Unsupervised classification for tiling arrays: chip-chip and transcriptome

DOI10.2202/1544-6115.1692zbMATH Open1296.92105arXiv1104.5429OpenAlexW2963959387WikidataQ46752384 ScholiaQ46752384MaRDI QIDQ2921164FDOQ2921164

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)

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.

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

Recommendations

• Fast wavelet based functional models for transcriptome analysis with tiling arrays
• Doubly stochastic continuous-time hidden Markov approach for analyzing genome tiling arrays
• Research in Computational Molecular Biology
• Mixture Modeling for Genome‐Wide Localization of Transcription Factors
• Scan statistics analysis for detection of introns in time-course tiling array data

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)

Cited In (8)

• 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
• 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
• Fast wavelet based functional models for transcriptome analysis with tiling arrays

Uses Software

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

This page was built for publication: Unsupervised classification for tiling arrays: chip-chip and transcriptome

Report a bug (only for logged in users!)Click here to report a bug for this page (MaRDI item Q2921164)