An ASP application in integrative biology: identification of functional gene units - Inria - Institut national de recherche en sciences et technologies du numérique Access content directly
Conference Papers Year : 2013

An ASP application in integrative biology: identification of functional gene units

Abstract

Integrating heterogeneous knowledge is necessary to eluci- date the regulations in biological systems. In particular, such an inte- gration is widely used to identify functional units, that are sets of genes that can be triggered by the same external stimuli, as biological stresses, and that are linked to similar responses of the system. Although several models and algorithms shown great success for detecting functional units on well-known biological species, they fail in identifying them when ap- plied to more exotic species, such as extremophiles, that are by nature unrefined. Indeed, approved methods on unrefined models suffer from an explosion in the number of solutions for functional units, that are merely combinatorial variations of the same set of genes. This paper overcomes this crucial limitation by introducing the concept of "genome segments". As a natural extension of recent studies, we rely on the declarative model- ing power of answer set programming (ASP) to encode the identification of shortest genome segments (SGS). This study shows, via experimental evidences, that SGS is a new model of functional units with a predic- tive power that is comparable to existing methods. We also demonstrate that, contrary to existing methods, SGS are stable in (i) computational time and (ii) ability to predict functional units when one deteriorates the biological knowledge, which simulates cases that occur for exotic species.
No file

Dates and versions

hal-00853762 , version 1 (23-08-2013)

Identifiers

  • HAL Id : hal-00853762 , version 1

Cite

Philippe Bordron, Damien Eveillard, Alejandro Maass, Anne Siegel, Sven Thiele. An ASP application in integrative biology: identification of functional gene units. LPNMR - 12th Conference on Logic Programming and Nonmonotonic Reasoning - 2013, Sep 2013, Corunna, Spain. ⟨hal-00853762⟩
529 View
0 Download

Share

Gmail Facebook X LinkedIn More