Surfing a genetic association interaction network to identify modulators of antibody response to smallpox vaccine

Genes and Immunity

Volumn 11, Issue 8, 2010, Pages 630-636

  Davis, N A ^a   Crowe Jr , J E ^b   Pajewski, N M ^c   McKinney, B A ^a  

^a UNIVERSITY OF TULSA   (United States)

^b VANDERBILT UNIVERSITY   (United States)

^c UNIVERSITY OF ALABAMA AT BIRMINGHAM   (United States)

Author keywords

eigenvector centrality; gene gene interaction; genetic association study; information theory; Markov chain; single nucleotide polymorphism

Indexed keywords

RETINOID X RECEPTOR ALPHA; SMALLPOX VACCINE;

ANTIBODY RESPONSE; ARTICLE; GENE INTERACTION; GENETIC ALGORITHM; GENETIC ANALYSIS; GENETIC ASSOCIATION; HUMAN; IMMUNOMODULATION; IMMUNOREGULATION; PRIORITY JOURNAL; SIGNAL TRANSDUCTION; SIMULATION; SINGLE NUCLEOTIDE POLYMORPHISM; SMALLPOX;

ALGORITHMS; ANTIBODY FORMATION; CYTOCHROME P-450 CYP1A1; GENE REGULATORY NETWORKS; GENES; GENOME-WIDE ASSOCIATION STUDY; HUMANS; MARKOV CHAINS; NADPH OXIDASE; PHENOTYPE; POLYMORPHISM, SINGLE NUCLEOTIDE; RETINOID X RECEPTOR ALPHA; SMALLPOX VACCINE;

VARIOLA VIRUS;

EID: 78649701338     PISSN: 14664879     EISSN: 14765470     Source Type: Journal    
DOI: 10.1038/gene.2010.37     Document Type: Article

References (21)

1. Poland GA, Ovsyannikova IG, Jacobson RM. Vaccine im-munogenetics: bedside to bench to population. Vaccine 2008; 26: 6183-6188.
2. Poland GA, Ovsyannikova IG, Jacobson RM, Smith DI. Heterogeneity in vaccine immune response: the role of immunogenetics and the emerging field of vaccinomics. Clin Pharmacol Ther 2007; 82: 653-664.
3. Altshuler D, Daly MJ, Lander ES. Genetic mapping in human disease. Science 2008; 322: 881-888.
4. McKinney BA, Crowe JE, Guo J, Tian D. Capturing the spectrum of interaction effects in genetic association studies by simulated evaporative cooling network analysis. PLoS Genet 2009; 5: e1000432.
5. Page L, Brin S, Motwani R, Winograd T. The PageRank citation ranking: bringing order to the web. Tech. rep. 1999-66, Standford Digital Library Technologies Project 1998.
6. Oldham MC, Horvath S, Geschwind DH. Conservation and evolution of gene coexpression networks in human and chimpanzee brains. Proc Natl Acad Sci USA 2006; 103: 17973-17978.
7. Oti M, Huynen MA, Brunner HG. The biological coherence of human phenome databases. Am J Hum Genet 2009; 85: 801-808.
8. Morrison JL, Breitling R, Higham DJ, Gilbert DR. GeneRank: using search engine technology for the analysis of microarray experiments. BMC Bioinformatics 2005; 6: 233.
9. Strang G. Linear Algebra and Its Applications. Saunders College Publishing: New York, 1988.
10. McKinney BA, Reif DM, White BC, Crowe Jr. JE, Moore JH. Evaporative cooling feature selection for genotypic data involving interactions. Bioinformatics 2007; 23: 2113-2120.
11. Greene CS, Penrod NM, Kiralis J, Moore JH. Spatially Uniform ReliefF (SURF) for computationally-efficient filtering of gene-gene interactions. BioData Min 2009; 2: 5.
12. Kononenko I. Estimating attributes: analysis and extensions of RELIEF. in European Conference on Machine Learning 1994: 171-182.
13. McNicholl JM, Downer MV, Udhayakumar V, Alper CA, Swerdlow DL. Host-pathogen interactions in emerging and re-emerging infectious diseases: a genomic perspective of tuberculosis, malaria, human immunodeficiency virus infection, hepatitis B, and cholera. Annu Rev Public Health 2000; 21: 15-46.
14. Packer BR et al. SNP500Cancer: a public resource for sequence validation, assay development, and frequency analysis for genetic variation in candidate genes. Nucleic Acids Res 2006; 34: D617-D621.
15. Reif DM et al. Genetic basis for adverse events after smallpox vaccination. J Infect Dis 2008; 198: 16-22.
16. Reif DM et al. Integrated analysis of genetic and proteomic data identifies biomarkers associated with adverse events following smallpox vaccination. Genes Immun 2009; 10: 112-119.
17. Talbot TR et al. Vaccination success rate and reaction profile with diluted and undiluted smallpox vaccine: a randomized controlled trial. JAMA 2004; 292: 1205-1212.
18. Purcell S et al. PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet 2007; 81: 559-575.
19. Garcia-Bates TM et al. Peroxisome proliferator-activated receptor gamma ligands enhance human B cell antibody production and differentiation. J Immunol 2009; 183: 6903-6912.
20. Ovsyannikova IG et al. Rubella vaccine-induced cellular immunity: evidence of associations with polymorphisms in the Toll-like, vitamin A and D receptors, and innate immune response genes. Hum Genet 2010; 127: 207-221.
21. Eden E, Navon R, Steinfeld I, Lipson D, Yakhini Z. GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists. BMC Bioinformatics 2009; 10: 48.