Methods, systems, apparatuses and computer readable media are provided for characterising a molecular phenotype of a biological sample using a biological interaction network. A biological interaction network may comprise a plurality of nodes, each node associated with a corresponding gene or protein, and a plurality of edges, each edge connecting a pair of nodes and indicative of an interaction between the genes or proteins to which each node of that associated pair of nodes corresponds. A method may comprise associating, with each node of the biological interaction network, a corresponding differential abundance value for the gene or protein to which that node corresponds, the differential abundance value derived from a comparison of a representative abundance value for the gene or protein in a biological sample exhibiting the molecular phenotype and a reference abundance value for the gene or protein. The method may comprise, using the differential abundance values of the nodes of the biological interaction network, performing a hill-climbing algorithm to partition the biological interaction network into clusters. The method may comprise determining, from the topology of the clusters, a signature of the molecular phenotype.
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