ProCAT: a data analysis approach for protein microarrays

被引：34

作者：

Zhu, Xiaowei

Gerstein, Mark

Snyder, Michael ^{[1
]}

机构：

[1] Yale Univ, Program Computat Biol & Bioinformat, New Haven, CT 06511 USA

[2] Yale Univ, Dept Mol Biophys & Biochem, New Haven, CT 06511 USA

[3] Yale Univ, Dept Comp Sci, New Haven, CT 06511 USA

[4] Yale Univ, Dept Mol Cellular & Dev Biol, New Haven, CT 06511 USA

来源：

GENOME BIOLOGY | 2006年 / 7卷 / 11期

关键词：

D O I：

10.1186/gb-2006-7-11-r110

中图分类号：

Q81 [生物工程学（生物技术）]; Q93 [微生物学];

学科分类号：

071005 ; 0836 ; 090102 ; 100705 ;

摘要：

Protein microarrays provide a versatile method for the analysis of many protein biochemical activities. Existing DNA microarray analytical methods do not translate to protein microarrays due to differences between the technologies. Here we report a new approach, ProCAT, which corrects for background bias and spatial artifacts, identifies significant signals, filters nonspecific spots, and normalizes the resulting signal to protein abundance. ProCAT provides a powerful and flexible new approach for analyzing many types of protein microarrays.

引用

页数：11

共 22 条

[1]

Belov L, 2001, CANCER RES, V61, P4483

[2]

CHERNOVEA I, 2006, ANAL BIOCHEM, V348, P19

[3]

Dudoit S, 2002, STAT SINICA, V12, P111

[4] Biochemical and genetic analysis of the yeast proteome with a movable ORF collection [J].

Gelperin, DM ;

White, MA ;

Wilkinson, ML ;

Kon, Y ;

Kung, LA ;

Wise, KJ ;

Lopez-Hoyo, N ;

Jiang, LX ;

Piccirillo, S ;

Yu, HY ;

Gerstein, M ;

Dumont, ME ;

Phizicky, EM ;

Snyder, M ;

Grayhack, EJ .

GENES & DEVELOPMENT, 2005, 19 (23) :2816-2826

[5] Bioconductor: open software development for computational biology and bioinformatics [J].

Gentleman, RC ;

Carey, VJ ;

Bates, DM ;

Bolstad, B ;

Dettling, M ;

Dudoit, S ;

Ellis, B ;

Gautier, L ;

Ge, YC ;

Gentry, J ;

Hornik, K ;

Hothorn, T ;

Huber, W ;

Iacus, S ;

Irizarry, R ;

Leisch, F ;

Li, C ;

Maechler, M ;

Rossini, AJ ;

Sawitzki, G ;

Smith, C ;

Smyth, G ;

Tierney, L ;

Yang, JYH ;

Zhang, JH .

GENOME BIOLOGY, 2004, 5 (10)

[6] Probing the proteome [J].

Gershon, D .

NATURE, 2003, 424 (6948) :581-+

[7] Regulation of gene expression by a metabolic enzyme [J].

Hall, DA ;

Zhu, H ;

Zhu, XW ;

Royce, T ;

Gerstein, M ;

Snyder, M .

SCIENCE, 2004, 306 (5695) :482-484

[8] THE MEANING AND USE OF THE AREA UNDER A RECEIVER OPERATING CHARACTERISTIC (ROC) CURVE [J].

HANLEY, JA ;

MCNEIL, BJ .

RADIOLOGY, 1982, 143 (01) :29-36

[9]

HOFFMANN R, 2002, GENOME BIOL, V3

[10] Analysis of variance for gene expression microarray data [J].

Kerr, MK ;

Martin, M ;

Churchill, GA .

JOURNAL OF COMPUTATIONAL BIOLOGY, 2000, 7 (06) :819-837

← 1 2 3 →