Unsupervised classification for tiling arrays: chip-chip and transcriptome

DOI10.2202/1544-6115.1692MaRDI QIDQ2921164zbMATH OpenOpenAlexWikidataFDO

Authors Caroline Bérard, Véronique Brunaud, Sébastien Aubourg, Stéphane Robin, Marie-Laure Martin-Magniette

Publication date 7 October 2014

Published in Statistical Applications in Genetics and Molecular Biology (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/1104.5429

zbMATH Keywords

hidden Markov modelunsupervised classificationtiling arraysbivariate Gaussian mixture

Mathematics Subject Classification ID

Applications of Markov chains and discrete-time Markov processes on general state spaces (social mobility, learning theory, industrial processes, etc.) (60J20) Biochemistry, molecular biology (92C40)

Abstract: Tiling arrays make possible a large scale exploration of the genome thanks to probes which cover the whole genome with very high density until 2 000 000 probes. Biological questions usually addressed are either the expression difference between two conditions or the detection of transcribed regions. In this work we propose to consider simultaneously both questions as an unsupervised classification problem by modeling the joint distribution of the two conditions. In contrast to previous methods, we account for all available information on the probes as well as biological knowledge like annotation and spatial dependence between probes. Since probes are not biologically relevant units we propose a classification rule for non-connected regions covered by several probes. Applications to transcriptomic and ChIP-chip data of Arabidopsis thaliana obtained with a NimbleGen tiling array highlight the importance of a precise modeling and the region classification.

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Cited in

(8)

• Fast wavelet based functional models for transcriptome analysis with tiling arrays
• Statistical metrics for quality assessment of high-density tiling array data
• Doubly stochastic continuous-time hidden Markov approach for analyzing genome tiling arrays
• Research in Computational Molecular Biology
• Error rate control for classification rules in multiclass mixture models
• Hidden Markov models with mixtures as emission distributions
• Variational Bayes approach for model aggregation in unsupervised classification with Markovian dependency
• Inference in finite state space non parametric hidden Markov models and applications

Describes a project that uses

Uses Software

• GENEVESTIGATOR
• NTAP
• TileMap
• TAHMMAnnot
• EUGENE
• R
• mclust

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