Bioinformatics Advance Access originally published online on December 14, 2004
Bioinformatics 2005 21(8):1542-1549; doi:10.1093/bioinformatics/bti214
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Boolean relationships among genes responsive to ionizing radiation in the NCI 60 ACDS
1Department of Electrical Engineering, Texas A&M University College Station, TX 77843, USA
2National Cancer Institute NIH Bethesda, MD 20892, USA
3Translational Genomics Research Institute 400 North Fifth Street, Suite 1600, Phoenix, AZ 85004, USA
4University of Texas M.D. Anderson Cancer Center Houston, TX 77030, USA
*To whom correspondence should be addressed.
Motivation: An early use of gene-expression data coming from microarrays was to discover non-linear multivariate intergene relationships. Pursuing this direction, the motivation for this paper is 2-fold: (1) to discover and elucidate multivariate logical predictive relations among gene expressions in a dataset arising from radiation studies using the NCI 60 Anti-Cancer Drug Screen (ACDS) cell lines; and (2) to demonstrate how these logical relations based on coarse quantization reflect corresponding relations in the continuous data.
Results: Using the coefficient of determination, a large number of logical relationships have been discovered among genes in the NCI 60 ACDS cell lines. Moreover, these relationships can be seen directly in the original continuous data, and many are robust relative to the thresholds used to obtain the logical data from the continuous data. A key observation is that a number of intergene relationships appear to be considerably stronger when p53 is functional as compared to when it is not, which is consistent with earlier findings in the literature.
Availability: The appendix is available at http://gsp.tamu.edu/Publications/supplement.htm
Contact: edward{at}ee.tamu.edu