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Bioinformatics Advance Access originally published online on November 23, 2007
Bioinformatics 2008 24(3):420-421; doi:10.1093/bioinformatics/btm582
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© The Author 2007. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

GEAR: genomic enrichment analysis of regional DNA copy number changes

Tae-Min Kim 1,3, Yu-Chae Jung 1, Mun-Gan Rhyu 1, Myeong Ho Jung 3,4 and Yeun-Jun Chung 1,2,*

1Department of Microbiology, 2Integrated Research Center for Genomic Polymorphism, College of Medicine, The Catholic University of Korea, Seoul 137-701, 3Division of Metabolic Diseases, Center for Biomedical Science, National Institute of Health, Seoul and 4School of Oriental Medicine, Pusan National University, Busan, Korea

*To whom correspondence should be addressed.


  Abstract

Summary: We developed an algorithm named GEAR (genomic enrichment analysis of regional DNA copy number changes) for functional interpretation of genome-wide DNA copy number changes identified by array-based comparative genomic hybridization. GEAR selects two types of chromosomal alterations with potential biological relevance, i.e. recurrent and phenotype-specific alterations. Then it performs functional enrichment analysis using a priori selected functional gene sets to identify primary and clinical genomic signatures. The genomic signatures identified by GEAR represent functionally coordinated genomic changes, which can provide clues on the underlying molecular mechanisms related to the phenotypes of interest. GEAR can help the identification of key molecular functions that are activated or repressed in the tumor genomes leading to the improved understanding on the tumor biology.

Availability: GEAR software is available with online manual in the website, http://www.systemsbiology.co.kr/GEAR/.

Contact: yejun{at}catholic.ac.kr

Associate Editor: Dmitrij Frishman

Received on March 22, 2007; revised on November 3, 2007; accepted on November 20, 2007

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