Doubly stochastic continuous-time hidden Markov approach for analyzing genome tiling arrays

DOI10.1214/09-AOAS248zbMATH Open1196.62141arXiv0910.2090OpenAlexW3105098933MaRDI QIDQ985036FDOQ985036

Authors: W. Evan Johnson, X. Shirley Liu, Jun S. Liu 

Publication date: 20 July 2010

Published in: The Annals of Applied Statistics (Search for Journal in Brave)

Abstract: Microarrays have been developed that tile the entire nonrepetitive genomes of many different organisms, allowing for the unbiased mapping of active transcription regions or protein binding sites across the entire genome. These tiling array experiments produce massive correlated data sets that have many experimental artifacts, presenting many challenges to researchers that require innovative analysis methods and efficient computational algorithms. This paper presents a doubly stochastic latent variable analysis method for transcript discovery and protein binding region localization using tiling array data. This model is unique in that it considers actual genomic distance between probes. Additionally, the model is designed to be robust to cross-hybridized and nonresponsive probes, which can often lead to false-positive results in microarray experiments. We apply our model to a transcript finding data set to illustrate the consistency of our method. Additionally, we apply our method to a spike-in experiment that can be used as a benchmark data set for researchers interested in developing and comparing future tiling array methods. The results indicate that our method is very powerful, accurate and can be used on a single sample and without control experiments, thus defraying some of the overhead cost of conducting experiments on tiling arrays.

Full work available at URL: https://arxiv.org/abs/0910.2090

Recommendations

• Research in Computational Molecular Biology
• Generalized Hierarchical Markov Models for the Discovery of Length‐Constrained Sequence Features from Genome Tiling Arrays
• Fast wavelet based functional models for transcriptome analysis with tiling arrays
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zbMATH Keywords

Markov chain Monte Carloforward-backward algorithmhidden Markov modelBayesian hierarchical modelcontinuous-space Markov chainexpectation conditional maximizationtiling microarray

Mathematics Subject Classification ID

Bayesian inference (62F15) Applications of statistics to biology and medical sciences; meta analysis (62P10) Numerical analysis or methods applied to Markov chains (65C40) Biochemistry, molecular biology (92C40) Genetics and epigenetics (92D10)

Cites Work

• Bioinformatics and computational biology solutions using R and Bioconductor.
• Maximum likelihood estimation via the ECM algorithm: A general framework
• Title not available (Why is that?)
• Title not available (Why is that?)
• Mixture Modeling for Genome‐Wide Localization of Transcription Factors
• Doubly stochastic continuous-time hidden Markov approach for analyzing genome tiling arrays
• A Flexible and Powerful Bayesian Hierarchical Model for ChIP-Chip Experiments
• ChIP‐chip: Data, Model, and Analysis

Cited In (9)

• Generalized Hierarchical Markov Models for the Discovery of Length‐Constrained Sequence Features from Genome Tiling Arrays
• Statistical metrics for quality assessment of high-density tiling array data
• Research in Computational Molecular Biology
• Doubly stochastic continuous-time hidden Markov approach for analyzing genome tiling arrays
• Unsupervised classification for tiling arrays: chip-chip and transcriptome
• Scan statistics analysis for detection of introns in time-course tiling array data
• A continuous-time HMM approach to modeling the magnitude-frequency distribution of earthquakes
• Acquisition Times of Contiguous and Distributed Marker Sequences: A Cross-Bifix Analysis
• Fast wavelet based functional models for transcriptome analysis with tiling arrays

Uses Software

• xMAN

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