Berlin 2008 – scientific programme
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BP: Fachverband Biologische Physik
BP 28: Molecular Recognition
BP 28.4: Talk
Friday, February 29, 2008, 11:30–11:45, PC 203
Physical-Chemistry Analysis of Microarray Data — •K. Myriam Kroll1, Gerard Barkema2,3, and Enrico Carlon1 — 1Institute for Theoretical Physics, KU Leuven, Celestijnenlaan 200D, B-3000 Leuven, Belgium — 2Institute for Theoretical Physics, Universiteit Utrecht, Leuvenlaan 4, 3584 CE, Utrecht, The Netherlands — 3Institute-Lorentz for Theoretical Physics, University of Leiden, Niels Bohrweg 2, 2333 CA Leiden, The Netherlands
DNA microarrays are comparably novel devices which allow to monitor the gene expression level of thousands of genes simultaneouly on a genome-wide scale. The underlying principle of these DNA chips is the hybridization process between surface-bound DNA sequences (probes) and the so-called target sequences (DNA or RNA) which are floating in solution. From the amount of hybridized targets, information about the presence of certain genes in solution can be extracted and conclusions concerning the gene expression level can be drawn. However, due to non-specific binding the measured signal contains a noisy background component which makes the data analysis and interpretation rather difficult. In this talk, we focus on the theoretical analysis of the publicly available data of microarray experiments performed on Affymetrix GeneChips. By combining well-established models from physical chemistry (Nearest Neighbor Model) and statistical mechanics, we construct a functional to predict the background intensity on every single spot on the chip. We then compare the results to other background subtraction schemes and show that our approach performs better on a global scale.