hoyle,Junyuan Wu,Saianand Balu,Darshan Singh,Jan F. Prins,James Stephen Marron,Joel S. Parker,Charles M. Perou,Jinze Liu,Dennis T. Maglinte,Philip H. Lai,Moiz S. Bootwalla,David Van Den Berg,Timothy J. Triche,Juok Cho,Daniel DiCara,David I. Heiman,Pei Lin,William Mallard,Douglas Voet,Hailei Zhang,Lihua Zou,Michael S. Noble,Nils Gehlenborg,Helga Thorvaldsdottir,Marc Danie Nazaire,James T. Robinson,B. Arman Aksoy,Giovanni Ciriello,Barry S. Taylor,Gideon Dresdner,Jianjiong Gao,Benjamin Gross,Venkatraman E. Seshan,Boris Reva,S. Onur Sumer,Nils Weinhold,Chris Sander,Sam Ng,Jingchun Zhu,Christopher C. Benz,Christina Yau,David Haussler,Paul T. Spellman,Patrick K. Kimes,Bradley M. Broom,Jing Wang,Yiling Lu,Patrick Kwok Shing Ng,Lixia Diao,Wenbin Liu,Christopher I. Amos,Rehan Akbani,Gordon B. Mills,Erin Curley,Joseph Paulauskis,Kevin Lau,Scott Morris,Troy Shelton,David Mallery,Johanna Gardner,Robert Penny,Charles Saller,Katherine Tarvin,William G. Richards,Robert J. Cerfolio,Ayesha S. Bryant,Daniel P. Raymond,Nathan A. Pennell,Carol Farver,Christine Czerwinski,Lori Huelsenbeck-Dill,Mary Iacocca,Nicholas J. Petrelli,Brenda Rabeno,Jennifer Brown,Thomas L. Bauer,Cureline Oleg Dolzhanskiy,Olga Potapova,D L Rotin,Olga Voronina,Elena Nemirovich-Danchenko,Konstantin V. Fedosenko,Anthony A. Gal,Madhusmita Behera,Suresh S. Ramalingam,Gabriel Sica,Douglas B. Flieder,Jeff Boyd,Jo Ellen Weaver,Bernard Kohl,Dang Huy Quoc Thinh,George E. Sandusky,Hartmut Juhl,Edwina Duhig,Peter B. Illei,Edward Gabrielson,James Shin,Beverly Lee,Kristen Rogers,Dante Trusty,Malcolm V. Brock,Christina Williamson,Eric J. Burks,Kimberly M. Rieger-Christ,Antonia H. Holway,Travis Sullivan,Michael K. Asiedu,Farhad Kosari,Natasha Rekhtman,Maureen F. Zakowski,Valerie W. Rusch,Paul Zippile,James Suh,Harvey I. Pass,Chandra Goparaju,Yvonne Owusu-Sarpong,John M. S. Bartlett,Sugy Kodeeswaran,Jeremy Parfitt,Harmanjatinder S. Sekhon,Monique Albert,John Eckman,Jerome Myers,Carl Morrison,Carmelo Gaudioso,Jeffrey A. Borgia,Philip Bonomi,Mark Pool,Michael J. Liptay,Fedor Moiseenko,Irina Zaytseva,Hendrik Dienemann,Michael Meister,Philipp A. Schnabel,Thomas Muley,Martin Peifer,Carmen Gomez-Fernandez,Lynn M. Herbert,Sophie C. Egea,Mei Huang,Leigh B. Thorne,Lori Boice,Ashley H. Salazar,William K. Funkhouser,W. Kimryn Rathmell,Rajiv Dhir,Samuel A. Yousem,Sanja Dacic,Frank Schneider,Jill M. Siegfried,Richard A. Hajek,Mark A. Watson,Sandra McDonald,Bryan F. Meyers,Belinda E. Clarke,Ian A. Yang,Kwun M. Fong,Lindy Hunter,Morgan Windsor,Rayleen V. Bowman,Solange Peters,Igor Letovanec,Khurram Z. Khan,Mark A. Jensen,Eric E. Snyder,Deepak Srinivasan,Ari B. Kahn,Julien Baboud,David Pot,Kenna R. Mills Shaw,Margi Sheth,Tanja Davidsen,John A. Demchok,Liming Yang,Zhining Wang,Roy Tarnuzzer,Jean C. Zenklusen,Bradley A. Ozenberger,Heidi J. Sofia,Richard T. Cheney +318 more
TL;DR: In this paper, the authors report molecular profiling of 230 resected lung adnocarcinomas using messenger RNA, microRNA and DNA sequencing integrated with copy number, methylation and proteomic analyses.
Journal ArticleDOI
ONCOMINE: A Cancer Microarray Database and Integrated Data-Mining Platform
Daniel R. Rhodes,Jianjun Yu,K. Shanker,Nandan P. Deshpande,Radhika Varambally,Debashis Ghosh,Terrence R. Barrette,Akhilesh Pandey,Arul M. Chinnaiyan +8 more
TL;DR: ONCOMINE is presented, a cancer microarray database and web-based data-mining platform aimed at facilitating discovery from genome-wide expression analyses and novel biomarkers and therapeutic targets are discovered.
Comprehensive molecular profiling of lung adenocarcinoma
TL;DR: High rates of somatic mutation were seen, including RIT1 activating mutations and newly described loss-of-function MGA mutations which are mutually exclusive with focal MYC amplification, and MAPK and PI(3)K pathway activity was explained by known mutations in only a fraction of cases, suggesting additional, unexplained mechanisms of pathway activation.
Journal ArticleDOI
Gene expression correlates of clinical prostate cancer behavior.
Dinesh Singh,Phillip G. Febbo,Phillip G. Febbo,Kenneth N. Ross,Donald G. Jackson,Judith Manola,Christine Ladd,Pablo Tamayo,Andrew A. Renshaw,Anthony V. D'Amico,Jerome P. Richie,Eric S. Lander,Massimo Loda,Philip W. Kantoff,Todd R. Golub,William R. Sellers +15 more
TL;DR: The results support the notion that the clinical behavior of prostate cancer is linked to underlying gene expression differences that are detectable at the time of diagnosis.
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