Journal article
General nonlinear framework for the analysis of gene interaction via multivariate expression arrays
Journal of Biomedical Optics, Vol.5(4), pp.411-424
10/2000
Handle:
https://hdl.handle.net/2376/106729
PMID: 11092429
Abstract
A
DNA microarray is a complex biochemical-optical system whose purpose is the simultaneous measurement of gene expression for thousands of genes. In this paper we propose a general statistical approach to finding associations between the expression patterns of genes 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. The method allows incorporation of knowledge of other conditions relevant to the prediction, such as the application of particular stimuli or the presence of inactivating gene mutations, as predictive elements affecting the expression level of a given gene. Various aspects of the method are discussed: prediction quantification, unconstrained prediction, constrained prediction using ternary perceptrons, and design of predictors given small numbers of replicated microarrays. The method is applied to a set of genes undergoing genotoxic stress for validation according to the manner in which it points toward previously known and unknown relationships. The entire procedure is supported by software that can be applied to large gene sets, has a number of facilities to simplify data analysis, and provides graphics for visualizing experimental data, multiple gene interaction, and prediction logic. ©
Metrics
11 Record Views
Details
- Title
- General nonlinear framework for the analysis of gene interaction via multivariate expression arrays
- Creators
- Seungchan Kim - Texas A&M University, Department of Electrical Engineering, College Station, Texas 77843-3128Edward R Dougherty - Texas A&M University, Department of Electrical Engineering, College Station, Texas 77843-3128Michael L Bittner - National Institutes for Health, National Human Genome Research Institute, Laboratory for Cancer GeneticsYidong Chen - National Institutes for Health, National Human Genome Research Institute, Laboratory for Cancer GeneticsKrishnamoorthy Sivakumar - Washington State University, Department of Electrical Engineering, Pullman, Washington 99163Paul Meltzer - National Institutes for Health, National Human Genome Research Institute, Laboratory for Cancer GeneticsJeffrey M Trent - National Institutes for Health, National Human Genome Research Institute, Laboratory for Cancer Genetics
- Publication Details
- Journal of Biomedical Optics, Vol.5(4), pp.411-424
- Academic Unit
- Voiland College of Engineering and Architecture
- Identifiers
- 99900546958001842
- Language
- English
- Resource Type
- Journal article