title: Network-based methods for identifying critical pathways of complex diseases: a survey.
abstract: Biological pathways play important roles in the development of complex diseases, such as cancers, which are multifactorial complex diseases that are generally caused by mutation of multiple genes or dysregulation of pathways. It has become one of the most important issues to analyze pathways through combining multiple types of high-throughput data, such as genomics and proteomics, to understand the mechanisms of complex diseases. Currently, several network-based pathway analysis methods have been proposed. In this overview, we review seven major network-based pathway analysis methods and enumerate their benefits and limitations from an algorithmic perspective to provide a reference for the next generation of pathway analysis methods. Finally, we discuss the challenges that the next generation of methods faces.
authors.affiliation: School of Computer Science and Technology, Harbin Institute of Technology, China. jieli@hit.edu.cn.
authors.forename: Qiaosheng
authors.initials: Q
authors.lastname: Zhang
authors.forename: Jie
authors.initials: J
authors.lastname: Li
authors.forename: Hanqing
authors.initials: H
authors.lastname: Xue
authors.forename: Leilei
authors.initials: L
authors.lastname: Kong
authors.forename: Yadong
authors.initials: Y
authors.lastname: Wang
mesh_terms: D000465:Algorithms; D000818:Animals; D019295:Computational Biology / Q000379:methods*; D053263:Gene Regulatory Networks; D006801:Humans; D053858:Metabolic Networks and Pathways; D008954:Models, Biological; D015398:Signal Transduction; D049490:Systems Biology / Q000379:methods*