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A unified framework for unraveling the functional interaction structure of a biomolecular network based on stimulus-response experimental data.

Abstract：

:We propose a unified framework for the identification of functional interaction structures of biomolecular networks in a way that leads to a new experimental design procedure. In developing our approach, we have built upon previous work. Thus we begin by pointing out some of the restrictions associated with existing structure identification methods and point out how these restrictions may be eased. In particular, existing methods use specific forms of experimental algebraic equations with which to identify the functional interaction structure of a biomolecular network. In our work, we employ an extended form of these experimental algebraic equations which, while retaining their merits, also overcome some of their disadvantages. Experimental data are required in order to estimate the coefficients of the experimental algebraic equation set associated with the structure identification task. However, experimentalists are rarely provided with guidance on which parameters to perturb, and to what extent, to perturb them. When a model of network dynamics is required then there is also the vexed question of sample rate and sample time selection to be resolved. Supplying some answers to these questions is the main motivation of this paper. The approach is based on stationary and/or temporal data obtained from parameter perturbations, and unifies the previous approaches of Kholodenko et al. (PNAS 99 (2002) 12841-12846) and Sontag et al. (Bioinformatics 20 (2004) 1877-1886). By way of demonstration, we apply our unified approach to a network model which cannot be properly identified by existing methods. Finally, we propose an experiment design methodology, which is not limited by the amount of parameter perturbations, and illustrate its use with an in numero example.

journal_name

FEBS Lett

journal_title

FEBS letters

authors

Cho KH,Choo SM,Wellstead P,Wolkenhauer O

doi

10.1016/j.febslet.2005.07.025

keywords:

subject

Has Abstract

pub_date

2005-08-15 00:00:00

pages

4520-8

issue

eissn

0014-5793

issn

1873-3468

pii

S0014-5793(05)00875-6

journal_volume

579

pub_type

杂志文章

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A unified framework for unraveling the functional interaction structure of a biomolecular network based on stimulus-response experimental data.