title: Pathway detection from protein interaction networks and gene expression data using color-coding methods and A∗ search algorithms.
abstract: With the large availability of protein interaction networks and microarray data supported, to identify the linear paths that have biological significance in search of a potential pathway is a challenge issue. We proposed a color-coding method based on the characteristics of biological network topology and applied heuristic search to speed up color-coding method. In the experiments, we tested our methods by applying to two datasets: yeast and human prostate cancer networks and gene expression data set. The comparisons of our method with other existing methods on known yeast MAPK pathways in terms of precision and recall show that we can find maximum number of the proteins and perform comparably well. On the other hand, our method is more efficient than previous ones and detects the paths of length 10 within 40 seconds using CPU Intel 1.73 GHz and 1 GB main memory running under windows operating system.
authors.affiliation: Department of Computer Science, National Tsing Hua University, Hsinchu 300, Taiwan.
authors.forename: Cheng-Yu
authors.initials: CY
authors.lastname: Yeh
authors.forename: Hsiang-Yuan
authors.initials: HY
authors.lastname: Yeh
authors.forename: Carlos Roberto
authors.initials: CR
authors.lastname: Arias
authors.forename: Von-Wun
authors.initials: VW
authors.lastname: Soo
mesh_terms: D000465:Algorithms; D000818:Animals; D003116:Color; D019295:Computational Biology; D030562:Databases, Protein; D005656:Fungal Proteins / Q000235:genetics; D015966:Gene Expression Regulation, Fungal; D015972:Gene Expression Regulation, Neoplastic; D005800:Genes, Fungal; D052138:Genes, Neoplasm; D006801:Humans; D008297:Male; D010675:Pheromones / Q000378:metabolism; D011471:Prostatic Neoplasms / Q000235:genetics*; D040081:Protein Array Analysis; D025941:Protein Interaction Mapping / Q000379:methods*; D060066:Protein Interaction Maps; D015398:Signal Transduction; D012984:Software; D015003:Yeasts / Q000235:genetics
chemical_list: D005656:Fungal Proteins; D010675:Pheromones