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. 2008:6:17-23.
doi: 10.4137/cin.s342. Epub 2008 Feb 9.

Global associations between copy number and transcript mRNA microarray data: an empirical study

Wenjuan Gu  1 , Hyungwon Choi, Debashis Ghosh
Affiliations

Global associations between copy number and transcript mRNA microarray data: an empirical study

Wenjuan Gu et al. Cancer Inform. 2008.

Abstract

With an increasing number of cancer profiling studies assaying both transcript mRNA and copy number expression levels, a natural question then involves the potential to combine information across the two types of genomic data. In this article, we perform a study to assess the nature of association between the two types of data across several experiments. We report on several interesting findings: 1) global correlation between gene expression and copy number is relatively weak but consistent across studies; 2) there is strong evidence for a cis-dosage effect of copy number on gene expression; 3) segmenting the copy number levels helps to improve correlations.

Keywords: circular binary segmentation; high-dimensional data; machine learning; two-color microarray platform.

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