Evolving DNA motifs to predict GeneChip probe performance.docVIP

Algorithms for Molecular Biology BioMedCentral Research Open Access Evolving DNA motifs to predict GeneChip probe performance WB Langdon*1 and AP Harrison2 Address: 1Department of Computer Science, Kings College London, Strand, London, WC2R 2LS, UK and 2Biological Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK Email: WB Langdon* - wlangdon@essex.ac.uk; AP Harrison - harry@essex.ac.uk * Corresponding author Published: 19 March 2009 Received: 20 November 2008 Accepted: 19 March 2009 Algorithms for Molecular Biology 2009, 4:6 doi:10.1186/1748-7188-4-6 This article is available from: /content/4/1/6 ? 2009 Langdon and Harrison; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Abstract Background: Affymetrix High Density Oligonuclotide Arrays (HDONA) simultaneously measure expression of thousands of genes using millions of probes. We use correlations between measurements for the same gene across 6685 human tissue samples from NCBIs GEO database to indicated the quality of individual HG-U133A probes. Low correlation indicates a poor probe. Results: Regular expressions can be automatically created from a Backus-Naur form (BNF) context-free grammar using strongly typed genetic programming. Conclusion: The automatically produced motif is better at predicting poor DNA sequences than an existing human generated RE, suggesting runs of Cytosine and Guanine and mixtures should all be avoided. Background probeset as a heatmap (yellow/lighter corresponds to greater consistency between pairs of probes). Figure 2 sug- gests that in Affymetrix probeset 200660_at two probes do not measure the gene as well as the other nine. Typically Affymetrix GeneChips (e.g. HG-U133A) meas-