tailieunhanh - Báo cáo y học: "Characterizing regulatory path motifs in integrated networks using perturbational data"

Tuyển tập các báo cáo nghiên cứu về y học được đăng trên tạp chí y học Wertheim cung cấp cho các bạn kiến thức về ngành y đề tài: Characterizing regulatory path motifs in integrated networks using perturbational data. | Joshi et al. Genome Biology 2010 11 R32 http 2010 11 3 R32 w Genome Biology SOFTWARE Open Access Characterizing regulatory path motifs in integrated networks using perturbational data Anagha Joshi 1 2 Thomas Van Parys1 2 Yves Van de Peer1 2 and Tom Michoel 1 2 Abstract We introduce Pathicular http software details Pathicular. a Cytoscape plugin for studying the cellular response to perturbations of transcription factors by integrating perturbational expression data with transcriptional protein-protein and phosphorylation networks. Pathicular searches for regulatory path motifs short paths in the integrated physical networks which occur significantly more often than expected between transcription factors and their targets in the perturbational data. A case study in Saccharomyces cerevisiae identifies eight regulatory path motifs and demonstrates their biological significance. Rationale When a cell is perturbed by external stimuli it responds by adjusting the amount at which different types of proteins are needed. Transcriptional regulatory networks form the core of this cellular response system. However the static wiring of these networks does not reveal which parts of the network are active under certain conditions and how perturbations are propagated through the network. For this reason there has been much interest in integrating the static network topology with gene expression data which reflect the dynamical or functional state of the network. In a pioneering paper large changes were identified in the subnetworks of the transcriptional regulatory network of 5. cerevisiae active under five different conditions 1 . In reality the transcriptional regulatory network cannot be considered in isolation but it is integrated with other networks such as the protein-protein interaction network 2 . In 3 a framework was developed which integrates protein-protein and pro-tein-DNA interactions to identify active subnetworks of .