A pattern-oriented specification of gene network inference processes

• Published in: Computers in biology and medicine Vol. 43; no. 10; pp. 1415 - 1427
• Main Authors: Trepode, Nestor W, de Farias, Cléver R.G, Barrera, Junior
• Format: Journal Article
• Language: English
• Published: United States Elsevier Ltd 01.10.2013; Elsevier Limited
• Subjects: Breeding of animals; Computational Biology - methods; Data mining; Dynamical system identification; Experiments; Gene expression; Gene network inference; Gene Regulatory Networks; Genetic regulatory networks; Hypotheses; Integrated software; Internal Medicine; Mathematical models; Microarray data analysis; Oligonucleotide Array Sequence Analysis; Other; Pattern Recognition, Automated - methods; Patterns; Process modeling; Studies; Visual aids; Microarray data analysis; Process modeling; Genetic regulatory networks; Dynamical system identification; Patterns; Gene network inference
• ISSN: 0010-4825; 1879-0534
• DOI: 10.1016/j.compbiomed.2013.07.008

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.