IGENT: Efficient entropy based algorithm for genome-wide gene-gene interaction analysis

BMC Medical Genomics

Volumn 7, Issue SUPPL.1, 2014, Pages

  Kwon, Min Seok ^a   Park, Mira ^b   Park, Taesung ^a  

^a Seoul National University   (South Korea)

^b Eulji University   (South Korea)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; AUTOMATION; BIPOLAR DISORDER; CLINICAL EFFECTIVENESS; COMPUTER ANALYSIS; COMPUTER MODEL; COMPUTER SYSTEM; CONTROLLED STUDY; DATA ANALYSIS; ENTROPY; GENE FREQUENCY; GENE IDENTIFICATION; GENE INTERACTION; GENETIC ALGORITHM; GENETIC ASSOCIATION; GENETIC VARIABILITY; GENOTYPE ENVIRONMENT INTERACTION; HERITABILITY; HIGH THROUGHPUT SEQUENCING; INTERMETHOD COMPARISON; MATHEMATICAL COMPUTING; PERFORMANCE MEASUREMENT SYSTEM; PRIORITY JOURNAL; PROCESS CONTROL; PROCESS DESIGN; PROCESS DEVELOPMENT; PROCESS MODEL; PROCESS TECHNOLOGY; RETINA MACULA AGE RELATED DEGENERATION; SINGLE NUCLEOTIDE POLYMORPHISM; SYSTEM ANALYSIS; ALGORITHM; BIOLOGICAL MODEL; EPISTASIS; GENETICS; GENOMICS; HUMAN; MACULAR DEGENERATION; PROCEDURES; TIME;

ALGORITHMS; BIPOLAR DISORDER; ENTROPY; EPISTASIS, GENETIC; GENOMICS; HUMANS; MACULAR DEGENERATION; MODELS, GENETIC; TIME FACTORS;

EID: 84900434301     PISSN: None     EISSN: 17558794     Source Type: Journal    
DOI: 10.1186/1755-8794-7-S1-S6     Document Type: Article

References (35)

1. The success of the genome-wide association approach: a brief story of a long struggle. Seng KC, Seng CK, Eur J Hum Genet 2008 16 554 64 10.1038/ejhg.2008.12 18285837 (Pubitemid 351594121)
2. Missing heritability and strategies for finding the underlying causes of complex disease. Eichler EE, Flint J, Gibson G, Kong A, Leal SM, Moore JH, Nadeau JH, Nat Rev Genet 2010 11 446 50 10.1038/nrg2809 20479774
3. Detecting gene-gene interactions that underlie human diseases. Cordell HJ, Nat Rev Genet 2009 10 392 404 10.1038/nrg2579 19434077
4. A support vector machine approach for detecting gene-gene interaction. Chen SH, Sun J, Dimitrov L, Turner AR, Adams TS, Meyers DA, Chang BL, Zheng SL, Grönberg H, Xu J, Hsu FC, Genet Epidemiol 2008 32 152 67 10.1002/gepi.20272 17968988 (Pubitemid 351288032)
5. SNP interaction detection with random forests in high-dimensional genetic data. Winham SJ, Colby CL, Freimuth RR, Wang X, de Andrade M, Huebner M, Biernacka JM, BMC bioinformatics 2012 13 164 10.1186/1471-2105-13-164 22793366
6. Multifactor-dimensionality reduction reveals high-order interactions among estrogen-metabolism genes in sporadic breast cancer. Ritchie MD, Hahn LW, Roodi N, Bailey LR, Dupont WD, Parl FF, Moore JH, Am J Hum Genet 2001 69 138 47 10.1086/321276 11404819 (Pubitemid 32614026)
7. A computationally efficient hypothesis testing method for epistasis analysis using multifactor dimensionality reduction. Pattin KA, White BC, Barney N, Gui J, Nelson HH, Kelsey KT, Andrew AS, Karagas MR, Moore JH, Genet Epidemiol 2009 33 87 94 10.1002/gepi.20360 18671250
8. BOOST: A fast approach to detecting gene-gene interactions in genome-wide case-control studies. Wan X, Yang C, Yang Q, Xue H, Fan X, Tang NL, Yu W, Am J Hum Genet 2010 87 325 40 10.1016/j.ajhg.2010.07.021 20817139
9. Gene mapping and marker clustering using Shannon's mutual information. Dawy Z, Goebel B, Hagenauer J, Andreoli C, Meitinger T, Mueller JC, IEEE/ACM Trans Comput Biol Bioinform 2006 3 47 56 10.1109/TCBB.2006.9 17048392 (Pubitemid 43269826)
10. Information-theoretic metrics for visualizing gene-environment interactions. Chanda P, Zhang A, Brazeau D, Sucheston L, Freudenheim JL, Ambrosone C, Ramanathan M, Am J Hum Genet 2007 81 939 63 10.1086/521878 17924337 (Pubitemid 47580248)
11. An entropy test for single-locus genetic association analysis. Ruiz-Marín M, Matilla-García M, Cordoba JA, Susillo- González JL, Romo-Astorga A, González-Pérez A, Ruiz A, Gayán J, BMC Genet. 2010 11 19 20331859
12. A mathematical theory of communication. Shannon CE, Bell Syst Tech J 1948 23 379 423
13. A modified entropy-based approach for identifying gene-gene interactions in case-control study. Yee J, Kwon MS, Park T, Park M, PLoS ONE 2013 8 69321 10.1371/journal.pone.0069321 23874943
14. An approximation to the distribution of finite sample size mutual information estimates. Goebel B, Dawy Z, Hagenauer J, Muller J, Proc IEEE Int'l Conf Comm 2005, May
15. New evaluation measures for multifactor dimensionality reduction classifiers in gene-gene interaction analysis. Namkung J, Kim K, Yi S, Chung W, Kwon MS, Park T, Bioinformatics 2009 25 338 45 10.1093/bioinformatics/btn629 19164302
16. Power of multifactor dimensionality reduction for detecting gene-gene interactions in the presence of genotyping error, missing data, phenocopy, and genetic heterogeneity. Ritchie MD, Hahn LW, Moore JH, Genet Epidemiol 2003 24 150 7 10.1002/gepi.10218 12548676 (Pubitemid 36158211)
17. Alternative contingency table measures improve the power and detection of multifactor dimensionality reduction. Bush WS, Edwards TL, Dudek SM, McKinney BA, Ritchie MD, BMC Bioinformatics 2008 9 238 244 10.1186/1471-2105-9-238 18485205 (Pubitemid 351801767)
18. A balanced accuracy function for epistasis modeling in imbalanced datasets using multifactor dimensionality reduction. Velez DR, White BC, Motsinger AA, Bush WS, Ritchie MD, Williams SM, Moore JH, Genet Epidemiol 2007 31 306 15 10.1002/gepi.20211 17323372 (Pubitemid 46642095)
19. Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls. Wellcome Trust Case Control Consortium, Nature 2007 447 661 78 10.1038/nature05911 17554300 (Pubitemid 46889737)
20. PLINK: a tool set for whole-genome association and population-based linkage analyses. Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MA, Bender D, Maller J, Sklar P, de Bakker PI, Daly MJ, Sham PC, Am J Hum Genet 2007 81 559 75 10.1086/519795 17701901 (Pubitemid 47330214)
21. A fast and flexible statistical model for large-scale population genotype data: applications to inferring missing genotypes and haplotypic phase. Scheet P, Stephens M, Am J Hum Genet 2006 78 629 44 10.1086/502802 16532393
22. Complement factor H polymorphism in age-related macular degeneration. Klein RJ, Zeiss C, Chew EY, Tsai JY, Sackler RS, Haynes C, Henning AK, SanGiovanni JP, Mane SM, Mayne ST, Bracken MB, Ferris FL, Ott J, Barnstable C, Hoh J, Science 2005 308 385 9 10.1126/science.1109557 15761122 (Pubitemid 40530070)
23. LIBSVM: A library for support vector machines. Chang CC, Lin CJ, ACM Transactions on Intelligent Systems and Technology 2011 2 3 1 27
24. Random Forests. Breiman L, Machine Learning 2001 45 5 32 10.1023/A:1010933404324 (Pubitemid 32933532)
25. Genetic utility of broadly defined bipolar schizoaffective disorder as a diagnostic concept. Hamshere ML, Green EK, Jones IR, Jones L, Moskvina V, Kirov G, Grozeva D, Nikolov I, Vukcevic D, Caesar S, Gordon-Smith K, Fraser C, Russell E, Breen G, St Clair D, Collier DA, Young AH, Ferrier IN, Farmer A, McGuffin P, Wellcome Trust Case Control Consortium, Holmans PA, Owen MJ, O'Donovan MC, Craddock N, Br J Psychiatry 2009 195 23 9 10.1192/bjp.bp.108.061424 19567891
26. Bipolar disorder: from genes to behavior pathways. Martinowich K, Schloesser RJ, Manji HK, J Clin Invest 2009 119 726 36 10.1172/JCI37703 19339764
27. Genome-wide association study of suicidal ideation emerging during citalopram treatment of depressed outpatients. Laje G, Allen AS, Akula N, Manji H, John Rush A, McMahon FJ, Pharmacogenet Genomics 2009 19 666 74 10.1097/FPC.0b013e32832e4bcd 19724244
28. A genome-wide association study of bipolar disorder in Norwegian individuals, followed by replication in Icelandic sample. Djurovic S, Gustafsson O, Mattingsdal M, Athanasiu L, Bjella T, Tesli M, Agartz I, Lorentzen S, Melle I, Morken G, Andreassen OA, J Affect Disord 2010 126 312 6 10.1016/j.jad.2010. 04.007 20451256
29. Survey of the effect of genetic variations on gene expression in human prefrontal cortex and its application to genetics of psychiatric disorders. Iwamoto K, Ueda J, Bundo M, Kojima T, Kato T, Neurosci Res 2011 70 238 42 10.1016/j.neures.2011.02.012 21382426
30. Family-based analysis of genetic variation underlying psychosis-inducing effects of cannabis: sibling analysis and proband follow-up. van Winkel R, Genetic Risk and Outcome of Psychosis (GROUP) Investigators, Arch Gen Psychiatry 2011 68 148 57 10.1001/archgenpsychiatry.2010.152 21041608
31. A navigator for human genome epidemiology. Yu W, Gwinn M, Clyne M, Yesupriya A, Khoury MJ, Nat Genet 2008 40 124 5 10.1038/ng0208-124 18227866 (Pubitemid 351171407)
32. Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. Hindorff LA, Sethupathy P, Junkins HA, Ramos EM, Mehta JP, Collins FS, Manolio TA, Proc Natl Acad Sci USA 2009 106 9362 7 10.1073/pnas.0903103106 19474294
33. Discovering genotypes underlying human phenotypes: past successes for mendelian disease, future approaches for complex disease. Botstein D, Risch N, Nat Genet 2003 33 Suppl 228 37 12610532 (Pubitemid 36278833)
34. Strategy for detecting susceptibility genes with weak or no marginal effect. Kotti S, Bickeboller H, Clerget-Darpoux F, Hum Hered 2007 63 85 92 10.1159/000099180 17283437
35. A perspective on epistasis: limits of models displaying no main effect. Culverhouse R, Suarez BK, Lin J, Reich T, Am J Hum Genet 2002 70 461 71 10.1086/338759 11791213 (Pubitemid 34112299)