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2D Gel Correlation Analysis and Perspectives on Systems Biology

Werner Van Belle1* - werner@yellowcouch.org, werner.van.belle@gmail.com

1- Department of Medical Genetics (MEDGEN); Northern Norwegian Hospital; Tromsø; Norway

Abstract :  Two-dimensional gel electrophoresis is a powerful technique to discriminate post-translationally modified protein isoforms. The first part of our presentation will focus on a technique we developed to relate such 2D gel images to specific external conditions. We will present the different steps of the technique, its validation on simulated images and give examples of its use on the analysis of P53-isoforms in AML patients. The second part of the presentation focuses on a recent experiment on biological networks. Microarray & qPCR make it easy to measure protein/transcription levels in cell systems. This technology can be used to sample the direct and indirect changes induced by cell system alterations, such as constitutive activation of genes or interfering with gene transciption (siRNAs). To provide a better overview of the effects on such alterations, we integrated a microarray measurement into a human protein interaction map. This made it possible to rank and cluster the proteins according to their expected relation towards the original change. Aside from providing a valuable tool for our research, our approach also revealed a number of substantial limitations which we will discuss in detail.

Keywords:  2D Gel Correlation Analysis, Gel Electrophoresis, Confidence Intervals Micro-Arrays, systems biology, systems description, small worlds, noise propagation, oscillation
Reference:  Werner Van Belle; 2D Gel Correlation Analysis and Perspectives on Systems Biology; Presented at Friedrich Miescher Institute for Biomedical Research, Basel; Switzerland; October 2007
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