Robust meta-analysis of gene expression using the elastic net

被引：92

作者：

Hughey, Jacob J. ^{[1
]}

Butte, Atul J. ^{[1
]}

机构：

[1] Stanford Univ, Dept Pediat, Div Syst Med, Stanford, CA 94305 USA

来源：

NUCLEIC ACIDS RESEARCH | 2015年 / 43卷 / 12期

基金：

美国国家卫生研究院;

关键词：

LUNG ADENOCARCINOMA; BREAST-CANCER; CLASSIFICATION; PREDICTION; PROFILES; REGULARIZATION; NORMALIZATION; METHYLATION; REGRESSION; SELECTION;

D O I：

10.1093/nar/gkv229

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

Meta-analysis of gene expression has enabled numerous insights into biological systems, but current methods have several limitations. We developed a method to perform a meta-analysis using the elastic net, a powerful and versatile approach for classification and regression. To demonstrate the utility of our method, we conducted a meta-analysis of lung cancer gene expression based on publicly available data. Using 629 samples from five data sets, we trained a multinomial classifier to distinguish between four lung cancer subtypes. Our meta-analysis-derived classifier included 58 genes and achieved 91% accuracy on leave-one-study-out cross-validation and on three independent data sets. Our method makes meta-analysis of gene expression more systematic and expands the range of questions that a meta-analysis can be used to address. As the amount of publicly available gene expression data continues to grow, our method will be an effective tool to help distill these data into knowledge.

引用

页数：11

共 41 条

[1] NCBI GEO: archive for functional genomics data sets-update [J].

Barrett, Tanya ;

Wilhite, Stephen E. ;

Ledoux, Pierre ;

Evangelista, Carlos ;

Kim, Irene F. ;

Tomashevsky, Maxim ;

Marshall, Kimberly A. ;

Phillippy, Katherine H. ;

Sherman, Patti M. ;

Holko, Michelle ;

Yefanov, Andrey ;

Lee, Hyeseung ;

Zhang, Naigong ;

Robertson, Cynthia L. ;

Serova, Nadezhda ;

Davis, Sean ;

Soboleva, Alexandra .

NUCLEIC ACIDS RESEARCH, 2013, 41 (D1) :D991-D995

[2] Classification of human lung carcinomas by mRNA expression profiling reveals distinct adenocarcinoma subclasses [J].

Bhattacharjee, A ;

Richards, WG ;

Staunton, J ;

Li, C ;

Monti, S ;

Vasa, P ;

Ladd, C ;

Beheshti, J ;

Bueno, R ;

Gillette, M ;

Loda, M ;

Weber, G ;

Mark, EJ ;

Lander, ES ;

Wong, W ;

Johnson, BE ;

Golub, TR ;

Sugarbaker, DJ ;

Meyerson, M .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2001, 98 (24) :13790-13795

[3] Biomarker Discovery in Non-Small Cell Lung Cancer: Integrating Gene Expression Profiling, Meta-analysis, and Tissue Microarray Validation [J].

Botling, Johan ;

Edlund, Karolina ;

Lohr, Miriam ;

Hellwig, Birte ;

Holmberg, Lars ;

Lambe, Mats ;

Berglund, Anders ;

Ekman, Simon ;

Bergqvist, Michael ;

Ponten, Fredrik ;

Koenig, Andre ;

Fernandes, Oswaldo ;

Karlsson, Mats ;

Helenius, Gisela ;

Karlsson, Christina ;

Rahnenfuehrer, Joerg ;

Hengstler, Jan G. ;

Micke, Patrick .

CLINICAL CANCER RESEARCH, 2013, 19 (01) :194-204

[4] A Meta-analysis of Lung Cancer Gene Expression Identifies PTK7 as a Survival Gene in Lung Adenocarcinoma [J].

Chen, Ron ;

Khatri, Purvesh ;

Mazur, Pawel K. ;

Polin, Melanie ;

Zheng, Yanyan ;

Vaka, Dedeepya ;

Hoang, Chuong D. ;

Shrager, Joseph ;

Xu, Yue ;

Vicent, Silvestre ;

Butte, Atul J. ;

Sweet-Cordero, E. Alejandro .

CANCER RESEARCH, 2014, 74 (10) :2892-2902

[5] Evolving gene/transcript definitions significantly alter the interpretation of GeneChip data [J].

Dai, MH ;

Wang, PL ;

Boyd, AD ;

Kostov, G ;

Athey, B ;

Jones, EG ;

Bunney, WE ;

Myers, RM ;

Speed, TP ;

Akil, H ;

Watson, SJ ;

Meng, F .

NUCLEIC ACIDS RESEARCH, 2005, 33 (20) :e175.1-e175.9

[6] Regularization Paths for Generalized Linear Models via Coordinate Descent [J].

Friedman, Jerome ;

Hastie, Trevor ;

Tibshirani, Rob .

JOURNAL OF STATISTICAL SOFTWARE, 2010, 33 (01) :1-22

[7] Diversity of gene expression in adenocarcinoma of the lung [J].

Garber, ME ;

Troyanskaya, OG ;

Schluens, K ;

Petersen, S ;

Thaesler, Z ;

Pacyna-Gengelbach, M ;

van de Rijn, M ;

Rosen, GD ;

Perou, CM ;

Whyte, RI ;

Altman, RB ;

Brown, PO ;

Botstein, D ;

Petersen, I .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2001, 98 (24) :13784-13789

[8] Systematic identification of genomic markers of drug sensitivity in cancer cells [J].

Garnett, Mathew J. ;

Edelman, Elena J. ;

Heidorn, Sonja J. ;

Greenman, Chris D. ;

Dastur, Anahita ;

Lau, King Wai ;

Greninger, Patricia ;

Thompson, I. Richard ;

Luo, Xi ;

Soares, Jorge ;

Liu, Qingsong ;

Iorio, Francesco ;

Surdez, Didier ;

Chen, Li ;

Milano, Randy J. ;

Bignell, Graham R. ;

Tam, Ah T. ;

Davies, Helen ;

Stevenson, Jesse A. ;

Barthorpe, Syd ;

Lutz, Stephen R. ;

Kogera, Fiona ;

Lawrence, Karl ;

McLaren-Douglas, Anne ;

Mitropoulos, Xeni ;

Mironenko, Tatiana ;

Thi, Helen ;

Richardson, Laura ;

Zhou, Wenjun ;

Jewitt, Frances ;

Zhang, Tinghu ;

O'Brien, Patrick ;

Boisvert, Jessica L. ;

Price, Stacey ;

Hur, Wooyoung ;

Yang, Wanjuan ;

Deng, Xianming ;

Butler, Adam ;

Choi, Hwan Geun ;

Chang, JaeWon ;

Baselga, Jose ;

Stamenkovic, Ivan ;

Engelman, Jeffrey A. ;

Sharma, Sreenath V. ;

Delattre, Olivier ;

Saez-Rodriguez, Julio ;

Gray, Nathanael S. ;

Settleman, Jeffrey ;

Futreal, P. Andrew ;

Haber, Daniel A. .

NATURE, 2012, 483 (7391) :570-U87

[9] Classification of the Four Main Types of Lung Cancer Using a MicroRNA-Based Diagnostic Assay [J].

Gilad, Shlomit ;

Lithwick-Yanai, Gila ;

Barshack, Iris ;

Benjamin, Sima ;

Krivitsky, Irit ;

Edmonston, Tina Bocker ;

Bibbo, Marluce ;

Thurm, Craig ;

Horowitz, Laurie ;

Huang, Yajue ;

Feinmesser, Meora ;

Hou, J. Steve ;

St Cyr, Brianna ;

Burnstein, Ilanit ;

Gibori, Hadas ;

Dromi, Nir ;

Sanden, Mats ;

Kushnir, Michal ;

Aharonov, Ranit .

JOURNAL OF MOLECULAR DIAGNOSTICS, 2012, 14 (05) :510-517

[10]

Hastie T., 2009, The elements of statistical learning: data mining, inference, and pre- diction, V2nd ed

← 1 2 3 4 5 →