Inferring gene regulatory networks by singular value decomposition and gravitation field algorithm

• Published in: PloS one 2012-12, Vol.7 (12), p.e51141-e51141
• Main Authors: Zheng, Ming, Wu, Jia-nan, Huang, Yan-xin, Liu, Gui-xia, Zhou, You, Zhou, Chun-guang
• Format: Article
• Language: English
• Subjects: Algorithms; Bayesian analysis; Biology; Cell cycle; Computer applications; Computer programs; Computer Science; Computer Simulation; Decomposition; Differential equations; Gene expression; Gene Expression Regulation, Fungal; Gene Regulatory Networks - genetics; Genes; Genetic algorithms; Genomes; Gravitation; Gravity (Force); Heuristic; Inference; Mathematical models; Mathematics; Methods; Molecular biology; Networks; Neural networks; Saccharomyces cerevisiae - genetics; Simulated annealing; Singular value decomposition; Solution space
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0051141

Reconstruction of gene regulatory networks (GRNs) is of utmost interest and has become a challenge computational problem in system biology. However, every existing inference algorithm from gene expression profiles has its own advantages and disadvantages. In particular, the effectiveness and efficiency of every previous algorithm is not high enough. In this work, we proposed a novel inference algorithm from gene expression data based on differential equation model. In this algorithm, two methods were included for inferring GRNs. Before reconstructing GRNs, singular value decomposition method was used to decompose gene expression data, determine the algorithm solution space, and get all candidate solutions of GRNs. In these generated family of candidate solutions, gravitation field algorithm was modified to infer GRNs, used to optimize the criteria of differential equation model, and search the best network structure result. The proposed algorithm is validated on both the simulated scale-free network and real benchmark gene regulatory network in networks database. Both the Bayesian method and the traditional differential equation model were also used to infer GRNs, and the results were used to compare with the proposed algorithm in our work. And genetic algorithm and simulated annealing were also used to evaluate gravitation field algorithm. The cross-validation results confirmed the effectiveness of our algorithm, which outperforms significantly other previous algorithms.