GenePath: a system for inference of genetic networks and proposal of genetic experiments

  • Authors:

  • Bla Zupan;Ivan Bratko;Janez Demšar;Peter Juvan;Toma Curk;Urban Borštnik;J.Robert Beck;John Halter;Adam Kuspa;Gad Shaulsky

  • Affiliations:

  • Faculty of Computer and Information Science, University of Ljubljana, Trzaska 25, SI-1000 Ljubljana, Slovenia and Department of Molecular and Human Genetics, Baylor College of Medicine, 1 Baylor P ...;Faculty of Computer and Information Science, University of Ljubljana, Trzaska 25, SI-1000 Ljubljana, Slovenia and Joef Stefan Institute, Jamova 39, SI-1000 Ljubljana, Slovenia;Faculty of Computer and Information Science, University of Ljubljana, Trzaska 25, SI-1000 Ljubljana, Slovenia;Faculty of Computer and Information Science, University of Ljubljana, Trzaska 25, SI-1000 Ljubljana, Slovenia;Faculty of Computer and Information Science, University of Ljubljana, Trzaska 25, SI-1000 Ljubljana, Slovenia;Faculty of Computer and Information Science, University of Ljubljana, Trzaska 25, SI-1000 Ljubljana, Slovenia;Fox Chase Cancer Center, 7701 Burholme Avenue, Philadelphia, PA 19111, USA;Department of PM&R, Molecular and Cellular Biology and Division of Neuroscience, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA;Department of Biochemistry and Molecular Biology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA and Department of Molecular and Human Genetics, Baylor College of Medicine, 1 B ...;Department of Molecular and Human Genetics, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA

  • Venue:
  • Artificial Intelligence in Medicine
  • Year:
  • 2003

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Abstract

A genetic network is a formalism that is often used in biology to represent causalities and reason about biological phenomena related to genetic regulation. We present GenePath, a computer-based system that supports the inference of genetic networks from a set of genetic experiments. Implemented in Prolog, GenePath uses abductive inference to elucidate network constraints based on background knowledge and experimental results. Additionally, it can propose genetic experiments that may further refine the discovered network and establish relations between genes that could not be related based on the original experimental data. We illustrate GenePath's approach and utility on analysis of data on aggregation and sporulation of the soil amoeba Dictyostelium discoideum.