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BMCBI
2006

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

8 years 12 months ago
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...
Kasper Munch, Paul P. Gardner, Peter Arctander, An
Added 10 Dec 2010
Updated 10 Dec 2010
Type Journal
Year 2006
Where BMCBI
Authors Kasper Munch, Paul P. Gardner, Peter Arctander, Anders Krogh
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