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Journal
2010 | 8 | 4 | 672-682
Article title

Predicting disease-related genes by topological similarity in human protein-protein interaction network

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EN
Abstracts
EN
Predicting genes likely to be involved in human diseases is an important task in bioinformatics field. Nowadays, the accumulation of human protein-protein interactions (PPIs) data provides us an unprecedented opportunity to gain insight into human diseases. In this paper, we adopt the topological similarity in human protein-protein interaction network to predict disease-related genes. As a computational algorithm to speed up the identification of disease-related genes, the topological similarity has substantial advantages over previous topology-based algorithms. First of all, it provides a global measurement of similarity between two vertices. Secondly, quantity which can measure new topological feature has been integrated into the notion of topological similarity. Our method is specially designed for predicting disease-related genes of single disease-gene family. The proposed method is applied to human protein-protein interaction and hepatocellular carcinoma (HCC) data. The results show a significant enrichment of disease-related genes that are characterized by higher topological similarity than other genes.
Publisher

Journal
Year
Volume
8
Issue
4
Pages
672-682
Physical description
Dates
published
1 - 8 - 2010
online
22 - 5 - 2010
Contributors
author
  • Department of physics, University of Xiangtan, Xiangtan, 411105, Hunan, China, twinsheros@126.com
author
  • Department of physics, University of Xiangtan, Xiangtan, 411105, Hunan, China
author
  • Department of physics, University of Xiangtan, Xiangtan, 411105, Hunan, China, tang_yii@126.com
References
  • [1] T. P. Dryja et al., Nature 343, 364 (1990) http://dx.doi.org/10.1038/343364a0[Crossref]
  • [2] M. L. Drumm et al., Cell 62, 1227 (1990) http://dx.doi.org/10.1016/0092-8674(90)90398-X[Crossref]
  • [3] S. Fields, O. Song, Nature 340, 245 (1989) http://dx.doi.org/10.1038/340245a0[Crossref]
  • [4] A. Kumar, M. Snyder, Nature 415, 123 (2002) http://dx.doi.org/10.1038/415123a[Crossref]
  • [5] T. K. Gandhi et al., Nat. Genet. 38, 285 (2006) http://dx.doi.org/10.1038/ng1747[Crossref]
  • [6] K. R. Brown, I. Jurisica, Bioinformatics 21, 2076 (2005) http://dx.doi.org/10.1093/bioinformatics/bti273[Crossref]
  • [7] N. Lopez-Bigas, C. A. Ouzounis, Nucleic Acids Res. 32, 3108 (2004) http://dx.doi.org/10.1093/nar/gkh605[Crossref]
  • [8] M. A. Van-Driel, K. Cuelenaere, J. A. Leunissen, H. G. Brunner, Eur. J. Hum. Genet. 11, 57 (2003) http://dx.doi.org/10.1038/sj.ejhg.5200918[Crossref]
  • [9] M. Oti, B. Snel, M. A. Huynen, H. G. Brunner, J. Med. Genet. 43, 691 (2006) http://dx.doi.org/10.1136/jmg.2006.041376[Crossref]
  • [10] J. Z. Xu, Y. J. Li, Bioinformatics 22, 2800 (2006) http://dx.doi.org/10.1093/bioinformatics/btl467[Crossref]
  • [11] T. Ideker, R. Sharan, Genome. Res. 18, 644 (2008) http://dx.doi.org/10.1101/gr.071852.107[Crossref]
  • [12] Z. Tu et al., BMC Genomics 7, 1471 (2006) http://dx.doi.org/10.1186/1471-2164-7-31[Crossref]
  • [13] E. A. Leicht, P. Holme, M. E. J. Newman, Phys. Rev. E 73, 026120 (2006) http://dx.doi.org/10.1103/PhysRevE.73.026120[Crossref]
  • [14] W. H. Su et al., Nucleic Acids Res. 35, D727 (2007) http://dx.doi.org/10.1093/nar/gkl845[Crossref]
  • [15] C. C. Schimanski et al., Oncol. Rep. 16, 109 (2006) [PubMed]
  • [16] B. Schmau├čer et al., Clin. Exp. Immunol. 139, 323 (2005) http://dx.doi.org/10.1111/j.1365-2249.2005.02703.x[Crossref]
  • [17] S. Maekawa et al., Oncol. Rep. 19, 1461 (2008) [PubMed]
  • [18] M. Furutani et al., Hepatology 24, 1441 (1996) [PubMed]
  • [19] J. F. Bromberg et al., Cell 98, 295 (1999) http://dx.doi.org/10.1016/S0092-8674(00)81959-5[Crossref]
  • [20] T. Yoshida et al., J. Exp. Med. 196, 641 (2002) http://dx.doi.org/10.1084/jem.20012127[Crossref]
  • [21] H. Yoshikawa et al., Nat. Genet. 28, 29 (2001) http://dx.doi.org/10.1038/88225[Crossref]
  • [22] S. Xi et al., J. Natl. Cancer I. 98, 181 (2006) http://dx.doi.org/10.1093/jnci/djj020[Crossref]
  • [23] N Diaz et al., Clin. Cancer Res. 12, 20 (2006) http://dx.doi.org/10.1158/1078-0432.CCR-04-1749[Crossref]
  • [24] H Li et al., Clin. Cancer Res. 16, 5863 (2005) http://dx.doi.org/10.1158/1078-0432.CCR-05-0562[Crossref]
  • [25] T. K. Lee et al., Cancer Res. 66, 9948 (2006) http://dx.doi.org/10.1158/0008-5472.CAN-06-1092[Crossref]
  • [26] K. Tomoaki, N. Tamotsu, Y. Hideyo, Mol. Cell 8, 713 (2001) http://dx.doi.org/10.1016/S1097-2765(01)00349-5[Crossref]
  • [27] V. Nelson, G. E. Davis, S. A. Maxwell, Apoptosis 6, 221 (2001) http://dx.doi.org/10.1023/A:1011392811628[Crossref]
  • [28] W. T. David, J. Pathol. 180, 118 (1999)
  • [29] D. Miyamoto et al., Oncogene 27, 3508 (2008) http://dx.doi.org/10.1038/sj.onc.1211019[Crossref]
  • [30] X. He et al., Cancer Res. 68, 5591 (2008) http://dx.doi.org/10.1158/0008-5472.CAN-08-0025[Crossref]
  • [31] D. M. Euhus et al., Cancer Epidem. Biomar. 17, 1051 (2008) http://dx.doi.org/10.1158/1055-9965.EPI-07-2582[Crossref]
  • [32] C. F. Lee et al., World J. Gastroentero. 15, 356 (2009) http://dx.doi.org/10.3748/wjg.15.356[Crossref]
Document Type
Publication order reference
Identifiers
YADDA identifier
bwmeta1.element.-psjd-doi-10_2478_s11534-009-0114-9
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