title: Simulated annealing based algorithm for identifying mutated driver pathways in cancer.
abstract: With the development of next-generation DNA sequencing technologies, large-scale cancer genomics projects can be implemented to help researchers to identify driver genes, driver mutations, and driver pathways, which promote cancer proliferation in large numbers of cancer patients. Hence, one of the remaining challenges is to distinguish functional mutations vital for cancer development, and filter out the unfunctional and random "passenger mutations." In this study, we introduce a modified method to solve the so-called maximum weight submatrix problem which is used to identify mutated driver pathways in cancer. The problem is based on two combinatorial properties, that is, coverage and exclusivity. Particularly, we enhance an integrative model which combines gene mutation and expression data. The experimental results on simulated data show that, compared with the other methods, our method is more efficient. Finally, we apply the proposed method on two real biological datasets. The results show that our proposed method is also applicable in real practice.
authors: College of Information and Communication Technology, Qufu Normal University, Rizhao 276826, China.
authors: Hai-Tao
authors: HT
authors: Li
authors: College of Jia Sixie Agriculture, Weifang University of Science and Technology, Shouguang 262700, China.
authors: Yu-Lang
authors: YL
authors: Zhang
authors: College of Information and Communication Technology, Qufu Normal University, Rizhao 276826, China ; College of Electrical Engineering and Automation, Anhui University, Hefei 230000, China.
authors: Chun-Hou
authors: CH
authors: Zheng
authors: Intelligent Computing Lab, Hefei Institute of Intelligent Machines, Chinese Academy of Sciences, Hefei 230000, China.
authors: Hong-Qiang
authors: HQ
authors: Wang
mesh_terms: D000465:Algorithms; D003198:Computer Simulation; D052138:Genes, Neoplasm; D006801:Humans; D008175:Lung Neoplasms / Q000235:genetics; D008390:Markov Chains; D009010:Monte Carlo Method; D009154:Mutation / Q000235:genetics*; D009369:Neoplasms / Q000235:genetics*; D015398:Signal Transduction / Q000235:genetics*; D058570:TOR Serine-Threonine Kinases / Q000378:metabolism; D013997:Time Factors
chemical_list: D058570:TOR Serine-Threonine Kinases