Prediction of human disease-related gene clusters by clustering analysis

International Journal of Biological Sciences

Volumn 7, Issue 1, 2011, Pages 61-73

  Sun, Peng Gang ^a   Gao, Lin ^a   Han, Shan ^b  

^a XIDIAN UNIVERSITY   (China)

^b UNIVERSITY OF COPENHAGEN   (Denmark)

Author keywords

Clustering analysis; Disease related gene cluster; Gene expression data; PPI network

Indexed keywords

EID: 79952457046     PISSN: 14492288     EISSN: None     Source Type: Journal    
DOI: 10.7150/ijbs.7.61     Document Type: Article

References (29)

1. Kann M. G. Protein interactions and disease: Computational approaches to uncover the etiology of diseases. Brief. Bioin-form. 2007; 8: 333-346.
2. Ideker T., Sharan R. Protein networks in disease. Genome Res. 2008; 18: 644-652.
3. Qiu Y.-Q., Zhang S., Zhang X.-S., Chen L. Detecting disease associated modules and prioritizing active genes based on high throughput data. BMC Bioinformatics 2010; 11: 1-13.
4. Karni S., Soreq H., Sharan R. A network-based method for predicting disease-causing Genes. Journal of Computational Biology 2009; 16: 181-189.
5. Calvano S.E., Xiao W., Richards D.R., et al. A network-based analysis of systemic inflammation in humans. Nature 2005; 437: 1032-1037.
6. Ghazalpour A., Doss S., Zhang B., et al. Integrating genetic and network analysis to characterize genes related to mouse weight. PLoS Genet. 2006; 2: 1-12.
7. Lim J., Hao T., Shaw C., et al. A protein-protein interaction network for human inherited ataxias and disorders of Purkinje cell degeneration. Cell 2006; 125: 801-814.
8. Pujana M.A., Han J.D., Starita L.M., et al. Network modeling links breast cancer susceptibility and centrosome dysfunction. Nat. Genet. 2007; 39: 1338-1349.
9. Oti M., Snel B., Huynen M.A., Brunner H.G. Predicting disease genes using protein-protein interactions. J. Med. Genet. 2006; 43: 691-698.
10. Franke L., Bakel H., Fokkens L., et al. Reconstruction of a func-tional human gene network, with an application for prioritizing positional candidate genes. Am. J. Hum. Genet. 2006; 78: 1011-1025.
11. Chen J., Aronow B. J., Jegga A. G. Disease candidate gene iden-tification and prioritization using protein interaction networks. BMC Bioinformatics 2009; 10:73-82.
12. Lage K., Karlberg E.O., Storling Z.M., et al. A human phe-nome-interactome network of protein complexes implicated in genetic disorders. Nat. Biotechnol. 2007; 25: 309-316.
13. Fraser H.B., Plotkin J. B. Using protein complexes to predict phenotypic effects of gene. Mutation Genome Biology 2007; 8: 252-261.
14. Goh K.-I., Cusick M. E., Valle D., et al. The human disease network. PNAS 2007; 104: 8685-8690.
15. Jonsson P.F., Bates P.A. Global topological features of cancer proteins in the human interactome. Bioinformatics 2006; 22: 2291-2297.
16. Futreal P.A., Coin L., Marshall M., et al. A census of human cancer genes. Nat. Rev. Cancer 2004; 4: 177-183.
17. Hamosh A., Scott A.F., Amberger J.S., et al. Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders. Nucleic Acids Res. 2005; 33: D514-D517.
18. Rual, J.-F., Venkatesan K., Hao T., et al. Towards a prote-ome-scale map of the human protein-protein interaction net-work. Nature 2005; 437:1173-1178.
19. Stelzl U., Worm U., Lalowski M., et al. A human protein-protein interaction network: a resource for annotating the proteome. Cell 2005; 122: 957-968.
20. Ge X., Yamamoto S., Tsutsumi S., et al. Interpreting expression profiles of cancers by genome-wide survey of breadth-of-expression in normal tissues. Genomics 2005; 86: 127-141.
21. Bader G. D., Hogue C.W. An automated method for finding molecular complexes in large protein interaction networks. BMC Bioinformatics 2003; 4:1-17.
22. Dongen S.V. Graph clustering by flow simulation; PhD thesis. Centers for mathematics and computer science, University of Utrecht. 2000.
23. Enright A.J., Van Dongen S., Ouzounis C. A. An efficient algo-rithm for large-scale detection of protein families. Nucleic Acids Res. 2002; 30:1575-1584.
24. Palla G., Derényi I., Farkas I., Vicsek T. Uncovering the over-lapping community structure of complex networks in nature and society. Nature 2005; 435: 814-818.
25. Warrington J.A., NAIR A., Mahadevappa M., Tsyganskaya M. Comparison of human adult and fetal expression and identifi-cation of 535 housekeeping/maintenance genes. Physiol. Ge-nomics 2000; 2:143-147.
26. Watson J.D., Hopkins N.H., Roberts J.W., Steitz J.A., Weiner A.M. The functioning of higher eukaryotic genes. Molecular Biology of the Gene. 1965; 1:704-713.
27. Ashburner M., Ball C.A., Blake J. A. et al. The Gene Ontology Consortium Gene ontology: tool for the unification of biology. Nat. Genet. 2000; 25: 25-29.
28. Sharan R., Ideker T. Modeling cellular machinery through biological network comparison. Nat. Biotech. 2006; 24: 427-433.
29. Vanunu O., Magger O., Ruppin E., Tomer S., Sharan R. Asso-ciating Genes and Protein Complexes with Disease via Network Propagation. PLoS Comput. Biol. 2010; 6: 641-52.