Vavien: An algorithm for prioritizing candidate disease genes based on topological similarity of proteins in interaction networks

Journal of Computational Biology

Volumn 18, Issue 11, 2011, Pages 1561-1574

  Erten, Sinan ^a   Bebek, Gurkan ^b,c   Koyutürk, Mehmet ^a,b  

^a Case Western Reserve University   (United States)

^b CASE WESTERN RESERVE UNIVERSITY SCHOOL OF MEDICINE   (United States)

^c LERNER RESEARCH INSTITUTE   (United States)

Author keywords

algorithms; computational molecular biology

Indexed keywords

LINK PROTEIN; P2RX7 PROTEIN, HUMAN; PROTEOGLYCAN; PURINERGIC P2X7 RECEPTOR; SCLEROPROTEIN;

ALGORITHM; ARTICLE; BIOLOGICAL MODEL; COMPUTER SIMULATION; GENETIC ASSOCIATION; GENETICS; HUMAN; METHODOLOGY; NEOPLASM; PROTEIN PROTEIN INTERACTION; STATISTICAL MODEL;

ALGORITHMS; COMPUTER SIMULATION; EXTRACELLULAR MATRIX PROTEINS; GENOME-WIDE ASSOCIATION STUDY; HUMANS; LOGISTIC MODELS; MODELS, GENETIC; NEOPLASMS; PROTEIN INTERACTION MAPS; PROTEOGLYCANS; RECEPTORS, PURINERGIC P2X7;

EID: 80955159942     PISSN: 10665277     EISSN: None     Source Type: Journal    
DOI: 10.1089/cmb.2011.0154     Document Type: Article

References (58)

1. Adie, E., Adams, R., Evans, K., et al. 2006. SUSPECTS: enabling fast and effective prioritization of positional candidates. Bioinformatics 226, 773-774.
2. Aerts, S., Lambrechts, D., Maity, S., et al. 2006. Gene prioritization through genomic data fusion. Nat. Biotech. 24, 537-544.
3. Banks, E., Nabieva, E., Peterson, R., et al. 2008. NETGREP: fast network schema searches in interactomes. Genome Biol. 9, 9.
4. Barrett, T., Troup, D. B., and Edgar, R. 2009. NCBI GEO: archive for high-throughput functional genomic data. Nucleic Acids Res. 37, D885-D890.
5. Bebek, G., Patel, V., and Chance, M. R. 2010. PETALS: Proteomic evaluation and topological analysis of a mutated locus' signaling. BMC Bioinform. 11, 596.
6. Bebek, G., and Yang, J. 2007. Pathfinder: mining signal transduction pathway segments from protein-protein interaction networks. BMC Bioinform. 8, 335.
7. Bogdanov, P., and Singh, A. K. 2010. Molecular function prediction using neighborhood features. IEEE/ACM Trans. Comput. Biol. Bioinform. 7, 208-217.
8. Brunner, H. G., and van Driel, M. A. 2004. From syndrome families to functional genomics. Nat. Rev. Genet. 5, 545-551. (Pubitemid 38868510)
9. Chen, J., Aronow, B., and Jegga, A. 2009a. Disease candidate gene identification and prioritization using protein interaction networks. BMC Bioinform. 10, 73.
10. Chen, J., Bardes, E. E., Aronow, B. J., et al. 2009b. TOPP-gene suite for gene list enrichment analysis and candidate gene prioritization. Nucleic Acids Res. 37, gkp427.
11. Erten, S., Bebek, G., Ewing, R. M., et al. 2011. DADA-degree-aware disease gene prioritization. BioData Mining 4 (19).
12. Erten, S., and Koyutürk, M. 2010. Role of centrality in network-based prioritization of disease genes. Lect. Notes Comput. Sci. 6023, 13-25.
13. Ewing, R. M., Chu, P., Elisma, F., et al. 2007. Large-scale mapping of human protein-protein interactions by mass spectrometry. Mol. Syst. Biol. 3.
14. Franke, L., Bakel, H., Fokkens, L., et al. 2006. Reconstruction of a functional human gene network, with an application for prioritizing positional candidate genes. Am. J. Hum. Genet. 78, 1011-1025. (Pubitemid 43787692)
15. Glazier, A. M., Nadeau, J. H., and Aitman, T. J. 2002. Finding genes that underlie complex traits. Science 298, 2345-2349. (Pubitemid 36014199)
16. Goh, K.-I., Cusick, M. E., Valle, D., et al. 2007. The human disease network. Proc. Natl. Acad. Sci. USA 104, 8685-8690. (Pubitemid 47175372)
17. Goldberg, D. S., and Roth, F. P. 2003. Assessing experimentally derived interactions in a small world. Proc. Natl. Acad. Sci. USA 100, 4372-4376. (Pubitemid 36457736)
18. Halberg, R. B., Chen, X., Amos-Landgraf, J. M., et al. 2008. The pleiotropic phenotype of apc mutations in the mouse: allele specificity and effects of the genetic background. Genetics 180, 601-609.
19. Ideker, T. and Sharan, R. 2008. Protein networks in disease. Genome Res. 18, 644-652. (Pubitemid 351482789)
20. Karni, S., Soreq, H., and Sharan, R. 2009. A network-based method for predicting disease-causing genes. J. Comput. Biol. 16, 181-189.
21. Kelley, B. P., Sharan, R., and Ideker, T. 2003. Conserved pathways within bacteria and yeast as revealed by global protein network alignment. Proc. Natl. Acad. Sci. USA 100, 11394-11399. (Pubitemid 37205946)
22. Kelley, R., and Ideker, T. 2005. Systematic interpretation of genetic interactions using protein networks. Nat. Biotechnol. 23, 561-566. (Pubitemid 41724894)
23. Kirac, M., Özsoyoglu, G., and Yang, J. 2006. Annotating proteins by mining protein interaction networks. Proc. ISMB 260-270.
24. Kirac, M., and Özsoyoglu, G. 2008. Protein function prediction based on patterns in biological networks. Proc. RECOMB 197-213.
25. Köhler, S., Bauer, S., Horn, D., et al. 2008. Walking the interactome for prioritization of candidate disease genes. Am. J. Hum. Genet. 82, 949-958.
26. Koyutürk, M., Kim, Y., Topkara, U., et al. 2006. Pairwise alignment of protein interaction networks. J. Comput Biol. 13, 182-199.
27. Lage, K., Karlberg, E., Storling, Z., et al. 2007. A human phenome-interactome network of protein complexes implicated in genetic disorders. Nat. Biol. 25, 309-316. (Pubitemid 46402863)
28. Li, J., Lee, B., and Lee, A. S. 2006. Endoplasmic reticulum stress-induced apoptosis. J. Biol. Chem. 281, 7260-7270.
29. Lovász, L. 1996. Random walks on graphs: a survey. Paul Erdos is Eighty. Combinatorics 2, 353-398.
30. Macropol, K., Can, T., and Singh, A. 2009. RRW: repeated random walks on genome-scale protein networks for local cluster discovery. BMC Bioinform. 10, 283.
31. Maglott, D., Ostell, J., Pruitt, K. D., et al. 2007. ENTREZ GENE: gene-centered information at NCBI. Nucleic Acids Res. 35, D26-D31. (Pubitemid 46056164)
32. Marsh, V., Winton, D. J., Williams, G. T., et al. 2008. Epithelial PTEN is dispensable for intestinal homeostasis but suppresses adenoma development and progression after APC mutation. Nat. Genet. 40, 1436-1444.
33. Mewes, H. W., Amid, C., Arnold, R., et al. 2004. MIPS: analysis and annotation of proteins from whole genomes. Nucleic Acids Res. 32, D41-D44. (Pubitemid 38081600)
34. Missiuro, P. V. V., Liu, K., Zou, L., et al. 2009. Information flow analysis of interactome networks. PLoS comput. Biol. 5, e1000350.
35. Nabieva, E., Jim, K., Agarwal, A., et al. 2005. Whole-proteome prediction of protein function via graph-theoretic analysis of interaction maps. Bioinformatics 21, i302-i310. (Pubitemid 41794502)
36. Navlakha, S., and Kingsford, C. 2010. The power of protein interaction networks for associating genes with diseases. Bioinformatics 26, 1057-1063.
37. Nica, A. C., and Dermitzakis, E. T. 2008. Using gene expression to investigate the genetic basis of complex disorders. Hum. Mol. Genet. 17, ddn285-134.
38. Oti, M., Snel, B., Huynen, M. A., et al. 2006. Predicting disease genes using protein-protein interactions. J. Med. Genet. jmg. 2006. 041376.
39. Pandey, J., Koyutürk, M., and Grama, A. 2010. Functional characterization and topological modularity of molecular interaction networks. BMC Bioinform. 11, S35.
40. Pandey, J., Koyutürk, M., Kim, Y., et al. 2007. Functional annotation of regulatory pathways. Bioinformatics 23, i377-i386. (Pubitemid 47244423)
41. Patel, V. N., Bebek, G., Mariadason, J. M., et al. 2010. Prediction and testing of biological networks underlying intestinal cancer. PLoS ONE 5, e12497.
42. Rhodes, D. R., and Chinnaiyan, A. M. 2005. Integrative analysis of the cancer transcriptome. Nat. Genet. 37 Suppl.
43. Sharan, R., Suthram, S., Kelley, R. M., et al. 2005. Conserved patterns of protein interaction in multiple species. Proc. Natl. Acad. Sci. USA 102, 1974-1979. (Pubitemid 40261997)
44. Sjöblom, T., Jones, S., Wood, L. D., et al. 2006. The consensus coding sequences of human breast and colorectal cancers. Science 314, 268-274. (Pubitemid 44571966)
45. Smialowski, P., Pagel, P., Wong, P., et al. 2010. The Negatome Database: a reference set of non-interacting protein pairs. Nucleic Acids Res. 38, D540-D544.
46. Spielman, D. A., and Srivastava, N. 2008. Graph sparsification by effective resistances. Proc. STOC 563-568.
47. Sprenger, J., Lynn Fink, J., Karunaratne, S., et al. 2008. LOCATE: a mammalian protein subcellular localization database. Nucleic Acids Res. 36, D230-D233. (Pubitemid 351149727)
48. Stumpf, M. P. H., Thorne, T., and de Silva, E. A. 2008. Estimating the size of the human interactome. Proc. Natl. Acad. Sci. USA 105, 6959-6964. (Pubitemid 351754512)
49. Suthram, S., Shlomi, T., Ruppin, E., et al. 2006. A direct comparison of protein interaction confidence assignment schemes. BMC Bioinform. 7, 360.
50. Tetali, P. 1991. Random walks and the effective resistance of networks. J. Theor. Probabil. 4, 101-109.
51. Tong, H., and Faloutsos, C. 2006. Center-piece subgraphs: problem definition and fast solutions. Proc. 12th ACM SIGKDD 404-413. (Pubitemid 44535537)
52. Tong, H., Faloutsos, C., and Pan, J.-Y. 2008. Random walk with restart: fast solutions and applications. Knowledge Inform. Syst. 14, 327-346.
53. Turner, F., Clutterbuck, D., and Semple, C. 2003. POCUS: mining genomic sequence annotation to predict disease genes. Genome Biol. 4, R75.
54. van Driel, M. A., Bruggeman, J., Vriend, G., et al. 2006. A text-mining analysis of the human phenome. EJHG 14, 535-542.
55. Vanunu, O., Magger, O., Ruppin, E., et al. 2010. Associating genes and protein complexes with disease via network propagation. PLoS Comput. Biol. 6, e1000641.
56. Wood, L. D., Parsons, D. W., Jones, S., et al. 2007. The genomic landscapes of human breast and colorectal cancers. Science 318, 1108-1113. (Pubitemid 350134889)
57. Wu, X., Jiang, R., Zhang, M. Q., et al. 2008. Network-based global inference of human disease genes. Mol. Syst. Biol. 4.
58. Zhang, L., Hu, K., and Tang, Y. 2010. Predicting disease-related genes by topological similarity in human proteinprotein interaction network. Central Eur. J. Phys. 8, 672-682.