Here, we discuss Systems Genetics applications for systematic evaluation of candidate causal genes together with follow-up bioinformatics pathway analysis. The aim of this chapter is to illustrate analytic procedures and we provide examples in the context of Type 1 diabetes (T1day), the risk of which is conferred by over 60 loci. We also describe the Type 1 Diabetes Systems Genetics website and provide a guide for its use and application to other diseases.
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