title: A comprehensive molecular interaction map of the budding yeast cell cycle.
abstract: With the accumulation of data on complex molecular machineries coordinating cell-cycle dynamics, coupled with its central function in disease patho-physiologies, it is becoming increasingly important to collate the disparate knowledge sources into a comprehensive molecular network amenable to systems-level analyses. In this work, we present a comprehensive map of the budding yeast cell-cycle, curating reactions from ∼600 original papers. Toward leveraging the map as a framework to explore the underlying network architecture, we abstract the molecular components into three planes--signaling, cell-cycle core and structural planes. The planar view together with topological analyses facilitates network-centric identification of functions and control mechanisms. Further, we perform a comparative motif analysis to identify around 194 motifs including feed-forward, mutual inhibitory and feedback mechanisms contributing to cell-cycle robustness. We envisage the open access, comprehensive cell-cycle map to open roads toward community-based deeper understanding of cell-cycle dynamics.
authors.affiliation: Department of Science and Technology, Keio University, Kanagawa, Japan.
authors.forename: Kazunari
authors.initials: K
authors.lastname: Kaizu
authors.forename: Samik
authors.initials: S
authors.lastname: Ghosh
authors.forename: Yukiko
authors.initials: Y
authors.lastname: Matsuoka
authors.forename: Hisao
authors.initials: H
authors.lastname: Moriya
authors.forename: Yuki
authors.initials: Y
authors.lastname: Shimizu-Yoshida
authors.forename: Hiroaki
authors.initials: H
authors.lastname: Kitano
mesh_terms: D020816:Amino Acid Motifs; D002453:Cell Cycle; D018797:Cell Cycle Proteins / Q000378:metabolism; D005656:Fungal Proteins / Q000378:metabolism; D015966:Gene Expression Regulation, Fungal; D008954:Models, Biological; D015233:Models, Statistical; D016366:Open Reading Frames; D004718:Saccharomycetales / Q000235:genetics / Q000502:physiology*; D015398:Signal Transduction
chemical_list: D018797:Cell Cycle Proteins; D005656:Fungal Proteins