Using the clustered circular layout as an informative method for visualizing protein-protein interaction networks

Proteomics

Volumn 10, Issue 14, 2010, Pages 2723-2727

  Fung, David C Y ^a   Wilkins, Marc R ^b   Hart, David ^c   Hong, Seok Hee ^a  

^a UNIVERSITY OF SYDNEY   (Australia)

^b UNIVERSITY OF NEW SOUTH WALES   (Australia)

^c Axogenic Proprietary Limited   (Australia)

Author keywords

Bioinformatics visualization; Clustered circular layout; Force directed layout; Human protein protein interaction network; Visual analytics

Indexed keywords

ARTICLE; CLUSTER ANALYSIS; CONTROLLED STUDY; DATA BASE; DNA REPLICATION; HUMAN; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN INTERACTION; PROTEIN LOCALIZATION;

ALGORITHMS; CLUSTER ANALYSIS; COMPUTER GRAPHICS; DNA REPLICATION; HUMANS; PROTEIN BINDING; PROTEIN INTERACTION MAPPING;

EID: 77954718394     PISSN: 16159853     EISSN: 16159861     Source Type: Journal    
DOI: 10.1002/pmic.201000046     Document Type: Article

References (17)

1. Suderman, M., Hallett, M., Tools for visually exploring biological networks. Bioinformatics 2007, 23, 2651-2659. (Pubitemid 350048327)
2. Merico, D., Gfeller, D., Bader, G. D., How to visually interpret biological data using networks? Nat. Biotech. 2009, 27, 921-924.
3. Kim, P. M., Lu, L. J., Xia, Y., Gerstein, M. B., Relating three-dimensional structures to protein networks provide evolutionary insights. Science 2006, 314, 1938-1941. (Pubitemid 46026118)
4. Han, J. D., Bertin, N., Hao, T., Goldberg, D. S. et al., Evidence for dynamically organized modularity in the yeast protein-protein interaction network. Nature 2004, 430, 88-95.
5. Yu, H., Kim, P. M., Sprecher, E., Trifonov, V., Gerstein, M., The importance of bottlenecks in protein networks: correlation with gene essentiality and expression dynamics. PLoS Computational. Biol. 2007, 3, e59.
6. Tornow, S., Mewes, H. W., Functional modules by relating protein interaction networks and gene expression. Nucleic Acids Res. 2003, 31, 6283-6289. (Pubitemid 37442357)
7. Rives, A. W., Galitski, T., Modular organization of cellular network. Proc. Natl. Acad. Sci. USA 2003, 100, 1128-1133.
8. Alon, U., Network motifs in developmental, signal transduction, and the neuronal networks. In: An Introduction to Systems Biology: Design Principles of Biological Circuits, Mathematical and Computational Biology Series, Chapman & Hall/CRC, London, Boca Rotan 2007, pp. 97-134.
9. Fruchterman, T. M. J., Rheingold, E. M., Graph drawing by force-directed placement. Software Pract. Exper. 1991, 21, 1129-1164.
10. Gene Ontology Consortium. The Gene Ontology (GO) project in 2006. Nucleic Acids Res. 2006, 34, D322-D326.
11. Iragne, F., Nikolski, M., Mathieu, B., Auber, D., Sherman, D., ProViz: protein interaction visualization and exploration. Bioinformatics 2005, 21, 272-274. (Pubitemid 40202032)
12. Breitkreutz, B. J., Stark, C., Reguly, T., Boucher, L. et al., The BioGRID Interaction database: 2008 update. Nucleic Acids Res. 2008, 36, D637-D640.
13. Ahmed, A., Dwyer, T., Forster, M., Xu, K. et al., GEOMI: geometry for maximum insight. Lect. Notes in Computer Sci. 2006, 3843, 468-479.
14. Ho, E., Webber, R., Wilkins, M. R., Interactive three-dimensional visualization and contextual analysis of protein interaction networks. J. Proteome Res. 2008, 7, 104-112. (Pubitemid 351171121)
15. Dafonesca, C. J., Shu, F., Zhang, J. J., Identification of two residuals in MCM5 critical for the assembly of the MCM complexes and Stat1-mediated transcription activation in response to IFN-γ. Proc. Natl. Acad. Sci. USA 2001, 98, 3034-3039.
16. Fan, Z., Beresford, P. J., Zhang, D., Lieberman, J., HMG2 interacts with the nucleosome assembly protein SET and is a target of the cytotoxic T-lymphocyte protease granzyme A. Mol. Cell. Biol. 2002, 22, 2810-2820.
17. Bustin, M., Regulation of DNA-dependent activities by the functional motifs of the high-mobility-group chromosomal proteins. Mol. Cell. Biol. 1999, 19, 5237-5246.