Encore: Genetic association interaction network centrality pipeline and application to SLE exome data

Genetic Epidemiology

Volumn 37, Issue 6, 2013, Pages 614-621

  Davis, Nicholas A ^a,c   Lareau, Caleb A ^a,b,c   White, Bill C ^a   Pandey, Ahwan ^a   Wiley, Graham ^b   Montgomery, Courtney G ^b   Gaffney, Patrick M ^b   Mckinney, B A ^a  

^a The University of Tulsa   (United States)

^b OKLAHOMA MEDICAL RESEARCH FOUNDATION   (United States)

^c UNIVERSITY OF OKLAHOMA TULSA   (United States)

Author keywords

Epistasis network; Machine learning; Network analysis; Network centrality; Systemic Lupus Erythematous

Indexed keywords

ARTICLE; EXOME; GENE INTERACTION; GENETIC ASSOCIATION; GENETIC PREDISPOSITION; HUMAN; RANDOM FOREST; SYSTEMIC LUPUS ERYTHEMATOSUS;

EPISTASIS NETWORK; MACHINE LEARNING; NETWORK ANALYSIS; NETWORK CENTRALITY; SYSTEMIC LUPUS ERYTHEMATOUS;

ALGORITHMS; EPISTASIS, GENETIC; EXOME; GENE REGULATORY NETWORKS; GENETIC PREDISPOSITION TO DISEASE; GENOME-WIDE ASSOCIATION STUDY; HLA-DR BETA-CHAINS; HUMANS; LINKAGE DISEQUILIBRIUM; LUPUS ERYTHEMATOSUS, SYSTEMIC; NADPH OXIDASE; SIALYLTRANSFERASES; SOFTWARE;

EID: 84881616745     PISSN: 07410395     EISSN: 10982272     Source Type: Journal    
DOI: 10.1002/gepi.21739     Document Type: Article

References (31)

1. Becker CG, Artola A, Gerardy-Schahn R, Becker T, Welzl H, Schachner M. 1996. The polysialic acid modification of the neural cell adhesion molecule is involved in spatial learning and hippocampal long-term potentiation. J Neurosci Res 45(2):143-152.
2. Benjamini Y, Hochberg Y. 1995. Controlling the false discovery rate-a practical and powerful approach to multiple testing. J R Stat Soc Ser B 57(1):289-300.
3. Blankenberg D, Von Kuster G, Coraor N, Ananda G, Lazarus R, Mangan M, Nekrutenko A, Taylor J. 2010. Galaxy: a web-based genome analysis tool for experimentalists. Curr Protoc Mol Biol 10:1-21.
4. Breiman L. 2001. Random forests. Mach Learn 45(1):5-32.
5. Busslinger M. 2004. Transcriptional control of early B cell development. Annu Rev Immunol 22:55-79.
6. Cunninghame Graham DS, Morris DL, Bhangale TR, Criswell LA, Syvanen AC, Ronnblom L, Behrens TW, Graham RR, Vyse TJ. 2011. Association of NCF2, IKZF1, IRF8, IFIH1, and TYK2 with systemic lupus erythematosus. PLoS Genet 7(10):e1002341.
7. Davis NA, Crowe JE Jr., Pajewski NM, McKinney BA. 2010. Surfing a genetic association interaction network to identify modulators of antibody response to smallpox vaccine. Genes Immun 11(8):630-636.
8. Davis NA, Pandey A, McKinney BA. 2011. Real-world comparison of CPU and GPU implementations of SNPrank: a network analysis tool for GWAS. Bioinformatics 27(2):284-285.
9. Drake PM, Nathan JK, Stock CM, Chang PV, Muench MO, Nakata D, Reader JR, Gip P, Golden KP, Weinhold B and others. 2008. Polysialic acid, a glycan with highly restricted expression, is found on human and murine leukocytes and modulates immune responses. J Immunol 181(10):6850-6858.
10. Ehlin-Henriksson B, Liang W, Cagigi A, Mowafi F, Klein G, Nilsson A. 2009. Changes in chemokines and chemokine receptor expression on tonsillar B cells upon Epstein-Barr virus infection. Immunology 127(4):549-557.
11. Eichler EE, Flint J, Gibson G, Kong A, Leal SM, Moore JH, Nadeau JH. 2010. Missing heritability and strategies for finding the underlying causes of complex disease. Nat Rev Genet 11(6):446-450.
12. Hu T, Sinnott-Armstrong NA, Kiralis JW, Andrew AS, Karagas MR, Moore JH. 2011. Characterizing genetic interactions in human disease association studies using statistical epistasis networks. BMC Bioinformatics 12:364.
13. Iyengar SK, Elston RC. 2007. The genetic basis of complex traits: rare variants or "common gene, common disease"? Methods Mol Biol 376:71-84.
14. Li H, Durbin R. 2009. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25(14):1754-1760.
15. Maher B. 2008. Personal genomes: the case of the missing heritability. Nature 456(7218):18-21.
16. McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M and others. 2010. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res 20(9):1297-1303.
17. McKinney BA, Crowe JE, Guo J, Tian D. 2009. Capturing the spectrum of interaction effects in genetic association studies by simulated evaporative cooling network analysis. PLoS Genet 5(3):e1000432.
18. McKinney BA, Pajewski NM. 2011. Six degrees of epistasis: statistical network models for GWAS. Front Genet 2:109.
19. OpenMP. Application Program Interface. 2008. Available from http://www. openmp.org/mp-documents/spec30.pdf
20. Ovsyannikova IG, Kennedy RB, O'Byrne M, Jacobson RM, Pankratz VS, Poland GA. 2012. Genome-wide association study of antibody response to smallpox vaccine. Vaccine 30(28):4182-4189.
21. Pandey A, Davis NA, White BC, Pajewski NM, Savitz J, Drevets WC, McKinney BA. 2012. Epistasis network centrality analysis yields pathway replication across two GWAS cohorts for bipolar disorder. Transl Psychiatry 2:e154.
22. Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MA, Bender D, Maller J, Sklar P, de Bakker PI, Daly MJ and others. 2007. PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet 81(3):559-575.
23. Raelson JV, Little RD, Ruether A, Fournier H, Paquin B, Van Eerdewegh P, Bradley WE, Croteau P, Nguyen-Huu Q, Segal J and others. 2007. Genome-wide association study for Crohn's disease in the Quebec Founder Population identifies multiple validated disease loci. Proc Natl Acad Sci USA 104(37):14747-14752.
24. Robnik-Sikonja M, Kononenko I. 2003. Theoretical and empirical analysis of ReliefF and RReliefF. Mach Learn 53(1-2):23-69.
25. Salloum R, Franek BS, Kariuki SN, Rhee L, Mikolaitis RA, Jolly M, Utset TO, Niewold TB. 2010. Genetic variation at the IRF7/PHRF1 locus is associated with autoantibody profile and serum interferon-alpha activity in lupus patients. Arthritis Rheum 62(2):553-561.
26. Schwarz DF, Konig IR, Ziegler A. 2010. On safari to Random Jungle: a fast implementation of Random Forests for high-dimensional data. Bioinformatics 26(14):1752-1758.
27. Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T. 2003. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 13(11):2498-2504.
28. Vene R, Delfino L, Castellani P, Balza E, Bertolotti M, Sitia R, Rubartelli A. 2010. Redox remodeling allows and controls B-cell activation and differentiation. Antioxid Redox Signal 13(8):1145-1155.
29. Warton K, Foster NC, Gold WA, Stanley KK. 2004. A novel gene family induced by acute inflammation in endothelial cells. Gene 342(1):85-95.
30. Watford WT, Hissong BD, Bream JH, Kanno Y, Muul L, O'Shea JJ. 2004. Signaling by IL-12 and IL-23 and the immunoregulatory roles of STAT4. Immunol Rev 202:139-156.
31. You Y, Zhao W, Chen S, Tan W, Dan Y, Hao F, Deng G. 2010. Association of TBX21 gene haplotypes in a Chinese population with systemic lupus erythematosus. Scand J Rheumatol 39(3):254-258.