Qualitative simulation of genetic regulatory networks using piecewise-linear models

Autor: Céline Hernandez, Hidde de Jong, Johannes Geiselmann, Jean-Luc Gouzé, Tewfik Sari, Michel Page
Přispěvatelé: Computer science and genomics (HELIX), Inria Grenoble - Rhône-Alpes, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Laboratoire Adaptation et pathogénie des micro-organismes [Grenoble] (LAPM), Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS), Université Joseph Fourier - Grenoble 1 (UJF), Centre National de la Recherche Scientifique (CNRS)-Université Joseph Fourier - Grenoble 1 (UJF)
Rok vydání: 2004
Předmět:
Theoretical computer science
Java
Differential equation
MESH: Genes
Regulator
General Mathematics
Immunology
Genomics
01 natural sciences
General Biochemistry
Genetics and Molecular Biology
MESH: Linear Models
010305 fluids & plasmas
03 medical and health sciences
MESH: Computer Simulation
Genes
Regulator
0103 physical sciences
Computer Simulation
[SDV.BBM]Life Sciences [q-bio]/Biochemistry
Molecular Biology
MESH: Models
Genetic
030304 developmental biology
General Environmental Science
computer.programming_language
Mathematics
Pharmacology
0303 health sciences
Mathematical and theoretical biology
Class (computer programming)
Models
Genetic
MESH: Genomics
General Neuroscience
Linear model
Qualitative simulation
Quantitative Biology::Genomics
Computational Theory and Mathematics
Linear Models
Graph (abstract data type)
General Agricultural and Biological Sciences
computer
Zdroj: Bulletin of Mathematical Biology
Bulletin of Mathematical Biology, 2004, 66 (2), pp.301-40. ⟨10.1016/j.bulm.2003.08.010⟩
Bulletin of Mathematical Biology, Springer Verlag, 2004, 66 (2), pp.301-40. ⟨10.1016/j.bulm.2003.08.010⟩
ISSN: 0092-8240
1522-9602
DOI: 10.1016/j.bulm.2003.08.010
Popis: In order to cope with the large amounts of data that have become available in genomics, mathematical tools for the analysis of networks of interactions between genes, proteins, and other molecules are indispensable. We present a method for the qualitative simulation of genetic regulatory networks, based on a class of piecewise-linear (PL) differential equations that has been well-studied in mathematical biology. The simulation method is well-adapted to state-of-the-art measurement techniques in genomics, which often provide qualitative and coarse-grained descriptions of genetic regulatory networks. Given a qualitative model of a genetic regulatory network, consisting of a system of PL differential equations and inequality constraints on the parameter values, the method produces a graph of qualitative states and transitions between qualitative states, summarizing the qualitative dynamics of the system. The qualitative simulation method has been implemented in Java in the computer tool Genetic Network Analyzer.
Databáze: OpenAIRE
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