Coexpression analysis of human genes across many microarray data sets

被引：562

作者：

Lee, HK

Hsu, AK

Sajdak, J

Qin, J

Pavlidis, P ^{[1
]}

机构：

[1] Columbia Univ, Columbia Genome Ctr, New York, NY 10032 USA

[2] Columbia Univ, Coll Phys & Surg, New York, NY 10032 USA

[3] Columbia Univ, Dept Biomed Informat, New York, NY 10032 USA

来源：

GENOME RESEARCH | 2004年 / 14卷 / 06期

关键词：

D O I：

10.1101/gr.1910904

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：

We present a large-scale analysis of mRNA coexpression based on 60 large human data sets containing a total of 3924 microarrays. We sought pairs of genes that were reliably coexpressed (based on the correlation of their expression profiles) in Multiple data sets, establishing a high-confidence network of 88O5 genes connected by 220,649 "coexpression links" that are observed in at least three data sets. Confirmed positive correlations between genes were much more common than confirmed negative correlations. We show that confirmation of coexpression in multiple data sets is correlated with functional relatedness, and show how cluster analysis of the network can reveal functionally coherent groups of genes. Our findings demonstrate how the large body of accumulated microarray data can be exploited to increase the reliability of inferences about gene function.

引用

页码：1085 / 1094

页数：10

共 93 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]

Allander SV, 2001, CANCER RES, V61, P8624

[3]

[Anonymous], 1993, Resampling-based multiple testing: Examples and methods for P-value adjustment

[4] MLL translocations specify a distinct gene expression profile that distinguishes a unique leukemia [J].

Armstrong, SA ;

Staunton, JE ;

Silverman, LB ;

Pieters, R ;

de Boer, ML ;

Minden, MD ;

Sallan, SE ;

Lander, ES ;

Golub, TR ;

Korsmeyer, SJ .

NATURE GENETICS, 2002, 30 (01) :41-47

[5] 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

[6] An automated method for finding molecular complexes in large protein interaction networks [J].

Bader, GD ;

Hogue, CW .

BMC BIOINFORMATICS, 2003, 4 (1)

[7] Emergence of scaling in random networks [J].

Barabási, AL ;

Albert, R .

SCIENCE, 1999, 286 (5439) :509-512

[8]

Batagelj V., 1998, Connections, V21, P47

[9] A duplication growth model of gene expression networks [J].

Bhan, A ;

Galas, DJ ;

Dewey, TG .

BIOINFORMATICS, 2002, 18 (11) :1486-1493

[10] 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

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