Identifying pre-post chemotherapy differences in gene expression in breast tumours: a statistical method appropriate for this aim

被引：19

作者：

Korn, EL

McShane, LM

Troendle, JF

Rosenwald, A

Simon, R

机构：

[1] NCI, Biometr Res Branch, Bethesda, MD 20892 USA

[2] NICHHD, Biometry & Math Stat Branch, Bethesda, MD 20892 USA

[3] NCI, Metab Branch, Bethesda, MD 20892 USA

来源：

BRITISH JOURNAL OF CANCER | 2002年 / 86卷 / 07期

关键词：

cluster analysis; doxorubicin; gene expression; microarray; multiple comparisons; statistical methods;

D O I：

10.1038/sj/bjc/6600216

中图分类号：

R73 [肿瘤学];

学科分类号：

100214 ;

摘要：

Although widely used for the analysis of gene expression microarray data, cluster analysis may not be the most appropriate statistical technique for some study aims. We demonstrate this by considering a previous analysis of microarray data obtained on breast tumour specimens, many of which were paired specimens from the same patient before and after chemotherapy. Reanalysing the data using statistical methods that appropriately utilise the paired differences for identification of differentially expressed genes, we find 17 genes that we can confidently identify as more. expressed after chemotherapy than before. These findings were not reported by the original investigators who analysed the data using cluster analysis techniques. (C) 2002 Cancer Research UK.

引用

页码：1093 / 1096

页数：4

共 12 条

[1] Microarray expression profiling identifies genes with altered expression in HDL-deficient mice [J].

Callow, MJ ;

Dudoit, S ;

Gong, EL ;

Speed, TP ;

Rubin, EM .

GENOME RESEARCH, 2000, 10 (12) :2022-2029

[2] Increased AP-1 activity in drug resistant human breast cancer MCF-7 cells [J].

Daschner, PJ ;

Ciolino, HP ;

Plouzek, CA ;

Yeh, GC .

BREAST CANCER RESEARCH AND TREATMENT, 1999, 53 (03) :229-240

[3] Cluster analysis and display of genome-wide expression patterns [J].

Eisen, MB ;

Spellman, PT ;

Brown, PO ;

Botstein, D .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 1998, 95 (25) :14863-14868

[4] Molecular classification of cancer: Class discovery and class prediction by gene expression monitoring [J].

Golub, TR ;

Slonim, DK ;

Tamayo, P ;

Huard, C ;

Gaasenbeek, M ;

Mesirov, JP ;

Coller, H ;

Loh, ML ;

Downing, JR ;

Caligiuri, MA ;

Bloomfield, CD ;

Lander, ES .

SCIENCE, 1999, 286 (5439) :531-537

[5] Gene-expression profiles in hereditary breast cancer. [J].

Hedenfalk, I ;

Duggan, D ;

Chen, YD ;

Radmacher, M ;

Bittner, M ;

Simon, R ;

Meltzer, P ;

Gusterson, B ;

Esteller, M ;

Kallioniemi, OP ;

Wilfond, B ;

Borg, Å ;

Trent, J ;

Raffeld, M ;

Yakhini, Z ;

Ben-Dor, A ;

Dougherty, E ;

Kononen, J ;

Bubendorf, L ;

Fehrle, W ;

Pittaluga, S ;

Gruvberger, S ;

Loman, N ;

Johannsoson, O ;

Olsson, H ;

Sauter, G .

NEW ENGLAND JOURNAL OF MEDICINE, 2001, 344 (08) :539-548

[6]

Miller R. G., 1981, SIMULTANEOUS STATIST, P67

[7] Molecular portraits of human breast tumours [J].

Perou, CM ;

Sorlie, T ;

Eisen, MB ;

van de Rijn, M ;

Jeffrey, SS ;

Rees, CA ;

Pollack, JR ;

Ross, DT ;

Johnsen, H ;

Akslen, LA ;

Fluge, O ;

Pergamenschikov, A ;

Williams, C ;

Zhu, SX ;

Lonning, PE ;

Borresen-Dale, AL ;

Brown, PO ;

Botstein, D .

NATURE, 2000, 406 (6797) :747-752

[8] ROBUST MULTIPLE COMPARISONS [J].

RINGLAND, JT .

JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION, 1983, 78 (381) :145-151

[9] Extracellular matrix proteins protect small cell lung cancer cells against apoptosis:: A mechanism for small cell lung cancer growth and drug resistance in vivo [J].

Sethi, T ;

Rintoul, RC ;

Moore, SM ;

MacKinnon, AC ;

Salter, D ;

Choo, C ;

Chilvers, ER ;

Dransfield, I ;

Donnelly, SC ;

Strieter, R ;

Haslett, C .

NATURE MEDICINE, 1999, 5 (06) :662-668

[10] Interpreting patterns of gene expression with self-organizing maps: Methods and application to hematopoietic differentiation [J].

Tamayo, P ;

Slonim, D ;

Mesirov, J ;

Zhu, Q ;

Kitareewan, S ;

Dmitrovsky, E ;

Lander, ES ;

Golub, TR .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 1999, 96 (06) :2907-2912

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