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A Stochastic Segmentation Model for Joint DNA-RNA Microarray Data Analysis

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dc.contributor.advisor Powers, Scott en_US
dc.contributor.author Su, Yi en_US
dc.contributor.other Department of Applied Mathematics and Statistics en_US
dc.date.accessioned 2013-05-22T17:35:40Z
dc.date.accessioned 2015-04-24T14:45:41Z
dc.date.available 2013-05-22T17:35:40Z
dc.date.available 2015-04-24T14:45:41Z
dc.date.issued 2012-12-01
dc.identifier Su_grad.sunysb_0771E_11231 en_US
dc.identifier.uri http://hdl.handle.net/1951/59879 en_US
dc.identifier.uri http://hdl.handle.net/11401/71042 en_US
dc.description 68 pg. en_US
dc.description.abstract DNA copy number change and epigenetic alteration often induce abnormal RNA expression level and have been linked to the development and progression of cancer. While various methods have been proposed for studying microarray DNA copy number and RNA expression data respectively, little statistical work has been done in modeling the relationship between the two. We propose for the joint analysis of the two types of data a new stochastic change-point model with latent variables, and an associated estimation procedure. Our method integrates hidden Markov model with Bayesian statistics to yield joint posterior distribution of DNA and RNA signal intensities throughout the whole genome. Explicit formulas of the posterior means are derived, which can be used to give direct estimates of the signal intensities without performing segmentation. A subsequent segmentation procedure is further provided to identify change-points and yield piecewise constant estimates of the signal intensities on each segment. Other quantities can also be derived from the posterior distribution for assessing the confidence of coincident and non-coincident change-points in the DNA and RNA sequences. Based on these estimates, chromosomal regions with genetic and potential epigenetic aberrations can be identified. For computational simplicity we propose an approximation method to keep computation time linear in sequence length, hence the method can be readily applied to the new generation of higher-throughput arrays. The proposed method is illustrated through simulation studies and application to a real data set. en_US
dc.description.sponsorship This work is sponsored by the Stony Brook University Graduate School in compliance with the requirements for completion of degree. en_US
dc.format Monograph en_US
dc.format.medium Electronic Resource en_US
dc.language.iso en_US en_US
dc.publisher The Graduate School, Stony Brook University: Stony Brook, NY. en_US
dc.subject.lcsh Statistics en_US
dc.subject.other Bayes Theory, Markov Chain, Segmentation en_US
dc.title A Stochastic Segmentation Model for Joint DNA-RNA Microarray Data Analysis en_US
dc.type Dissertation en_US
dc.mimetype Application/PDF en_US
dc.contributor.committeemember Green, David en_US
dc.contributor.committeemember Powers, Scott en_US
dc.contributor.committeemember Xing, Haipeng en_US
dc.contributor.committeemember Zhu, Wei en_US
dc.contributor.committeemember Shen, Ronglai en_US

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