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De novo network enrichment approaches have become increasingly popular. Although existing approaches differ in many relevant aspects (optimization criteria, algorithmic implementation, scoring function, etc.), they all aim for extracting connected subnetworks from a larger interaction network. These are significantly enriched with active, i.e. deregulated, biological entities (genes, proteins, metabolites).
(List et al., 2016) KeyPathwayMinerWeb: online multi-omics network enrichment. Nucleic Acids Res.