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A protein interaction atlas for the nuclear receptors: properties and quality of a hub-based dimerisation network

Grigoris Amoutzias UGent, Elgar E. Pichler, Nina Mian, David De Graaf, Anastasia Imsiridou, Marc Robinson-Rechavi, Erich Bornberg-Bauer, David L. Robertson and Stephen G. Oliver (2007) BMC SYSTEMS BIOLOGY. 1.
abstract
Background: The nuclear receptors are a large family of eukaryotic transcription factors that constitute major pharmacological targets. They exert their combinatorial control through homotypic heterodimerisation. Elucidation of this dimerisation network is vital in order to understand the complex dynamics and potential cross-talk involved. Results: Phylogeny, protein-protein interactions, protein-DNA interactions and gene expression data have been integrated to provide a comprehensive and up-to-date description of the topology and properties of the nuclear receptor interaction network in humans. We discriminate between DNA-binding and non-DNA-binding dimers, and provide a comprehensive interaction map, that identifies potential cross-talk between the various pathways of nuclear receptors. Conclusion: We infer that the topology of this network is hub-based, and much more connected than previously thought. The hub-based topology of the network and the wide tissue expression pattern of NRs create a highly competitive environment for the common heterodimerising partners. Furthermore, a significant number of negative feedback loops is present, with the hub protein SHP [ NR0B2] playing a major role. We also compare the evolution, topology and properties of the nuclear receptor network with the hub-based dimerisation network of the bHLH transcription factors in order to identify both unique themes and ubiquitous properties in gene regulation. In terms of methodology, we conclude that such a comprehensive picture can only be assembled by semi-automated text-mining, manual curation and integration of data from various sources.
Please use this url to cite or link to this publication:
author
organization
year
type
journalArticle (original)
publication status
published
keyword
EXPRESSION, SUPERFAMILY, X-RECEPTOR, HORMONE RECEPTORS, ESTROGEN-RECEPTORS, ORPHAN RECEPTORS, GENE NETWORKS, DNA-BINDING, SMALL-WORLD, UNION-OF-PHARMACOLOGY
journal title
BMC SYSTEMS BIOLOGY
BMC Syst. Biol.
volume
1
Web of Science type
Article
Web of Science id
000250004000001
ISSN
1752-0509
language
English
UGent publication?
yes
classification
A1
id
744049
handle
http://hdl.handle.net/1854/LU-744049
date created
2009-09-09 09:01:06
date last changed
2012-09-19 14:04:34
@article{744049,
  abstract     = {Background: The nuclear receptors are a large family of eukaryotic transcription factors that constitute major pharmacological targets. They exert their combinatorial control through homotypic heterodimerisation. Elucidation of this dimerisation network is vital in order to understand the complex dynamics and potential cross-talk involved.

Results: Phylogeny, protein-protein interactions, protein-DNA interactions and gene expression data have been integrated to provide a comprehensive and up-to-date description of the topology and properties of the nuclear receptor interaction network in humans. We discriminate between DNA-binding and non-DNA-binding dimers, and provide a comprehensive interaction map, that identifies potential cross-talk between the various pathways of nuclear receptors.

Conclusion: We infer that the topology of this network is hub-based, and much more connected than previously thought. The hub-based topology of the network and the wide tissue expression pattern of NRs create a highly competitive environment for the common heterodimerising partners. Furthermore, a significant number of negative feedback loops is present, with the hub protein SHP [ NR0B2] playing a major role. We also compare the evolution, topology and properties of the nuclear receptor network with the hub-based dimerisation network of the bHLH transcription factors in order to identify both unique themes and ubiquitous properties in gene regulation. In terms of methodology, we conclude that such a comprehensive picture can only be assembled by semi-automated text-mining, manual curation and integration of data from various sources.},
  author       = {Amoutzias, Grigoris and Pichler, Elgar E. and Mian, Nina and De Graaf, David and Imsiridou, Anastasia and Robinson-Rechavi, Marc and Bornberg-Bauer, Erich and Robertson, David L. and Oliver, Stephen G.},
  issn         = {1752-0509},
  journal      = {BMC SYSTEMS BIOLOGY},
  keyword      = {EXPRESSION,SUPERFAMILY,X-RECEPTOR,HORMONE RECEPTORS,ESTROGEN-RECEPTORS,ORPHAN RECEPTORS,GENE NETWORKS,DNA-BINDING,SMALL-WORLD,UNION-OF-PHARMACOLOGY},
  language     = {eng},
  title        = {A protein interaction atlas for the nuclear receptors: properties and quality of a hub-based dimerisation network},
  volume       = {1},
  year         = {2007},
}

Chicago
Amoutzias, Grigoris, Elgar E. Pichler, Nina Mian, David De Graaf, Anastasia Imsiridou, Marc Robinson-Rechavi, Erich Bornberg-Bauer, David L. Robertson, and Stephen G. Oliver. 2007. “A Protein Interaction Atlas for the Nuclear Receptors: Properties and Quality of a Hub-based Dimerisation Network.” Bmc Systems Biology 1.
APA
Amoutzias, G., Pichler, E. E., Mian, N., De Graaf, D., Imsiridou, A., Robinson-Rechavi, M., Bornberg-Bauer, E., et al. (2007). A protein interaction atlas for the nuclear receptors: properties and quality of a hub-based dimerisation network. BMC SYSTEMS BIOLOGY, 1.
Vancouver
1.
Amoutzias G, Pichler EE, Mian N, De Graaf D, Imsiridou A, Robinson-Rechavi M, et al. A protein interaction atlas for the nuclear receptors: properties and quality of a hub-based dimerisation network. BMC SYSTEMS BIOLOGY. 2007;1.
MLA
Amoutzias, Grigoris, Elgar E. Pichler, Nina Mian, et al. “A Protein Interaction Atlas for the Nuclear Receptors: Properties and Quality of a Hub-based Dimerisation Network.” BMC SYSTEMS BIOLOGY 1 (2007): n. pag. Print.