A comprehensive resource of interacting protein regions for refining human transcription factor networks

Etsuko Miyamoto-Sato, Shigeo Fujimori, Masamichi Ishizaka, Naoya Hirai, Kazuyo Masuoka, Rintaro Saito, Yosuke Ozawa, Katsuya Hino, Takanori Washio, Masaru Tomita, Tatsuhiro Yamashita, Tomohiro Oshikubo, Hidetoshi Akasaka, Jun Sugiyama, Yasuo Matsumoto, Hiroshi Yanagawa

Research output: Contribution to journalArticle

43 Citations (Scopus)

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.

Original languageEnglish
Article numbere9289
JournalPLoS One
Volume5
Issue number2
DOIs
Publication statusPublished - 2010 Feb 24

Fingerprint

refining
Refining
Transcription Factors
transcription factors
protein-protein interactions
Proteins
proteins
Sexual Partners
transcription (genetics)
Transcription
Electric network analysis
Display devices
Datasets
Messenger RNA

ASJC Scopus subject areas

  • Agricultural and Biological Sciences(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Medicine(all)

Cite this

Miyamoto-Sato, E., Fujimori, S., Ishizaka, M., Hirai, N., Masuoka, K., Saito, R., ... Yanagawa, H. (2010). A comprehensive resource of interacting protein regions for refining human transcription factor networks. PLoS One, 5(2), [e9289]. https://doi.org/10.1371/journal.pone.0009289

A comprehensive resource of interacting protein regions for refining human transcription factor networks. / Miyamoto-Sato, Etsuko; Fujimori, Shigeo; Ishizaka, Masamichi; Hirai, Naoya; Masuoka, Kazuyo; Saito, Rintaro; Ozawa, Yosuke; Hino, Katsuya; Washio, Takanori; Tomita, Masaru; Yamashita, Tatsuhiro; Oshikubo, Tomohiro; Akasaka, Hidetoshi; Sugiyama, Jun; Matsumoto, Yasuo; Yanagawa, Hiroshi.

In: PLoS One, Vol. 5, No. 2, e9289, 24.02.2010.

Research output: Contribution to journalArticle

Miyamoto-Sato, E, Fujimori, S, Ishizaka, M, Hirai, N, Masuoka, K, Saito, R, Ozawa, Y, Hino, K, Washio, T, Tomita, M, Yamashita, T, Oshikubo, T, Akasaka, H, Sugiyama, J, Matsumoto, Y & Yanagawa, H 2010, 'A comprehensive resource of interacting protein regions for refining human transcription factor networks', PLoS One, vol. 5, no. 2, e9289. https://doi.org/10.1371/journal.pone.0009289
Miyamoto-Sato E, Fujimori S, Ishizaka M, Hirai N, Masuoka K, Saito R et al. A comprehensive resource of interacting protein regions for refining human transcription factor networks. PLoS One. 2010 Feb 24;5(2). e9289. https://doi.org/10.1371/journal.pone.0009289
Miyamoto-Sato, Etsuko ; Fujimori, Shigeo ; Ishizaka, Masamichi ; Hirai, Naoya ; Masuoka, Kazuyo ; Saito, Rintaro ; Ozawa, Yosuke ; Hino, Katsuya ; Washio, Takanori ; Tomita, Masaru ; Yamashita, Tatsuhiro ; Oshikubo, Tomohiro ; Akasaka, Hidetoshi ; Sugiyama, Jun ; Matsumoto, Yasuo ; Yanagawa, Hiroshi. / A comprehensive resource of interacting protein regions for refining human transcription factor networks. In: PLoS One. 2010 ; Vol. 5, No. 2.
@article{990e3b7e4da2401f96a0ec976f05568d,
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.",
author = "Etsuko Miyamoto-Sato and Shigeo Fujimori and Masamichi Ishizaka and Naoya Hirai and Kazuyo Masuoka and Rintaro Saito and Yosuke Ozawa and Katsuya Hino and Takanori Washio and Masaru Tomita and Tatsuhiro Yamashita and Tomohiro Oshikubo and Hidetoshi Akasaka and Jun Sugiyama and Yasuo Matsumoto and Hiroshi Yanagawa",
year = "2010",
month = "2",
day = "24",
doi = "10.1371/journal.pone.0009289",
language = "English",
volume = "5",
journal = "PLoS One",
issn = "1932-6203",
publisher = "Public Library of Science",
number = "2",

}

TY - JOUR

T1 - A comprehensive resource of interacting protein regions for refining human transcription factor networks

AU - Miyamoto-Sato, Etsuko

AU - Fujimori, Shigeo

AU - Ishizaka, Masamichi

AU - Hirai, Naoya

AU - Masuoka, Kazuyo

AU - Saito, Rintaro

AU - Ozawa, Yosuke

AU - Hino, Katsuya

AU - Washio, Takanori

AU - Tomita, Masaru

AU - Yamashita, Tatsuhiro

AU - Oshikubo, Tomohiro

AU - Akasaka, Hidetoshi

AU - Sugiyama, Jun

AU - Matsumoto, Yasuo

AU - Yanagawa, Hiroshi

PY - 2010/2/24

Y1 - 2010/2/24

N2 - 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.

AB - 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.

UR - http://www.scopus.com/inward/record.url?scp=77949762977&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=77949762977&partnerID=8YFLogxK

U2 - 10.1371/journal.pone.0009289

DO - 10.1371/journal.pone.0009289

M3 - Article

VL - 5

JO - PLoS One

JF - PLoS One

SN - 1932-6203

IS - 2

M1 - e9289

ER -