Titlebook: Data Mining for Systems Biology; Methods and Protocol Hiroshi Mamitsuka,Charles DeLisi,Minoru Kanehisa Book 2013 Springer Science+Business

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https://doi.org/10.1007/978-3-663-07869-2ortant challenge to gain insight on a cell’s working mechanisms. We present SIRENE, a method to estimate a GRN from a collection of expression data. Contrary to most existing methods for GRN inference, SIRENE requires as input a list of known regulations, in addition to expression data, and implemen

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https://doi.org/10.1007/978-3-663-07869-2underlying network. We present a technique addressing this problem through focussing on a more limited problem: inferring direct targets of a transcription factor from short expression time series. The method is based on combining Gaussian process priors and ordinary differential equation models all

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https://doi.org/10.1007/978-3-663-07869-2iological networks. Currently, the most comprehensive and validated biological networks are metabolic networks. Complete metabolic networks are easily sourced from multiple online databases. These databases reveal metabolic networks to be large, highly complex structures. This complexity is sufficie

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https://doi.org/10.1007/978-3-663-07869-2terfaces may lead to the development of many diseases. In this chapter, we will briefly introduce the background knowledge of the protein–protein interaction, followed by the detailed explanation of varied analysis—from basic to advanced, as well as related tools and databases. VisANT (.)—a free Web

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https://doi.org/10.1007/978-3-663-07869-2sts of thousands of databases that were derived through computational inference of metabolic pathways from the MetaCyc pathway/genome database (PGDB). In some cases, these DBs underwent subsequent manual curation. Curated pathway DBs are now available for most of the major model organisms. Databases

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https://doi.org/10.1007/978-3-663-07869-2already a common procedure in identifying biomarkers or signatures of phenotypic states such as diseases or compound treatments. However, in most of the cases, especially in complex diseases, even given a list of biomarkers, the underlying biological mechanisms are still obscure to us. In other word