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Bioinformatics Advance Access published online on December 14, 2004
Bioinformatics, doi:10.1093/bioinformatics/bti214
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Bioinformatics © Oxford University Press 2004; all rights reserved.
Received September 27, 2004
Revised November 27, 2004
Accepted December 7, 2004

Article

Boolean relationships among genes responsive to ionizing radiation in the NCI 60 ACDS

Ranadip Pal 1, Aniruddha Datta 1, Albert J. Fornace 2, Michael L. Bittner 3, and Edward R. Dougherty 4*

1 Department of Electrical Engineering, Texas A&M University, College Station, TX, 77843, USA
2 National Cancer Institute, NIH Bethesda, Maryland 20892, USA
3 Translational Genomics Research Institute, 400 North Fifth Street, Suite 1600, Phoenix, AZ 85004, USA
4 Department of Electrical Engineering, Texas A&M University, College Station, TX, 77843, USA; University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA

* To whom correspondence should be addressed.
Edward R. Dougherty, E-mail: edward{at}ee.tamu.edu


  Abstract

Motivation: An early use of gene-expression data coming from microarrays was to discover nonlinear multivariate inter-gene relationships. Pursuing this direction, the motivation for this paper is twofold: (1) to discover and elucidate multivariate logical predictive relations among gene expressions in a data set 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 Anti-Cancer Drug Screen 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 inter-gene 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.


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