Automated analysis of multivariate nonlinear gene relations based on cDNA microarray expression data

Seungchan Kim; Edward R. Dougherty; Michael L. Bittner; Yidong Chen; Krishnamoorthy Sivakumar; Paul S. Meltzer; Jeffrey M. Trent

doi:10.1117/12.380506

22 March 2000 Automated analysis of multivariate nonlinear gene relations based on cDNA microarray expression data

Seungchan Kim, Edward R. Dougherty, Michael L. Bittner, Yidong Chen, Krishnamoorthy Sivakumar, Paul S. Meltzer, Jeffrey M. Trent

Author Affiliations +

Proceedings Volume 3926, Advances in Nucleic Acid and Protein Analyses, Manipulation, and Sequencing; (2000) https://doi.org/10.1117/12.380506
Event: BiOS 2000 The International Symposium on Biomedical Optics, 2000, San Jose, CA, United States

Abstract

A cDNA microarray is a complex biochemical-optical system whose purpose is the simultaneous measurement of gene expression for thousands of genes. This paper describes a general statistical environment for finding associations among gene expression patterns, and between genes and external conditions, via the coefficient of determination. This coefficient measures the degree to which the transcriptional levels of an observed gene set can be used to improve the prediction of the transcriptional state of a target gene relative to the best possible prediction in the absence of observations. Various aspects of the method are discussed: prediction quantification, deign of predictors given small numbers of replicated microarrays, and constrained prediction using ternary perceptrons. A main focus is the supporting software and its facilities for data analysis and visualization.

Citation Download Citation

Seungchan Kim, Edward R. Dougherty, Michael L. Bittner, Yidong Chen, Krishnamoorthy Sivakumar, Paul S. Meltzer, and Jeffrey M. Trent "Automated analysis of multivariate nonlinear gene relations based on cDNA microarray expression data", Proc. SPIE 3926, Advances in Nucleic Acid and Protein Analyses, Manipulation, and Sequencing, (22 March 2000); https://doi.org/10.1117/12.380506

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