GenePath: a System for Automated Construction of Genetic Networks from Mutant Data

Abstract

Motivation: Genetic pathways are often used in the analysis of biological phenomena. In classical genetics, they are constructed manually from experimental data on mutants. The field lacks formalism to guide such analysis, and accounting for all the data becomes complicated when large amounts of data are considered. Results: We have developed GenePath, an intelligent assistant that mimics expert geneticists in the analysis of genetic data. GenePath employs expert-defined patterns to uncover gene relations from the data, and uses these relations as constraints that guide the search for a plausible genetic network. GenePath provides formalism to genetic data analysis, facilitates the consideration of all the available data in a consistent and systematic manner, and aids in the examination of the large number of possible consequences of a planned experiment. It also provides an explanation mechanism that traces back every finding to the pertinent data. GenePath was successfully tested on several genetic problems. Availability: GenePath can be accessed at http://genepath.org. Supplementary information: Supplementary material is available at http://genepath.org/bi-supp.