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Signalling pathways are conserved across different species, therefore makingyeast a model organism to study these via disruption of kinase activity. Yeasthas 159 genes that encode protein kinases and phosphatases, and 136 of thesehave counterparts in humans. Therefore any insight in this model organism couldpotentially offer indications of mechanisms of action in the human kinome. Thestudy utilises a Prolog-based approach, data from a yeast kinase deletionsstrains study and publicly available kinase-protein associations. Prolog, aprogramming language that is well-suited for symbolic reasoning is used toreason over the data and infer compensatory kinase networks. This approach isbased on the idea that when a kinase is knocked out, other kinases maycompensate for this loss of activity. Background knowledge on kinases targetingproteins is used to guide the analysis. This knowledge is used to infer thepotential compensatory interactions between kinases based on the changes inphosphorylation observed in the phosphoproteomics data from the yeast study.The results demonstrate the effectiveness of the Prolog-based approach inanalysing complex cell signalling mechanisms in yeast. The inferredcompensatory kinase networks provide new insights into the regulation of cellsignalling in yeast and may aid in the identification of potential therapeutictargets for modulating signalling pathways in yeast and other organisms.

Inferring Compensatory Kinase Networks in Yeast using Prolog