title: Improving the accuracy of signal transduction pathway construction using Level-2 neighbours.
abstract: In this paper, we consider the problem of reconstructing a pathway for a given set of proteins based on available genomics and proteomics information such as gene expression data. In all previous approaches, the scoring function for a candidate pathway usually only depends on adjacent proteins in the pathway. We propose to also consider proteins that are of distance two in the pathway (we call them Level-2 neighbours). We derive a scoring function based on both adjacent proteins and Level-2 neighbours in the pathway and show that our scoring function can increase the accuracy of the predicted pathways through a set of experiments. The problem of computing the pathway with optimal score, in general, is NP-hard. We thus extend a randomised algorithm to make it work on our scoring function to compute the optimal pathway with high probability.
authors.affiliation: Faculty of Engineering, Department of Computer Science, The University of Hong Kong, Pokfulam Road, Hong Kong. kfwong@cs.hku.hk
authors.forename: Thomas K F
authors.initials: TK
authors.lastname: Wong
authors.forename: T W
authors.initials: TW
authors.lastname: Lam
authors.forename: S M
authors.initials: SM
authors.lastname: Yiu
authors.forename: Simon C K
authors.initials: SC
authors.lastname: Wong
mesh_terms: D000465:Algorithms; D019295:Computational Biology; D030562:Databases, Protein; D023281:Genomics; D047908:Intracellular Signaling Peptides and Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D040901:Proteomics; D015398:Signal Transduction
chemical_list: D047908:Intracellular Signaling Peptides and Proteins