Symmetric Epistasis Estimation (SEE) and its application to dissecting interaction map of Plasmodium falciparum

Molecular BioSystems

Volumn 8, Issue 5, 2012, Pages 1544-1552

  Huang, Yang ^a   Siwo, Geoffrey ^b   Wuchty, Stefan ^a   Ferdig, Michael T ^b   Przytycka, Teresa M ^a  

^a NATIONAL INSTITUTES OF HEALTH   (United States)

^b UNIVERSITY OF NOTRE DAME   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CHROMOSOME; CROSS BREEDING; GENE LINKAGE DISEQUILIBRIUM; GENETIC EPISTASIS; GENETIC TRANSCRIPTION; GENETICS; HUMAN; PLASMODIUM FALCIPARUM; QUANTITATIVE TRAIT LOCUS; SACCHAROMYCES CEREVISIAE;

CHROMOSOMES; CROSSES, GENETIC; EPISTASIS, GENETIC; HUMANS; LINKAGE DISEQUILIBRIUM; PLASMODIUM FALCIPARUM; QUANTITATIVE TRAIT LOCI; SACCHAROMYCES CEREVISIAE; TRANSCRIPTION, GENETIC;

PLASMODIUM FALCIPARUM;

EID: 84859812487     PISSN: 1742206X     EISSN: 17422051     Source Type: Journal    
DOI: 10.1039/c2mb05333k     Document Type: Article

References (32)

1. H. J. Cordell Detecting gene-gene interactions that underlie human diseases Nat. Rev. Genet. 2009 10 392 404
2. S. K. Musani D. Shriner N. Liu R. Feng C. S. Coffey et al., Detection of gene x gene interactions in genome-wide association studies of human population data Hum. Hered. 2007 63 67 84
3. R. A. Fisher The correlation between relatives on the supposition of Mendelian inheritance Philosophical Transactions of the Royal Society of Edinburgh 1918 52 399 433
4. P. C. Phillips Epistasis-the essential role of gene interactions in the structure and evolution of genetic systems Nat. Rev. Genet. 2008 9 855 867
5. H. J. Cordell Epistasis: what it means, what it doesn't mean, and statistical methods to detect it in humans Hum. Mol. Genet. 2002 11 2463 2468
6. J. Marchini P. Donnelly L. R. Cardon Genome-wide strategies for detecting multiple loci that influence complex diseases Nat. Genet. 2005 37 413 417
7. J. D. Storey J. M. Akey L. Kruglyak Multiple locus linkage analysis of genome-wide expression in yeast PLoS Biol. 2005 3 e267
8. G. Hannum R. Srivas A. Guenole H. van Attikum N. J. Krogan et al., Genome-wide association data reveal a global map of genetic interactions among protein complexes PLoS Genet. 2009 5 e1000782
9. O. Litvin H. C. Causton B. J. Chen D. Péer Modularity and interactions in the genetics of gene expression Proc. Natl. Acad. Sci. USA 2009
10. V. van Noort M. A. Huynen Combinatorial gene regulation in Plasmodium falciparum Trends Genet. 2006 22 73 78
11. W. Zhang J. Zhu E. E. Schadt J. S. Liu A Bayesian partition method for detecting pleiotropic and epistatic eQTL modules PLoS Comput. Biol. 2010 6 e1000642
12. J. M. Gonzales J. J. Patel N. Ponmee L. Jiang A. Tan et al., Regulatory hotspots in the malaria parasite genome dictate transcriptional variation PLoS Biol. 2008 6 e238
13. H. Jiang J. J. Patel M. Yi J. Mu J. Ding et al., Genome-wide compensatory changes accompany drug- selected mutations in the Plasmodium falciparum crt gene PLoS One 2008 3 e2484
14. R. B. Brem G. Yvert R. Clinton L. Kruglyak Genetic dissection of transcriptional regulation in budding yeast Science 2002 296 752 755
15. Y. Huang S. Wuchty M. T. Ferdig T. M. Przytycka Graph theoretical approach to study eQTL: a case study of Plasmodium falciparum Bioinformatics 2009 25 i15 20
16. J. D. Storey R. Tibshirani Statistical significance for genome-wide studies Proc. Natl. Acad. Sci. U. S. A. 2003 100 9440 9445
17. C. Hertz-Fowler C. S. Peacock V. Wood M. Aslett A. Kerhornou et al., GeneDB: a resource for prokaryotic and eukaryotic organisms Nucleic Acids Res. 2004 32 D339 343
18. B. Klenke M. P. Barrett R. Brun I. H. Gilbert Antiplasmodial activity of a series of 1,3,5-triazine-substituted polyamines J. Antimicrob. Chemother. 2003 52 290 293
19. X. Su L. A. Kirkman H. Fujioka T. E. Wellems Complex polymorphisms in an approximately 330 kDa protein are linked to chloroquine-resistant P. falciparum in Southeast Asia and Africa Cell 1997 91 593 603
20. M. Marti R. T. Good M. Rug E. Knuepfer A. F. Cowman Targeting malaria virulence and remodeling proteins to the host erythrocyte Science 2004 306 1930 1933
21. Y. S. Lee Y. Shibata A. Malhotra A. Dutta A novel class of small RNAs: tRNA-derived RNA fragments (tRFs) Genes Dev. 2009 23 2639 2649
22. M. Schaefer T. Pollex K. Hanna F. Tuorto M. Meusburger et al., RNA methylation by Dnmt2 protects transfer RNAs against stress-induced cleavage Genes Dev. 2010 24 1590 1595
23. S. Blanco A. Kurowski J. Nichols F. M. Watt S. A. Benitah et al., The RNA-Methyltransferase Misu (NSun2) Poises Epidermal Stem Cells to Differentiate PLoS Genet. 2011 7 e1002403
24. T. L. Campbell E. K. De Silva K. L. Olszewski O. Elemento M. Llinas Identification and Genome-Wide Prediction of DNA Binding Specificities for the ApiAP2 Family of Regulators from the Malaria Parasite PLoS Pathog. 2010 6 e1001165
25. J. V. Turatsinze M. Thomas-Chollier M. Defrance J. van Helden Using RSAT to scan genome sequences for transcription factor binding sites and cis-regulatory modules Nat. Protoc. 2008 3 1578 1588
26. K. Hayton D. Gaur A. Liu J. Takahashi B. Henschen et al., Erythrocyte binding protein PfRH5 polymorphisms determine species-specific pathways of Plasmodium falciparum invasion Cell Host Microbe 2008 4 40 51
27. X. Wang R. C. Elston X. Zhu Statistical interaction in human genetics: how should we model it if we are looking for biological interaction? Nat. Rev. Genet. 2011 12 74
28. E. K. De Silva A. R. Gehrke K. Olszewski I. Leon J. S. Chahal et al., Specific DNA-binding by apicomplexan AP2 transcription factors Proc. Natl. Acad. Sci. U. S. A. 2008 105 8393 8398
29. S. I. Lee D. Péer A. M. Dudley G. M. Church D. Koller Identifying regulatory mechanisms using individual variation reveals key role for chromatin modification Proc. Natl. Acad. Sci. U. S. A. 2006 103 14062 14067
30. R. W. Doerge G. A. Churchill Permutation tests for multiple loci affecting a quantitative character Genetics 1996 142 285 294
31. M. J. Anderson C. J. F. T. Braak Permutation tests for multi-factorial analysis of variance Journal of Statistical Computation and Simulation 2003 73 85 113
32. R. Breitling Y. Li B. M. Tesson J. Fu C. Wu et al., Genetical genomics: spotlight on QTL hotspots PLoS Genet. 2008 4 e1000232