Identification of functional CNV region networks using a CNV-gene mapping algorithm in a genome-wide scale

Chihyun Park, Jaegyoon Ahn, Youngmi Yoon, Sanghyun Park

Research output: Contribution to journalArticlepeer-review

2 Citations (Scopus)

Abstract

Motivation: Identifying functional relation of copy number variation regions (CNVRs) and gene is an essential process in understanding the impact of genotypic variations on phenotype. There have been many related works, but only a few attempts were made to normal populations.Results: To analyze the functions of genome-wide CNVRs, we applied a novel correlation measure called Correlation based on Sample Set (CSS) to paired Whole Genome TilePath array and messenger RNA (mRNA) microarray data from 210 HapMap individuals with normal phenotypes and calculated the confident CNVR-gene relationships. Two CNVR nodes form an edge if they regulate a common set of genes, allowing the construction of a global CNVR network. We performed functional enrichment on the common genes that were trans-regulated from CNVRs clustered together in our CNVR network. As a result, we observed that most of CNVR clusters in our CNVR network were reported to be involved in some biological processes or cellular functions, while most CNVR clusters from randomly constructed CNVR networks showed no evidence of functional enrichment. Those results imply that CSS is capable of finding related CNVR-gene pairs and CNVR networks that have functional significance.

Original languageEnglish
Article numberbts318
Pages (from-to)2045-2051
Number of pages7
JournalBioinformatics
Volume28
Issue number15
DOIs
Publication statusPublished - 2012 Aug

Bibliographical note

Funding Information:
Funding: This research was supported by Basic Science Research Program through the National Research Foundation of Korea (NRF) funded by the Ministry of Education, Science and Technology (2012-0002887)

All Science Journal Classification (ASJC) codes

  • Statistics and Probability
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Computational Theory and Mathematics
  • Computational Mathematics

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