Identifying Non-random Patterns from Gene Expression Profiles
PRIB '08 Proceedings of the Third IAPR International Conference on Pattern Recognition in Bioinformatics
Pervasive and Mobile Computing
Comparison of methods for identifying periodically varying genes
International Journal of Bioinformatics Research and Applications
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Motivation: Following the advent of microarray technology in recent years, the challenge for biologists is to identify genes of interest from the thousands of genetic expression levels measured in each microarray experiment. In many cases the aim is to identify pattern in the data series generated by successive microarray measurements. Results: Here we introduce a new method of detecting pattern in microarray data series which is independent of the nature of this pattern. Our approach provides a measure of the algorithmic compressibility of each data series. A series which is significantly compressible is much more likely to result from simple underlying mechanisms than series which are incompressible. Accordingly, the gene associated with a compressible series is more likely to be biologically significant. We test our method on microarray time series of yeast cell cycle and show that it blindly selects genes exhibiting the expected cyclic behaviour as well as detecting other forms of pattern. Our results successfully predict two independent non-microarray experimental studies. Contact: sea31@cam.ac.uk