A pattern-oriented specification of gene network inference processes

Abstract

Patterns have been widely used in Computer Science. A pattern describes a generic solution to an existing problem in a more readable and accessible form. A pattern-oriented process specification consists of a generic and abstract description of a process. This paper presents a pattern-oriented specification of a genetic regulatory network inference process performed from microarray data and prior biological knowledge. The proposed specification was conceived based on prior work on gene inference networks. The adequacy of the proposed solution was then evaluated with respect to modern tendencies of the genes network inference literature.

Keywords: Dynamical system identification; Gene network inference; Genetic regulatory networks; Microarray data analysis; Patterns; Process modeling.