Analysis of the robustness of network-based disease-gene prioritization methods reveals redundancy in the human interactome and functional diversity of disease-genes

PLoS ONE

Volumn 9, Issue 4, 2014, Pages

  Guney, Emre ^a   Oliva, Baldo ^b  

^a NORTHEASTERN UNIVERSITY   (United States)

^b UNIVERSITAT POMPEU FABRA   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BIOINFORMATICS; COMPUTER MODEL; COMPUTER PREDICTION; DISEASE ASSOCIATION; GENE IDENTIFICATION; GENE INTERACTION; GENE ONTOLOGY; GENE REGULATORY NETWORK; GENE TECHNOLOGY; GENETIC ASSOCIATION; GENETIC DATABASE; GENETIC VARIABILITY; GENOTYPE PHENOTYPE CORRELATION; INHERITANCE; MOLECULAR PATHOLOGY; PERFORMANCE MEASUREMENT SYSTEM; PROTEIN PROTEIN INTERACTION; SIGNAL NOISE RATIO; SYSTEMS BIOLOGY; ALGORITHM; AREA UNDER THE CURVE; BIOLOGICAL MODEL; BIOLOGY; GENE EXPRESSION REGULATION; GENETIC DISORDER; GENETICS; HUMAN; METABOLISM; MUTATION; PHENOTYPE; PROCEDURES; PROTEIN ANALYSIS; STATISTICAL MODEL;

PROTEIN;

ALGORITHMS; AREA UNDER CURVE; COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; GENE EXPRESSION REGULATION; GENE REGULATORY NETWORKS; GENETIC DISEASES, INBORN; HUMANS; MODELS, GENETIC; MODELS, STATISTICAL; MUTATION; PHENOTYPE; PROTEIN INTERACTION MAPPING; PROTEIN INTERACTION MAPS; PROTEINS;

EID: 84899643468     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0094686     Document Type: Article

References (46)

1. Morohashi M, Winn AE, Borisuk MT, Bolouri H, Doyle J, et al. (2002) Robustness as a measure of plausibility in models of biochemical networks. Journal of theoretical biology 216: 19-30. (Pubitemid 34748054)
2. Hartwell LH, Hopfield JJ, Leibler S, Murray AW (1999) From molecular to modular cell biology. Nature 402: C47-52.
3. Agrawal AA (2001) Phenotypic plasticity in the interactions and evolution of species. Science 294: 321-326. (Pubitemid 32963392)
4. Kitano H (2004) Biological robustness. Nat Rev Genet 5: 826-837. (Pubitemid 39457498)
5. Carlson JM, Doyle J (2002) Complexity and robustness. Proc Natl Acad Sci U S A 99 Suppl 1: 2538-2545. (Pubitemid 34165063)
6. Altshuler D, Daly MJ, Lander ES (2008) Genetic Mapping in Human Disease. Science 322: 881-888. doi:10.1126/science.1156409.
7. Oti M, Snel B, Huynen MA, Brunner HG (2006) Predicting disease genes using protein-protein interactions. J Med Genet 43: 691-698. (Pubitemid 44214908)
8. Xu J, Li Y (2006) Discovering disease-genes by topological features in human protein-protein interaction network. Bioinformatics 22: 2800-2805. (Pubitemid 44742401)
9. Pujana MA, Han JD, Starita LM, Stevens KN, Tewari M, et al. (2007) Network modeling links breast cancer susceptibility and centrosome dysfunction. Nat Genet 39: 1338-1349. (Pubitemid 350035000)
10. Kohler S, Bauer S, Horn D, Robinson PN (2008) Walking the Interactome for Prioritization of Candidate Disease Genes. The American Journal of Human Genetics 82: 949-958. doi:10.1016/j.ajhg.2008.02.013.
11. Chen J, Aronow B, Jegga A (2009) Disease candidate gene identification and prioritization using protein interaction networks. BMC bioinformatics 10: 73.
12. Navlakha S, Kingsford C (2010) The Power of Protein Interaction Networks for Associating Genes with Diseases. Bioinformatics 26: 1057-1063. doi:10.1093/bioinformatics/btq076.
13. Akula N, Baranova A, Seto D, Solka J, Nalls MA, et al. (2011) A Network-Based Approach to Prioritize Results from Genome-Wide Association Studies. PloS one 6: e24220.
14. Lee I, Blom UM, Wang PI, Shim JE, Marcotte EM (2011) Prioritizing candidate disease genes by network-based boosting of genome-wide association data. Genome Res 21: 1109-1121. doi:10.1101/gr.118992.110.
15. Guney E, Oliva B (2012) Exploiting Protein-Protein Interaction Networks for Genome-Wide Disease-Gene Prioritization. PLoS ONE 7: e43557. doi:10.1371/journal.pone.0043557.
16. Jeong H, Tombor B, Albert R, Oltvai ZN, Barabasi AL (2000) The large-scale organization of metabolic networks. Nature 407: 651-654.
17. Jeong H, Mason SP, Barabasi AL, Oltvai ZN (2001) Lethality and centrality in protein networks. Nature 411: 41-42. (Pubitemid 32428180)
18. Huang C-H, Fang J-F, Tsai J, Ng K-L (2006) Topological Robustness of the Protein-Protein Interaction Networks Systems Biology and Regulatory Genomics. In: Eskin E, Ideker T, Raphael B, Workman C, editors. Lecture Notes in Computer Science. Springer Berlin/Heidelberg. pp. 166-177. Available: http://dx.doi.org/10.1007/978-3-540-48540-7-14 DO-10.1007/978-3-540-48540-7-14.
19. Demongeot J, Ben Amor H, Elena A, Gillois P, Noual M, et al. (2009) Robustness in regulatory interaction networks. A generic approach with applications at different levels: physiologic, metabolic and genetic. Int J Mol Sci 10: 4437-4473.
20. Rizk A, Batt G, Fages F, Soliman S (2009) A General Computational Method for Robustness Analysis with Applications to Synthetic Gene Networks. Bioinformatics 25: i169-i178. doi:10.1093/bioinformatics/btp200.
21. Amberger J, Bocchini CA, Scott AF, Hamosh A (2009) McKusick's Online Mendelian Inheritance in Man (OMIM). Nucleic Acids Res 37: D793-D796. doi:10.1093/nar/gkn665.
22. Nabieva E, Jim K, Agarwal A, Chazelle B, Singh M (2005) Whole-proteome prediction of protein function via graph-theoretic analysis of interaction maps. Bioinformatics 21: i302-i310. doi:10.1093/bioinformatics/bti1054. (Pubitemid 41794502)
23. Goh KI, Cusick ME, Valle D, Childs B, Vidal M, et al. (2007) The human disease network. Proc Natl Acad Sci U S A 104: 8685.
24. Krauthammer M, Kaufmann CA, Gilliam TC, Rzhetsky A (2004) Molecular triangulation: bridging linkage and molecular-network information for identifying candidate genes in Alzheimer's disease. Proc Natl Acad Sci U S A 101: 15148-15153. (Pubitemid 39391733)
25. Cotterchio M, Nadalin V, Sauer M (2002) Human breast cancer and lymphomas may share a common aetiology involving Mouse Mammary Tumour Virus (MMTV). Medical hypotheses 59: 492-494.
26. Kitano H (2004) Cancer as a robust system: implications for anticancer therapy. Nature Reviews Cancer 4: 227-235. (Pubitemid 38337502)
27. Kitano H, Oda K, Kimura T, Matsuoka Y, Csete M, et al. (2004) Metabolic syndrome and robustness tradeoffs. Diabetes 53: S6-S15. (Pubitemid 39564516)
28. Whitacre JM (2012) Biological robustness: paradigms, mechanisms, and systems principles. Front Gene 3: 67. doi:10.3389/fgene.2012.00067.
29. Chuang H-Y, Hofree M, Ideker T (2010) A Decade of Systems Biology. Annual Review of Cell and Developmental Biology 26: 721-744. doi:10.1146/ annurevcellbio-100109-104122.
30. Tian T, Olson S, Whitacre JM, Harding A (2011) The origins of cancer robustness and evolvability. Integr Biol 3: 17-30. doi:10.1039/C0IB00046A.
31. Guney E, Sanz-Pamplona R, Sierra A, Oliva B (2012) Understanding Cancer Progression Using Protein Interaction Networks. In: Azmi AS, editor. Systems Biology in Cancer Research and Drug Discovery. Springer Netherlands. pp. 167-195. Available: http://link.springer.com/chapter/10.1007/978-94-007-4819-4- 7. Accessed 10 February 2014.
32. Ellis JD, Barrios-Rodiles M, Ç olak R, Irimia M, Kim T, et al. (2012) Tissue-Specific Alternative Splicing Remodels Protein-Protein Interaction Networks. Molecular Cell 46: 884-892. doi:10.1016/j.molcel.2012.05.037.
33. Guan Y, Gorenshteyn D, Burmeister M, Wong AK, Schimenti JC, et al. (2012) Tissue-Specific Functional Networks for Prioritizing Phenotype and Disease Genes. PLoS Comput Biol 8: e1002694. doi:10.1371/journal.pcbi.1002694.
34. Zanzoni A, Soler-Lopez M, Aloy P (2009) A network medicine approach to human disease. FEBS Letters 583: 1759-1765. doi:10.1016/j.febslet. 2009.03.001.
35. Hopkins AL (2008) Network pharmacology: the next paradigm in drug discovery. Nature Chemical Biology 4: 682-690. doi:10.1038/nchembio.118.
36. Yang K, Bai H, Ouyang Q, Lai L, Tang C (2008) Finding multiple target optimal intervention in disease-related molecular network. Molecular Systems Biology 4.
37. Vazquez A (2009) Optimal drug combinations and minimal hitting sets. BMC systems biology 3: 81.
38. Motter AE (2010) Improved network performance via antagonism: From synthetic rescues to multi-drug combinations. BioEssays 32: 236-245. doi:10.1002/bies.200900128.
39. Garcia-Garcia J, Guney E, Aragues R, Planas-Iglesias J, Oliva B (2010) Biana: a software framework for compiling biological interactions and analyzing networks. BMC Bioinformatics 11: 56. doi:10.1186/1471-2105-11-56.
40. Rual JF, Venkatesan K, Hao T, Hirozane-Kishikawa T, Dricot A, et al. (2005) Towards a proteome-scale map of the human protein-protein interaction network. Nature 437: 1173-1178. (Pubitemid 41509356)
41. Stelzl U, Worm U, Lalowski M, Haenig C, Brembeck FH, et al. (2005) A human protein-protein interaction network: a resource for annotating the proteome. Cell 122: 957-968. (Pubitemid 41345212)
42. Guney E, Oliva B (2011) Toward PWAS: discovering pathways associated with human disorders. BMC Bioinformatics 12: A12. doi:10.1186/1471-2105-12-S11-A12.
43. White S, Smyth P (2003) Algorithms for estimating relative importance in networks. Proceedings of the ninth ACM SIGKDD international conference on Knowledge discovery and data mining. KDD '03. New York, NY, USA: ACM. pp. 266-275. Available: http://doi.acm.org/10.1145/956750.956782. Accessed 22 February 2012.
44. Berriz GF, Beaver JE, Cenik C, Tasan M, Roth FP (2009) Next generation software for functional trend analysis. Bioinformatics 25: 3043-3044.
45. Yu G, Li F, Qin Y, Bo X, Wu Y, et al. (2010) GOSemSim: an R package for measuring semantic similarity among GO terms and gene products. Bioinformatics 26: 976-978. doi:10.1093/bioinformatics/btq064.
46. Wang JZ, Du Z, Payattakool R, Yu PS, Chen C-F (2007) A new method to measure the semantic similarity of GO terms. Bioinformatics 23: 1274-1281. doi:10.1093/bioinformatics/btm087. (Pubitemid 47050544)