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Bioinformatics Vol. 19 no. 3 2003
Pages 383-389
© 2003 Oxford University Press

GenePath: a system for automated construction of genetic networks from mutant data

Blaz Zupan 1,5, Janez Demsar 1, Ivan Bratko 1,2, Peter Juvan 1, John A. Halter 3, Adam Kuspa 4,5 and Gad Shaulsky 5,*

1 University of Ljubljana, Faculty of Computer and Information Science
2 Jozef Stefan Institute, Ljubljana, Slovenia, Departments of
3 PM&R and Division of Neuroscience,
4 Biochemistry and Molecular Biology
5 Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA

Received on May 8, 2002 ; revised on August 23, 2002 ; accepted on September 17, 2002

Motivation: Genetic networks 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 automates the analysis of genetic data. GenePath employs expert-defined patterns to uncover gene relations from the data, and uses these relations as constraints in the search for a plausible genetic network. GenePath formalizes genetic data analysis, facilitates the consideration of all the available data in a consistent manner, and the examination of the large number of possible consequences of planned experiments. It also provides an explanation mechanism that traces every finding to the pertinent data.

Availability: GenePath can be accessed at http://genepath.org

Contact: gadi{at}bcm.tmc.edu

Supplementary information: Supplementary material is available at http://genepath.org/bi-supp

* To whom correspondence should be addressed.


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