Gene co-expression network analysis reveals common system-level properties of prognostic genes across cancer types

被引：722

作者：

Yang, Yang ^{[1
,2
]}

Han, Leng ^{[2
]}

Yuan, Yuan ^{[2
,3
]}

Li, Jun ^{[2
]}

Hei, Nainan ^{[1
]}

Liang, Han ^{[2
,3
]}

机构：

[1] Univ Texas Hlth Sci Ctr Houston, Sch Publ Hlth, Div Biostat, Houston, TX 77030 USA

[2] Univ Texas Hlth Sci Ctr Houston, Dept Bioinformat & Computat Biol, Houston, TX 77030 USA

[3] Baylor Coll Med, Grad Program Struct & Computat Biol & Mol Biophys, Houston, TX 77030 USA

来源：

NATURE COMMUNICATIONS | 2014年 / 5卷

基金：

美国国家卫生研究院;

关键词：

EXPRESSION SIGNATURES; GENOMIC ANALYSIS; BREAST-CANCER; DISCOVERY; ESSENTIALITY; CELLS;

D O I：

10.1038/ncomms4231

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

Prognostic genes are key molecules informative for cancer prognosis and treatment. Previous studies have focused on the properties of individual prognostic genes, but have lacked a global view of their system-level properties. Here we examined their properties in gene co-expression networks for four cancer types using data from 'The Cancer Genome Atlas'. We found that prognostic mRNA genes tend not to be hub genes (genes with an extremely high connectivity), and this pattern is unique to the corresponding cancer-type-specific network. In contrast, the prognostic genes are enriched in modules (a group of highly interconnected genes), especially in module genes conserved across different cancer co-expression networks. The target genes of prognostic miRNA genes show similar patterns. We identified the modules enriched in various prognostic genes, some of which show cross-tumour conservation. Given the cancer types surveyed, our study presents a view of emergent properties of prognostic genes.

引用

页数：9

共 42 条

[1] Breast Cancer Biomarker Discovery in the Functional Genomic Age: A Systematic Review of 42 Gene Expression Signatures [J].

Abba, M. C. ;

Lacunza, E. ;

Butti, M. ;

Aldaz, C. M. .

BIOMARKER INSIGHTS, 2010, 5 :103-117

[2] From description to causality - Mechanisms of gene expression signatures in cancer [J].

Adler, Adam S. ;

Chang, Howard Y. .

CELL CYCLE, 2006, 5 (11) :1148-1151

[3] Improved scoring of functional groups from gene expression data by decorrelating GO graph structure [J].

Alexa, Adrian ;

Rahnenfuehrer, Joerg ;

Lengauer, Thomas .

BIOINFORMATICS, 2006, 22 (13) :1600-1607

[4] 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

[5] Network biology:: Understanding the cell's functional organization [J].

Barabási, AL ;

Oltvai, ZN .

NATURE REVIEWS GENETICS, 2004, 5 (02) :101-U15

[6] MicroRNAs: Target Recognition and Regulatory Functions [J].

Bartel, David P. .

CELL, 2009, 136 (02) :215-233

[7] Integrated genomic analyses of ovarian carcinoma [J].

Bell, D. ;

Berchuck, A. ;

Birrer, M. ;

Chien, J. ;

Cramer, D. W. ;

Dao, F. ;

Dhir, R. ;

DiSaia, P. ;

Gabra, H. ;

Glenn, P. ;

Godwin, A. K. ;

Gross, J. ;

Hartmann, L. ;

Huang, M. ;

Huntsman, D. G. ;

Iacocca, M. ;

Imielinski, M. ;

Kalloger, S. ;

Karlan, B. Y. ;

Levine, D. A. ;

Mills, G. B. ;

Morrison, C. ;

Mutch, D. ;

Olvera, N. ;

Orsulic, S. ;

Park, K. ;

Petrelli, N. ;

Rabeno, B. ;

Rader, J. S. ;

Sikic, B. I. ;

Smith-McCune, K. ;

Sood, A. K. ;

Bowtell, D. ;

Penny, R. ;

Testa, J. R. ;

Chang, K. ;

Dinh, H. H. ;

Drummond, J. A. ;

Fowler, G. ;

Gunaratne, P. ;

Hawes, A. C. ;

Kovar, C. L. ;

Lewis, L. R. ;

Morgan, M. B. ;

Newsham, I. F. ;

Santibanez, J. ;

Reid, J. G. ;

Trevino, L. R. ;

Wu, Y. -Q. ;

Wang, M. .

NATURE, 2011, 474 (7353) :609-615

[8] Metagenes and molecular pattern discovery using matrix factorization [J].

Brunet, JP ;

Tamayo, P ;

Golub, TR ;

Mesirov, JP .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2004, 101 (12) :4164-4169

[9] Use of gene-expression profiling to identify prognostic subclasses in adult acute myeloid leukemia [J].

Bullinger, L ;

Döhner, K ;

Bair, E ;

Fröhling, S ;

Schlenk, RF ;

Tibshirani, R ;

Döhner, H ;

Pollack, JR .

NEW ENGLAND JOURNAL OF MEDICINE, 2004, 350 (16) :1605-1616

[10] Validation and clinical utility of a 70-gene prognostic signature for women with node-negative breast cancer [J].

Buyse, Marc ;

Loi, Sherene ;

van't Veer, Laura ;

Viale, Giuseppe ;

Delorenzi, Mauro ;

Glas, Annuska M. ;

d'Assignies, Mahasti Saghatchian ;

Bergh, Jonas ;

Lidereau, Rosette ;

Ellis, Paul ;

Harris, Adrian ;

Bogaerts, Jan ;

Therasse, Patrick ;

Floore, Arno ;

Amakrane, Mohamed ;

Piette, Fanny ;

Rutgers, Emiel ;

Sotiriou, Christos ;

Cardoso, Fatima ;

Piccart, Martine J. .

JNCI-JOURNAL OF THE NATIONAL CANCER INSTITUTE, 2006, 98 (17) :1183-1192

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