A hidden Markov model approach for determining expression from genomic tiling micro arrays

Background: Genomic tiling micro arrays have great potential for identifying previously undiscovered coding as well as non-coding transcription. To-date, however, analyses of these data have been performed in an ad hoc fashion. Results: We present a probabilistic procedure, ExpressHMM, that adaptively models tiling data prior to predicting expression on genomic sequence. A hidden Markov model (HMM) is used to model the distributions of tiling array probe scores in expressed and non-expressed regions. The HMM is trained on sets of probes mapped to regions of annotated expression and non-expression. Subsequently, prediction of transcribed fragments is made on tiled genomic sequence. The prediction is accompanied by an expression probability curve for visual inspection of the supporting evidence. We test ExpressHMM on data from the Cheng et al. (2005) tiling array experiments on ten Human chromosomes [1]. Results can be downloaded and viewed from our web site [2]. Conclusion: The value o...

• Type: Journal
• Year: 2006
• Where: BMCBI
• Authors: Kasper Munch, Paul P. Gardner, Peter Arctander, Anders Krogh
• Keywords: BMCBI 2006, Genomic Sequence, Genomic Tiling Micro, Tiling Micro