Ghent University Academic Bibliography

Advanced

An exploration of alternative visualisations of the basic helix-loop-helix protein interaction network

Brian J. Holden, John W. Pinney, Simon C. Lovell, Grigoris Amoutzias UGent and David L. Robertson (2007) BMC BIOINFORMATICS. 8. p.289-1-289-12
abstract
Background: Alternative representations of biochemical networks emphasise different aspects of the data and contribute to the understanding of complex biological systems. In this study we present a variety of automated methods for visualisation of a protein-protein interaction network, using the basic helix-loop-helix ( bHLH) family of transcription factors as an example. Results: Network representations that arrange nodes ( proteins) according to either continuous or discrete information are investigated, revealing the existence of protein sub-families and the retention of interactions following gene duplication events. Methods of network visualisation in conjunction with a phylogenetic tree are presented, highlighting the evolutionary relationships between proteins, and clarifying the context of network hubs and interaction clusters. Finally, an optimisation technique is used to create a three-dimensional layout of the phylogenetic tree upon which the protein-protein interactions may be projected. Conclusion: We show that by incorporating secondary genomic, functional or phylogenetic information into network visualisation, it is possible to move beyond simple layout algorithms based on network topology towards more biologically meaningful representations. These new visualisations can give structure to complex networks and will greatly help in interpreting their evolutionary origins and functional implications. Three open source software packages (InterView, TVi and OptiMage) implementing our methods are available.
Please use this url to cite or link to this publication:
author
organization
year
type
journalArticle (original)
publication status
published
keyword
EVOLUTION, PHYLOGENETIC TREES, GENE DUPLICATION, HYPERBOLIC SPACE, GENOMICS, MAP, ENVIRONMENT, ALGORITHM, BIOLOGICAL NETWORKS, TRANSCRIPTION FACTORS
journal title
BMC BIOINFORMATICS
BMC BIOINFORMATICS
volume
8
pages
289-1 - 289-12
Web of Science type
Article
Web of Science id
000249274200001
JCR category
MATHEMATICAL & COMPUTATIONAL BIOLOGY
JCR impact factor
3.493 (2007)
JCR rank
3/24 (2007)
JCR quartile
1 (2007)
ISSN
1471-2105
DOI
10.1186/1471-2105-8-289
language
English
UGent publication?
yes
classification
A1
id
743832
handle
http://hdl.handle.net/1854/LU-743832
date created
2009-09-09 09:00:49
date last changed
2016-12-19 15:45:00
@article{743832,
  abstract     = {Background: Alternative representations of biochemical networks emphasise different aspects of the data and contribute to the understanding of complex biological systems. In this study we present a variety of automated methods for visualisation of a protein-protein interaction network, using the basic helix-loop-helix ( bHLH) family of transcription factors as an example.

Results: Network representations that arrange nodes ( proteins) according to either continuous or discrete information are investigated, revealing the existence of protein sub-families and the retention of interactions following gene duplication events. Methods of network visualisation in conjunction with a phylogenetic tree are presented, highlighting the evolutionary relationships between proteins, and clarifying the context of network hubs and interaction clusters. Finally, an optimisation technique is used to create a three-dimensional layout of the phylogenetic tree upon which the protein-protein interactions may be projected.

Conclusion: We show that by incorporating secondary genomic, functional or phylogenetic information into network visualisation, it is possible to move beyond simple layout algorithms based on network topology towards more biologically meaningful representations. These new visualisations can give structure to complex networks and will greatly help in interpreting their evolutionary origins and functional implications. Three open source software packages (InterView, TVi and OptiMage) implementing our methods are available.},
  author       = {Holden, Brian J. and Pinney, John W. and Lovell, Simon C. and Amoutzias, Grigoris and Robertson, David L.},
  issn         = {1471-2105},
  journal      = {BMC BIOINFORMATICS},
  keyword      = {EVOLUTION,PHYLOGENETIC TREES,GENE DUPLICATION,HYPERBOLIC SPACE,GENOMICS,MAP,ENVIRONMENT,ALGORITHM,BIOLOGICAL NETWORKS,TRANSCRIPTION FACTORS},
  language     = {eng},
  pages        = {289-1--289-12},
  title        = {An exploration of alternative visualisations of the basic helix-loop-helix protein interaction network},
  url          = {http://dx.doi.org/10.1186/1471-2105-8-289},
  volume       = {8},
  year         = {2007},
}

Chicago
Holden, Brian J., John W. Pinney, Simon C. Lovell, Grigoris Amoutzias, and David L. Robertson. 2007. “An Exploration of Alternative Visualisations of the Basic Helix-loop-helix Protein Interaction Network.” Bmc Bioinformatics 8: 289–1–289–12.
APA
Holden, B. J., Pinney, J. W., Lovell, S. C., Amoutzias, G., & Robertson, D. L. (2007). An exploration of alternative visualisations of the basic helix-loop-helix protein interaction network. BMC BIOINFORMATICS, 8, 289–1–289–12.
Vancouver
1.
Holden BJ, Pinney JW, Lovell SC, Amoutzias G, Robertson DL. An exploration of alternative visualisations of the basic helix-loop-helix protein interaction network. BMC BIOINFORMATICS. 2007;8:289–1–289–12.
MLA
Holden, Brian J., John W. Pinney, Simon C. Lovell, et al. “An Exploration of Alternative Visualisations of the Basic Helix-loop-helix Protein Interaction Network.” BMC BIOINFORMATICS 8 (2007): 289–1–289–12. Print.