title: A comprehensive resource of interacting protein regions for refining human transcription factor networks.
abstract: Large-scale data sets of protein-protein interactions (PPIs) are a valuable resource for mapping and analysis of the topological and dynamic features of interactome networks. The currently available large-scale PPI data sets only contain information on interaction partners. The data presented in this study also include the sequences involved in the interactions (i.e., the interacting regions, IRs) suggested to correspond to functional and structural domains. Here we present the first large-scale IR data set obtained using mRNA display for 50 human transcription factors (TFs), including 12 transcription-related proteins. The core data set (966 IRs; 943 PPIs) displays a verification rate of 70%. Analysis of the IR data set revealed the existence of IRs that interact with multiple partners. Furthermore, these IRs were preferentially associated with intrinsic disorder. This finding supports the hypothesis that intrinsically disordered regions play a major role in the dynamics and diversity of TF networks through their ability to structurally adapt to and bind with multiple partners. Accordingly, this domain-based interaction resource represents an important step in refining protein interactions and networks at the domain level and in associating network analysis with biological structure and function.
authors.affiliation: Advanced Research Centers, Keio University, Yokohama, Japan. nekoneko@educ.cc.keio.ac.jp
authors.forename: Etsuko
authors.initials: E
authors.lastname: Miyamoto-Sato
authors.forename: Shigeo
authors.initials: S
authors.lastname: Fujimori
authors.forename: Masamichi
authors.initials: M
authors.lastname: Ishizaka
authors.forename: Naoya
authors.initials: N
authors.lastname: Hirai
authors.forename: Kazuyo
authors.initials: K
authors.lastname: Masuoka
authors.forename: Rintaro
authors.initials: R
authors.lastname: Saito
authors.forename: Yosuke
authors.initials: Y
authors.lastname: Ozawa
authors.forename: Katsuya
authors.initials: K
authors.lastname: Hino
authors.forename: Takanori
authors.initials: T
authors.lastname: Washio
authors.forename: Masaru
authors.initials: M
authors.lastname: Tomita
authors.forename: Tatsuhiro
authors.initials: T
authors.lastname: Yamashita
authors.forename: Tomohiro
authors.initials: T
authors.lastname: Oshikubo
authors.forename: Hidetoshi
authors.initials: H
authors.lastname: Akasaka
authors.forename: Jun
authors.initials: J
authors.lastname: Sugiyama
authors.forename: Yasuo
authors.initials: Y
authors.lastname: Matsumoto
authors.forename: Hiroshi
authors.initials: H
authors.lastname: Yanagawa
mesh_terms: D001665:Binding Sites / Q000235:genetics; D030562:Databases, Protein; D020869:Gene Expression Profiling; D053263:Gene Regulatory Networks; D006801:Humans; D008958:Models, Molecular; D011485:Protein Binding; D011487:Protein Conformation; D025941:Protein Interaction Mapping / Q000379:methods*; D017434:Protein Structure, Tertiary; D040901:Proteomics; D014157:Transcription Factors / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism*
chemical_list: D014157:Transcription Factors