Inferring gene regulatory networks from temporal expression profiles under time-delay and noise

Authors:
Shinuk Kim;Junil Kim;Kwang-Hyun Cho
Affiliations:
Bio-MAX Institute, Seoul National University, Gwanak-gu, Seoul 151-818, Republic of Korea;Interdisciplinary Program in Bioinformatics, Seoul National University, Gwanak-gu, Seoul 151-747, Republic of Korea;Bio-MAX Institute, Seoul National University, Gwanak-gu, Seoul 151-818, Republic of Korea and College of Medicine, Seoul National University, Jongno-gu, Seoul 110-779, Republic of Korea
Venue:
Computational Biology and Chemistry
Year:
2007

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Abstract

Ordinary differential equations (ODE) have been widely used for modeling and analysis of dynamic gene networks in systems biology. In this paper, we propose an optimization method that can infer a gene regulatory network from time-series gene expression data. Specifically, the following four cases are considered: (1) reconstruction of a gene network from synthetic gene expression data with noise, (2) reconstruction of a gene network from synthetic gene expression data with time-delay, (3) reconstruction of a gene network from synthetic gene expression data with noise and time-delay, and (4) reconstruction of a gene network from experimental time-series data in budding yeast cell cycle.