Explaining Effects of Host Gene Knockouts on Brome Mosaic Virus Replication

Gene products are key players in the interaction networks within a cell. We analyze an experiment in which a yeast knockout library was assayed for the effects of host gene deletion on the replication of Brome Mosaic Virus (BMV). These observations, integrated with the partially known yeast interaction network, may be used to infer which host processes and gene products are involved in the mechanism of BMV’s replication. We approach this task using Inductive and Abductive Logic Programming (ILP and ALP). We use ALP to abduce causal explanations for each observation, including possible host interfaces with BMV. Some notable aspects of our task that differ from previous work using abduction in systems biology include a highly incomplete background model and a large number of observations to explain. Additionally, we expect that there are many interfaces between the host cell and the virus, and that each abduced interface will serve to explain a handful of observations. We determine that ILP is unable to identify general, informative models that characterize host-virus interactions accurately. Using ALP, however, we are able to construct causal explanations that link multiple observations to the same host interface.