Importance of collection in gene set enrichment analysis of drug response in cancer cell lines

被引：20

作者：

Bateman, Alain R. ^{[1
]}

El-Hachem, Nehme ^{[1
]}

Beck, Andrew H. ^{[2
,3
]}

Aerts, Hugo J. W. L. ^{[4
,5
,6
,7
]}

Haibe-Kains, Benjamin ^{[1
,8
]}

机构：

[1] Univ Montreal, Inst Rech Clin Montreal, Bioinformat & Computat Genom Lab, Montreal, PQ, Canada

[2] Beth Israel Deaconess Med Ctr, Dept Pathol, Boston, MA 02215 USA

[3] Harvard Univ, Sch Med, Boston, MA USA

[4] Dana Farber Canc Inst, Dept Biostat & Computat Biol, Boston, MA 02115 USA

[5] Dana Farber Canc Inst, Ctr Canc Computat Biol, Boston, MA 02115 USA

[6] Harvard Univ, Brigham & Womens Hosp, Sch Med,Dana Farber Canc Inst, Dept Radiat Oncol & Radiol, Boston, MA 02115 USA

[7] Maastricht Univ, Dept Radiat Oncol, Maastricht, Netherlands

[8] Univ Hlth Network, Princess Margaret Canc Ctr, Ontario Canc Inst, Toronto, ON, Canada

来源：

SCIENTIFIC REPORTS | 2014年 / 4卷

关键词：

EXPRESSION; ENCYCLOPEDIA; SENSITIVITY; SIGNATURES; DISCOVERY; CISPLATIN; PATHWAY; TOOL;

D O I：

10.1038/srep04092

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：

07 ; 0710 ; 09 ;

摘要：

Gene set enrichment analysis (GSEA) associates gene sets and phenotypes, its use is predicated on the choice of a pre-defined collection of sets. The defacto standard implementation of GSEA provides seven collections yet there are no guidelines for the choice of collections and the impact of such choice, if any, is unknown. Here we compare each of the standard gene set collections in the context of a large dataset of drug response in human cancer cell lines. We define and test a new collection based on gene co-expression in cancer cell lines to compare the performance of the standard collections to an externally derived cell line based collection. The results show that GSEA findings vary significantly depending on the collection chosen for analysis. Henceforth, collections should be carefully selected and reported in studies that leverage GSEA.

引用

页数：7

共 37 条

[1] Gene Ontology: tool for the unification of biology [J].

Ashburner, M ;

Ball, CA ;

Blake, JA ;

Botstein, D ;

Butler, H ;

Cherry, JM ;

Davis, AP ;

Dolinski, K ;

Dwight, SS ;

Eppig, JT ;

Harris, MA ;

Hill, DP ;

Issel-Tarver, L ;

Kasarskis, A ;

Lewis, S ;

Matese, JC ;

Richardson, JE ;

Ringwald, M ;

Rubin, GM ;

Sherlock, G .

NATURE GENETICS, 2000, 25 (01) :25-29

[2] 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

[3] The generation and utilization of a cancer-oriented representation of the human transcriptome by using expressed sequence tags [J].

Brentani, H ;

Caballero, OL ;

Camargo, AA ;

da Silva, AM ;

da Silva, WA ;

Neto, ED ;

Grivet, M ;

Gruber, A ;

Guimaraes, PEM ;

Hide, W ;

Iseli, C ;

Jongeneel, CV ;

Kelso, J ;

Nagai, MA ;

Ojopi, EPB ;

Osorio, EC ;

Reis, EMR ;

Riggins, GJ ;

Simpson, AJG ;

de Souza, S ;

Stevenson, BJ ;

Strausberg, RL ;

Tajara, EH ;

Verjovski-Almeida, S ;

Acencion, ML ;

Bengtsono, MH ;

Bettonip, F ;

Bodmerq, WF ;

Brionesr, MRS ;

Camargos, LP ;

Caveneet, W ;

Ceruttiu, JM ;

Coelho Andradev, LE ;

Costa dos Santosn, PC ;

Costaw, MCR ;

da Silvaw, IT ;

Esteciox, MRH ;

Ferreiraw, KS ;

Furnarit, FB ;

Faria, M ;

Galantep, PAF ;

Guimaraesy, GS ;

Holandaw, AJ ;

Kimuraz, ET ;

Leerkesp, MR ;

Xin, LA ;

Macielu, RMB ;

Martinsbb, EAL ;

Massirero, KB ;

Melor, ASA .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2003, 100 (23) :13418-13423

[4] Baseline gene expression predicts sensitivity to gefitinib in non-small cell lung cancer cell lines [J].

Coldren, Christopher D. ;

Helfrich, Barbara A. ;

Witta, Samir E. ;

Sugita, Michio ;

Lapadat, Razvan ;

Zeng, Chan ;

Baron, Anna ;

Franklin, Wilbur A. ;

Hirsch, Fred R. ;

Geraci, Mark W. ;

Bunn, Paul A., Jr. .

MOLECULAR CANCER RESEARCH, 2006, 4 (08) :521-528

[5] Reactome: a database of reactions, pathways and biological processes [J].

Croft, David ;

O'Kelly, Gavin ;

Wu, Guanming ;

Haw, Robin ;

Gillespie, Marc ;

Matthews, Lisa ;

Caudy, Michael ;

Garapati, Phani ;

Gopinath, Gopal ;

Jassal, Bijay ;

Jupe, Steven ;

Kalatskaya, Irina ;

Mahajan, Shahana ;

May, Bruce ;

Ndegwa, Nelson ;

Schmidt, Esther ;

Shamovsky, Veronica ;

Yung, Christina ;

Birney, Ewan ;

Hermjakob, Henning ;

D'Eustachio, Peter ;

Stein, Lincoln .

NUCLEIC ACIDS RESEARCH, 2011, 39 :D691-D697

[6] STRING v9.1: protein-protein interaction networks, with increased coverage and integration [J].

Franceschini, Andrea ;

Szklarczyk, Damian ;

Frankild, Sune ;

Kuhn, Michael ;

Simonovic, Milan ;

Roth, Alexander ;

Lin, Jianyi ;

Minguez, Pablo ;

Bork, Peer ;

von Mering, Christian ;

Jensen, Lars J. .

NUCLEIC ACIDS RESEARCH, 2013, 41 (D1) :D808-D815

[7] 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

[8] Molecular Target Class Is Predictive of In vitro Response Profile [J].

Greshock, Joel ;

Bachman, Kurtis E. ;

Degenhardt, Yan Y. ;

Jing, Junping ;

Wen, Yuan H. ;

Eastman, Stephen ;

McNeil, Elizabeth ;

Moy, Christopher ;

Wegrzyn, Ronald ;

Auger, Kurt ;

Hardwicke, Mary Ann ;

Wooster, Richard .

CANCER RESEARCH, 2010, 70 (09) :3677-3686

[9] Inconsistency in large pharmacogenomic studies [J].

Haibe-Kains, Benjamin ;

El-Hachem, Nehme ;

Birkbak, Nicolai Juul ;

Jin, Andrew C. ;

Beck, Andrew H. ;

Aerts, Hugo J. W. L. ;

Quackenbush, John .

NATURE, 2013, 504 (7480) :389-+

[10] A Three-Gene Model to Robustly Identify Breast Cancer Molecular Subtypes [J].

Haibe-Kains, Benjamin ;

Desmedt, Christine ;

Loi, Sherene ;

Culhane, Aedin C. ;

Bontempi, Gianluca ;

Quackenbush, John ;

Sotiriou, Christos .

JNCI-JOURNAL OF THE NATIONAL CANCER INSTITUTE, 2012, 104 (04) :311-325

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