Department of Computer Science, Yonsei University, South Korea, Seoul 120-749, South Korea.
Bioinformatics. 2012 Aug 1;28(15):2045-51. doi: 10.1093/bioinformatics/bts318. Epub 2012 May 30.
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.
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.
http://embio.yonsei.ac.kr/~ Park/cnv_net.php.
Supplementary data are available at Bioinformatics online.
鉴定拷贝数变异区域 (CNVRs) 和基因的功能关系是理解基因型变异对表型影响的重要过程。已经有许多相关的工作，但只有少数尝试针对正常人群进行。
为了分析全基因组 CNVRs 的功能，我们应用了一种称为基于样本集的相关性 (CSS) 的新相关性度量方法，对来自 210 名具有正常表型的 HapMap 个体的全基因组 TilePath 阵列和信使 RNA (mRNA) 微阵列数据进行分析，并计算了置信度的 CNVR-基因关系。如果两个 CNVR 节点调节一组共同的基因，则它们形成一个边缘，允许构建一个全局 CNVR 网络。我们对从我们的 CNVR 网络中聚集在一起的 CNVR 调节的共同基因进行了功能富集。结果表明，我们的 CNVR 网络中大多数 CNVR 簇被报道参与了一些生物过程或细胞功能，而从随机构建的 CNVR 网络中得到的大多数 CNVR 簇没有功能富集的证据。这些结果表明，CSS 能够找到具有功能意义的相关 CNVR-基因对和 CNVR 网络。
http://embio.yonsei.ac.kr/~Park/cnv_net.php。
补充数据可在 Bioinformatics 在线获取。
