Computational protocol: Systems Medicine as an Emerging Tool for Cardiovascular Genetics

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Protocol publication

[…] Along with network analysis, a pathway analysis has become a useful method for gaining a detailed insight into biomolecular mechanisms among genes, proteins, metabolites, etc., as it reduces complexity, has increased explanatory power () and investigates biological pathways rather than genome-scale networks. Methods and tools for pathway analysis have been developed and studied, such as Pathway-Express, an impact analysis including classical statistics along with crucial factors such as the magnitude of each gene’s expression change, their type and position in the given pathways, and their interactions (). Other pathway analysis methods and tools include KEGG, KegArray, PathVisio, Ingenuity, and others [for a detailed review, please refer to Wheelock et al. ()]. These methods integrate different data types and pathway information and perform subsequent pathway analyses, for example, whether certain pathways are enriched for genes differentially expressed under certain conditions (, ). These analyses will provide more information on molecular characteristics in the cell under disease conditions or perturbations. […]

Pipeline specifications

Software tools Pathway-Express, KegArray, PathVisio
Databases KEGG
Application Transcription analysis
Diseases Cardiovascular Diseases