Journal
BIOMETRICS
Volume 65, Issue 1, Pages 19-29Publisher
WILEY
DOI: 10.1111/j.1541-0420.2008.01052.x
Keywords
Array CGH; Integration; Microarray; Nonparametric statistics; Permutation test; Shrinkage
Ask authors/readers for more resources
The central dogma of molecular biology relates DNA with mRNA. Array CGH measures DNA copy number and gene expression microarrays measure the amount of mRNA. Methods that integrate data from these two platforms may uncover meaningful biological relationships that further our understanding of cancer. We develop nonparametric tests for the detection of copy number induced differential gene expression. The tests incorporate the uncertainty of the calling of genomic aberrations. The test is preceded by a tuning algorithm that discards certain genes to improve the overall power of the false discovery rate selection procedure. Moreover, the test statistics are shrunken to borrow information across neighboring genes that share the same array CGH signature. For each gene we also estimate its effect, its amount of differential expression due to copy number changes, and calculate the coefficient of determination. The method is illustrated on breast cancer data, in which it confirms previously reported findings, now with a more profound statistical underpinning.
Authors
I am an author on this paper
Click your name to claim this paper and add it to your profile.
Reviews
Recommended
No Data Available