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Proceedings Paper

Analysis of gene expression data of the NCl 60 cancer cell lines using Bayesian hierarchical effects model
Author(s): Jae K. Lee; Uwe Scherf; Lawrence H. Smith; Lorraine Tanabe; John N. Weinstein
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Paper Abstract

From the end of the last decade, NCI has been performing large screening of anticancer drug compounds and molecular targets on a pool of 60 cell lines of various types of cancer. In particular, a complete set of cDNA expression array data on the 60 cell lines are now available. To discover differentially-expressed genes in each type of cancer cell lines, we need to estimate a large number of genetic parameters, especially interaction effects for all combinations of cancer types and genes, by decomposing the total variance into biological and array instrumental components. This error decomposition is important to identify subtle genes with low biological variability. An innovative statistical method is required for simultaneously estimating more than 100,000 parameters of interaction effects and error components. We propose a Bayesian statistical approach based on the construction of a hierarchical model adopting parameterization of a liner effects model. The estimation of the model parameters is performed by Markov Chain Monte Carlo, a recent computer- intensive statistical resampling technique. We have identified novel genes whose effects have not been revealed by the previous clustering approaches to the gene expression data.

Paper Details

Date Published: 4 June 2001
PDF: 8 pages
Proc. SPIE 4266, Microarrays: Optical Technologies and Informatics, (4 June 2001); doi: 10.1117/12.427993
Show Author Affiliations
Jae K. Lee, Univ. of Virginia (United States)
Uwe Scherf, National Cancer Institute/National Institutes of Health (United States)
Lawrence H. Smith, National Cancer Institute/National Institutes of Health (United States)
Lorraine Tanabe, National Cancer Institute/National Institutes of Health (United States)
John N. Weinstein, National Cancer Institute/National Institutes of Health (United States)

Published in SPIE Proceedings Vol. 4266:
Microarrays: Optical Technologies and Informatics
Michael L. Bittner; Yidong Chen; Andreas N. Dorsel; Edward R. Dougherty, Editor(s)

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