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PMID: 17940530 Published · ppublish English Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't

Network-based classification of breast cancer metastasis.

Molecular systems biology ·Vol. 3 ·2007-00-00 ·Pages 140

Chuang HY, Lee E, Liu YT, Lee D, Ideker T

Abstract

Mapping the pathways that give rise to metastasis is one of the key challenges of breast cancer research. Recently, several large-scale studies have shed light on this problem through analysis of gene expression profiles to identify markers correlated with metastasis. Here, we apply a protein-network-based approach that identifies markers not as individual genes but as subnetworks extracted from protein interaction databases. The resulting subnetworks provide novel hypotheses for pathways involved in tumor progression. Although genes with known breast cancer mutations are typically not detected through analysis of differential expression, they play a central role in the protein network by interconnecting many differentially expressed genes. We find that the subnetwork markers are more reproducible than individual marker genes selected without network information, and that they achieve higher accuracy in the classification of metastatic versus non-metastatic tumors.

MeSH Terms
Biomarkers, Tumor/analysis Breast Neoplasms/genetics,pathology Computational Biology Female Gene Expression Profiling Gene Expression Regulation, Neoplastic Humans Neoplasm Metastasis/genetics,pathology Neoplasm Proteins/genetics Oligonucleotide Array Sequence Analysis
Chemicals
Biomarkers, Tumor Neoplasm Proteins
Authors & Affiliations
5 authors, click to expand affiliations / ORCID
Chuang Han-Yu
Bioinformatics Program, University of California San Diego, La Jolla, CA 92093, USA.
Lee Eunjung
Liu Yu-Tsueng
Lee Doheon
Ideker Trey
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Article Info
Journal
Molecular systems biology
Abbr.
Mol Syst Biol
ISSN
1744-4292
DOI
10.1038/msb4100180
Published
2007-00-00
Epub
2007-00-16
Pages
140
Language
English
Region
England
NLM ID
101235389
PMCID
PMC2063581
Subset
IM
Grants
NIEHS NIH HHS · R01 ES014811-01A1 · United States
NIEHS NIH HHS · R01 ES014811-05S1 · United States
NIEHS NIH HHS · R01 ES014811-04 · United States
NIEHS NIH HHS · R01 ES014811-05 · United States
NIEHS NIH HHS · R01 ES014811-02 · United States
NIEHS NIH HHS · R01 ES014811 · United States
NIEHS NIH HHS · ES14811-01 · United States
NIEHS NIH HHS · R01 ES014811-03 · United States
NIEHS NIH HHS · R01 ES014811-02S1 · United States
Corrections
CommentIn
PMID: 17940531
External Links
PubMed source DOI: 10.1038/msb4100180 PMC Full Text View journal details
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