title: Integer programming-based method for completing signaling pathways and its application to analysis of colorectal cancer.
abstract: Signaling pathways are often represented by networks where each node corresponds to a protein and each edge corresponds to a relationship between nodes such as activation, inhibition and binding. However, such signaling pathways in a cell may be affected by genetic and epigenetic alteration. Some edges may be deleted and some edges may be newly added. The current knowledge about known signaling pathways is available on some public databases, but most of the signaling pathways including changes upon the cell state alterations remain largely unknown. In this paper, we develop an integer programming-based method for inferring such changes by using gene expression data. We test our method on its ability to reconstruct the pathway of colorectal cancer in the KEGG database.
authors.affiliation: Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan. tamura@kuicr.kyoto-u.ac.jp.
authors.forename: Takeyuki
authors.initials: T
authors.lastname: Tamura
authors.forename: Yoshihiro
authors.initials: Y
authors.lastname: Yamanishi
authors.forename: Mao
authors.initials: M
authors.lastname: Tanabe
authors.forename: Susumu
authors.initials: S
authors.lastname: Goto
authors.forename: Minoru
authors.initials: M
authors.lastname: Kanehisa
authors.forename: Katsuhisa
authors.initials: K
authors.lastname: Horimoto
authors.forename: Tatsuya
authors.initials: T
authors.lastname: Akutsu
mesh_terms: D000465:Algorithms; D015179:Colorectal Neoplasms / Q000235:genetics* / Q000378:metabolism*; D019295:Computational Biology / Q000379:methods*; D003198:Computer Simulation; D016208:Databases, Factual; D044127:Epigenesis, Genetic; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic; D006801:Humans; D015398:Signal Transduction; D012984:Software