GenePath: software for genetic network exploration

Genetic pathways and networks are often used in the analysis of biological phenomena. They are constructed by determining the effect of mutations in different genes on the investigated phenomenon and by determining the relationships between the mutated genes. We describe a software tool named GenePath (http://genepath.org/) which serves as an assistant for genetic pathway discovery. The pathways and genetic networks are constructed in two steps. In the first step, genetic data are matched to a set of inference patterns of the type "If a combination of experiments is found in the data, THEN a relation between genes and phenotypic states can be assumed". The discovered relations impose constraints over the plausible genetic network, which is constructed in the second step such that all the constraints are satisfied. In addition to automation of the network discovery process, GenePath provides an 'explanation', the tracing of any network relation back to the pertinent experimental data. GenePath was trained on a genetic pathway that regulates the transition from growth to development in the social amoeba Dictyostelium discoideum and tested successfully on several other problems, demonstrating its utility as a general-purpose intelligent assistant to biologists in their explorative analysis of genetic data.