Design of studies using DNA microarrays

被引:119
作者
Simon, R [1 ]
Radmacher, MD [1 ]
Dobbin, K [1 ]
机构
[1] NCI, Biomet Res Branch, Bethesda, MD 20892 USA
关键词
gene expression; bioinformatics; biomarkers; computational biology;
D O I
10.1002/gepi.202
中图分类号
Q3 [遗传学];
学科分类号
071007 ; 090102 ;
摘要
DNA microarrays are assays that simultaneously provide information about expression levels of thousands of genes and are consequently finding wide use in biomedical research. In order to control the many sources of variation and the many opportunities for misanalysis, DNA microarray studies require careful planning. Different studies have different objectives, and important aspects of design and analysis strategy differ for different types of studies. We review several types of objectives of studies using DNA microarrays and address issues such as selection of samples, levels of replication needed, allocation of samples to dyes and arrays, sample size considerations, and analysis strategies. (C) 2002 Wiley-Liss, Inc.
引用
收藏
页码:21 / 36
页数:16
相关论文
共 25 条
  • [11] Bootstrapping cluster analysis: Assessing the reliability of conclusions from microarray experiments
    Kerr, MK
    Churchill, GA
    [J]. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2001, 98 (16) : 8961 - 8965
  • [12] Kerr MK, 2001, GENET RES, V77, P123
  • [13] KORN EL, 2001, 03 NATL CANC I BIOM
  • [14] Expression monitoring by hybridization to high-density oligonucleotide arrays
    Lockhart, DJ
    Dong, HL
    Byrne, MC
    Follettie, MT
    Gallo, MV
    Chee, MS
    Mittmann, M
    Wang, CW
    Kobayashi, M
    Horton, H
    Brown, EL
    [J]. NATURE BIOTECHNOLOGY, 1996, 14 (13) : 1675 - 1680
  • [15] *LYMPH LEUK MOL PR, 2002, IN PRESS N ENGL J ME
  • [16] MCSHANE LM, IN PRESS BIOINFORMAT
  • [17] RADMACHER MD, IN PRESS J COMPUTAT
  • [18] Relation of gene expression phenotype to immunoglobulin mutation genotype in B cell chronic lymphocytic leukemia
    Rosenwald, A
    Alizadeh, AA
    Widhopf, G
    Simon, R
    Davis, RE
    Yu, X
    Yang, LM
    Pickeral, OK
    Rassenti, LZ
    Powell, J
    Botstein, D
    Byrd, JC
    Grever, MR
    Cheson, BD
    Chiorazzi, N
    Wilson, WH
    Kipps, TJ
    Brown, PO
    Staudt, LM
    [J]. JOURNAL OF EXPERIMENTAL MEDICINE, 2001, 194 (11) : 1639 - 1647
  • [19] Systematic variation in gene expression patterns in human cancer cell lines
    Ross, DT
    Scherf, U
    Eisen, MB
    Perou, CM
    Rees, C
    Spellman, P
    Iyer, V
    Jeffrey, SS
    Van de Rijn, M
    Waltham, M
    Pergamenschikov, A
    Lee, JCE
    Lashkari, D
    Shalon, D
    Myers, TG
    Weinstein, JN
    Botstein, D
    Brown, PO
    [J]. NATURE GENETICS, 2000, 24 (03) : 227 - 235
  • [20] A DNA microarray system for analyzing complex DNA samples using two-color fluorescent probe hybridization
    Shalon, D
    Smith, SJ
    Brown, PO
    [J]. GENOME RESEARCH, 1996, 6 (07): : 639 - 645