Observation conflict resolution in steady-state metabolic network dynamics analysis.
Steady state metabolic network dynamics analysis (SMDA) is a recently proposed computational metabolomics tool that (i) captures a metabolic network and its rules via a metabolic network database, (ii) mimics the reasoning of a biochemist, given a set of metabolic observations, and (iii) locates efficiently all possible metabolic activation/inactivation (flux) alternatives. However, a number of factors may cause the SMDA algorithm to eliminate feasible flux scenarios. These factors include (i) inherent error margins in observations (measurements), (ii) lack of knowledge to classify measurements as normal versus abnormal, and (iii) choosing a highly constrained metabolic subnetwork to query against. In this work, we first present and formalize these obstacles. Then, we propose techniques to eliminate them and present an experimental evaluation of our proposed techniques.
Department of Electrical Engineering and Computer Science, Case Western Reserve University, 10900 Euclid Ave., Cleveland, OH 44106, USA. aec51@case.edu
A Ercument
AE
Cicek
Gultekin
G
Ozsoyoglu
D000465:Algorithms; D016208:Databases, Factual; D053858:Metabolic Networks and Pathways; D055432:Metabolomics