Revisiting Global Gene Expression Analysis

被引：443

作者：

Loven, Jakob ^{[1
]}

Orlando, David A. ^{[1
]}

Sigova, Alla A. ^{[1
]}

Lin, Charles Y. ^{[1
,2
]}

Rahl, Peter B. ^{[1
]}

Burge, Christopher B. ^{[3
]}

Levens, David L. ^{[4
]}

Lee, Tong Ihn ^{[1
]}

Young, Richard A. ^{[1
,3
]}

机构：

[1] Whitehead Inst Biomed Res, Cambridge, MA 02142 USA

[2] MIT, Computat & Syst Biol Program, Cambridge, MA 02139 USA

[3] MIT, Dept Biol, Cambridge, MA 02139 USA

[4] NCI, Gene Regulat Sect, Pathol Lab, Ctr Canc Res, Bethesda, MD 20892 USA

来源：

CELL | 2012年 / 151卷 / 03期

基金：

瑞典研究理事会; 美国国家卫生研究院;

关键词：

C-MYC; MOLECULAR CLASSIFICATION; BREAST-CANCER; RNA-SEQ; NORMALIZATION; ARRAYS; PREDICTION; DISCOVERY; ADENOCARCINOMA; MICROARRAYS;

D O I：

10.1016/j.cell.2012.10.012

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：

Gene expression analysis is a widely used and powerful method for investigating the transcriptional behavior of biological systems, for classifying cell states in disease, and for many other purposes. Recent studies indicate that common assumptions currently embedded in experimental and analytical practices can lead to misinterpretation of global gene expression data. We discuss these assumptions and describe solutions that should minimize erroneous interpretation of gene expression data from multiple analysis platforms.

引用

页码：476 / 482

页数：7

共 45 条

[1] Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling [J].

Alizadeh, AA ;

Eisen, MB ;

Davis, RE ;

Ma, C ;

Lossos, IS ;

Rosenwald, A ;

Boldrick, JG ;

Sabet, H ;

Tran, T ;

Yu, X ;

Powell, JI ;

Yang, LM ;

Marti, GE ;

Moore, T ;

Hudson, J ;

Lu, LS ;

Lewis, DB ;

Tibshirani, R ;

Sherlock, G ;

Chan, WC ;

Greiner, TC ;

Weisenburger, DD ;

Armitage, JO ;

Warnke, R ;

Levy, R ;

Wilson, W ;

Grever, MR ;

Byrd, JC ;

Botstein, D ;

Brown, PO ;

Staudt, LM .

NATURE, 2000, 403 (6769) :503-511

[2]

[Anonymous], P SOC PHOTO-OPT INS

[3] STUDY DESIGNS Studying and modelling dynamic biological processes using time-series gene expression data [J].

Bar-Joseph, Ziv ;

Gitter, Anthony ;

Simon, Itamar .

NATURE REVIEWS GENETICS, 2012, 13 (08) :552-564

[4] Gene-expression profiles predict survival of patients with lung adenocarcinoma [J].

Beer, DG ;

Kardia, SLR ;

Huang, CC ;

Giordano, TJ ;

Levin, AM ;

Misek, DE ;

Lin, L ;

Chen, GA ;

Gharib, TG ;

Thomas, DG ;

Lizyness, ML ;

Kuick, R ;

Hayasaka, S ;

Taylor, JMG ;

Iannettoni, MD ;

Orringer, MB ;

Hanash, S .

NATURE MEDICINE, 2002, 8 (08) :816-824

[5] Standardization of protocols in cDNA microarray analysis [J].

Benes, V ;

Muckenthaler, M .

TRENDS IN BIOCHEMICAL SCIENCES, 2003, 28 (05) :244-249

[6] Integrative analysis of the melanoma transcriptome [J].

Berger, Michael F. ;

Levin, Joshua Z. ;

Vijayendran, Krishna ;

Sivachenko, Andrey ;

Adiconis, Xian ;

Maguire, Jared ;

Johnson, Laura A. ;

Robinson, James ;

Verhaak, Roel G. ;

Sougnez, Carrie ;

Onofrio, Robert C. ;

Ziaugra, Liuda ;

Cibulskis, Kristian ;

Laine, Elisabeth ;

Barretina, Jordi ;

Winckler, Wendy ;

Fisher, David E. ;

Getz, Gad ;

Meyerson, Matthew ;

Jaffe, David B. ;

Gabriel, Stacey B. ;

Lander, Eric S. ;

Dummer, Reinhard ;

Gnirke, Andreas ;

Nusbaum, Chad ;

Garraway, Levi A. .

GENOME RESEARCH, 2010, 20 (04) :413-427

[7] 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

[8] Molecular classification of cutaneous malignant melanoma by gene expression profiling [J].

Bittner, M ;

Meitzer, P ;

Chen, Y ;

Jiang, Y ;

Seftor, E ;

Hendrix, M ;

Radmacher, M ;

Simon, R ;

Yakhini, Z ;

Ben-Dor, A ;

Sampas, N ;

Dougherty, E ;

Wang, E ;

Marincola, F ;

Gooden, C ;

Lueders, J ;

Glatfelter, A ;

Pollock, P ;

Carpten, J ;

Gillanders, E ;

Leja, D ;

Dietrich, K ;

Beaudry, C ;

Berens, M ;

Alberts, D ;

Sondak, V ;

Hayward, N ;

Trent, J .

NATURE, 2000, 406 (6795) :536-540

[9] A comparison of normalization methods for high density oligonucleotide array data based on variance and bias [J].

Bolstad, BM ;

Irizarry, RA ;

Åstrand, M ;

Speed, TP .

BIOINFORMATICS, 2003, 19 (02) :185-193

[10] BET Bromodomain Inhibition as a Therapeutic Strategy to Target c-Myc [J].

Delmore, Jake E. ;

Issa, Ghayas C. ;

Lemieux, Madeleine E. ;

Rahl, Peter B. ;

Shi, Junwei ;

Jacobs, Hannah M. ;

Kastritis, Efstathios ;

Gilpatrick, Timothy ;

Paranal, Ronald M. ;

Qi, Jun ;

Chesi, Marta ;

Schinzel, Anna C. ;

McKeown, Michael R. ;

Heffernan, Timothy P. ;

Vakoc, Christopher R. ;

Bergsagel, P. Leif ;

Ghobrial, Irene M. ;

Richardson, Paul G. ;

Young, Richard A. ;

Hahn, William C. ;

Anderson, Kenneth C. ;

Kung, Andrew L. ;

Bradner, James E. ;

Mitsiades, Constantine S. .

CELL, 2011, 146 (06) :903-916

← 1 2 3 4 5 →