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Please use this identifier to cite or link to this item: http://hdl.handle.net/1942/13799

Title: Fast Wavelet Based Functional Models for Transcriptome Analysis with Tiling Arrays
Authors: Clement, Lieven
De Beuf, Kristof
Thas, Olivier
Vuylsteke, Marnik
Irizarry, Rafael A.
Crainiceanu, Ciprian M.
Issue Date: 2012
Abstract: For a better understanding of the biology of an organism, a complete description is needed of all regions of the genome that are actively transcribed. Tiling arrays are used for this purpose. They allow for the discovery of novel transcripts and the assessment of differential expression between two or more experimental conditions such as genotype, treatment, tissue, etc. In tiling array literature, many efforts are devoted to transcript discovery, whereas more recent developments also focus on differential expression. To our knowledge, however, no methods for tiling arrays have been described that can simultaneously assess transcript discovery and identify differentially expressed transcripts. In this paper, we adopt wavelet based functional models to the context of tiling arrays. The high dimensionality of the data triggered us to avoid inference based on Bayesian MCMC methods. Instead, we introduce a fast empirical Bayes method that provides adaptive regularization of the functional effects. A simulation study and a case study illustrate that our approach is well suited for the simultaneous assessment of transcript discovery and differential expression in tiling array studies, and that it outperforms methods that accomplish only one of these tasks.
Notes: [Clement, Lieven] Katholieke Univ Leuven, Louvain, Belgium. [Clement, Lieven] Univ Hasselt, Hasselt, Belgium. [De Beuf, Kristof; Thas, Olivier] London S Bank Univ, Dept Math Modelling Stat & Bioinformat, London, England. [Vuylsteke, Marnik] London S Bank Univ, VIB Dept Plant Syst Biol, London, England. [Irizarry, Rafael A.; Crainiceanu, Ciprian M.] Johns Hopkins Univ, Bloomberg Sch Publ Hlth, Dept Biostat, Baltimore, MD 21218 USA.
URI: http://hdl.handle.net/1942/13799
DOI: 10.2202/1544-6115.1726
ISI #: 000305091700004
ISSN: 2194-6302
Category: A1
Type: Journal Contribution
Validation: ecoom, 2013
Appears in Collections: Research publications

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