Original Research Article

Applied Bioinformatics

, Volume 4, Issue 4, pp 263-276

Random Walk Models for Bayesian Clustering of Gene Expression Profiles

  • Fulvia FerrazziAffiliated withDipartimento di Informatica e Sistemistica, Università di Pavia Email author 
  • , Paolo MagniAffiliated withDipartimento di Informatica e Sistemistica, Università di Pavia
  • , Riccardo BellazziAffiliated withDipartimento di Informatica e Sistemistica, Università di Pavia

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Abstract

The analysis of gene expression temporal profiles is a topic of increasing interest in functional genomics. Model-based clustering methods are particularly interesting because they are able to capture the dynamic nature of these data and to identify the optimal number of clusters. We have defined a new Bayesian method that allows us to cope with some important issues that remain unsolved in the currently available approaches: the presence of time dislocations in gene expression, the non-stationarity of the processes generating the data, and the presence of data collected on an irregular temporal grid. Our method, which is based on random walk models, requires only mild a priori assumptions about the nature of the processes generating the data and explicitly models inter-gene variability within each cluster. It has first been validated on simulated datasets and then employed for the analysis of a dataset relative to serum-stimulated fibroblasts. In all cases, the results have been promising, showing that the method can be helpful in functional genomics research.