title: Inference of biological pathway from gene expression profiles by time delay boolean networks.
abstract: One great challenge of genomic research is to efficiently and accurately identify complex gene regulatory networks. The development of high-throughput technologies provides numerous experimental data such as DNA sequences, protein sequence, and RNA expression profiles makes it possible to study interactions and regulations among genes or other substance in an organism. However, it is crucial to make inference of genetic regulatory networks from gene expression profiles and protein interaction data for systems biology. This study will develop a new approach to reconstruct time delay boolean networks as a tool for exploring biological pathways. In the inference strategy, we will compare all pairs of input genes in those basic relationships by their corresponding p-scores for every output gene. Then, we will combine those consistent relationships to reveal the most probable relationship and reconstruct the genetic network. Specifically, we will prove that O(log n) state transition pairs are sufficient and necessary to reconstruct the time delay boolean network of n nodes with high accuracy if the number of input genes to each gene is bounded. We also have implemented this method on simulated and empirical yeast gene expression data sets. The test results show that this proposed method is extensible for realistic networks.
authors.affiliation: Green Energy and Environment Research Laboratories, Industrial Technology Research Institute, Chutung, Hsinchu, Taiwan, Republic of China.
authors.forename: Tung-Hung
authors.initials: TH
authors.lastname: Chueh
authors.forename: Henry Horng-Shing
authors.initials: HH
authors.lastname: Lu
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods; D005656:Fungal Proteins / Q000378:metabolism; D020869:Gene Expression Profiling; D015966:Gene Expression Regulation, Fungal; D053263:Gene Regulatory Networks; D005800:Genes, Fungal; D008954:Models, Biological; D008957:Models, Genetic; D015233:Models, Statistical; D011336:Probability; D012313:RNA / Q000378:metabolism; D015203:Reproducibility of Results; D012441:Saccharomyces cerevisiae / Q000378:metabolism; D017422:Sequence Analysis, DNA; D012984:Software; D049490:Systems Biology / Q000379:methods
chemical_list: D005656:Fungal Proteins; D012313:RNA