A knowledge-driven interaction analysis reveals potential neurodegenerative mechanism of multiple sclerosis susceptibility (original) (raw)

• Barcellos LF, Sawcer S, Ramsay PP, Baranzini SE, Thomson G, Briggs F et al. Heterogeneity at the HLA-DRB1 locus and risk for multiple sclerosis. Hum Mol Genet 2006; 15: 2813–2824.
  Article CAS Google Scholar
• The International Multiple Sclerosis Genetics Consortium. A second major histocompatibility complex susceptibility locus for multiple sclerosis. Ann Neurol 2007; 61: 228–236.
  Article Google Scholar
• Cordell HJ . Genome-wide association studies: detecting gene-gene interactions that underlie human diseases. Nat Rev Genet 2009; 10: 392–404.
  Article CAS Google Scholar
• Marchini J, Donnelly P, Cardon LR . Genome-wide strategies for detecting multiple loci that influence complex diseases. Nat Genet 2005; 37: 413–417.
  Article CAS Google Scholar
• Rodriguez Del CA, Vitale ML, Tchakarov L, Trifaro JM . Human platelets contain scinderin, a Ca(2+)-dependent actin filament-severing protein. Thromb Haemost 1992; 67: 248–251.
  Article Google Scholar
• Trifaro JM, Rose SD, Marcu MG . Scinderin, a Ca2+-dependent actin filament severing protein that controls cortical actin network dynamics during secretion. Neurochem Res 2000; 25: 133–144.
  Article CAS Google Scholar
• Greene CS, Penrod NM, Williams SM, Moore JH . Failure to replicate a genetic association may provide important clues about genetic architecture. PLoS One 2009; 4: e5639.
  Article Google Scholar
• Fraley TS, Pereira CB, Tran TC, Singleton C, Greenwood JA . Phosphoinositide binding regulates alpha-actinin dynamics: mechanism for modulating cytoskeletal remodeling. J Biol Chem 2005; 280: 15479–15482.
  Article CAS Google Scholar
• Kremerskothen J, Teber I, Wendholt D, Liedtke T, Bockers TM, Barnekow A . Brain-specific splicing of alpha-actinin 1 (ACTN1) mRNA. Biochem Biophys Res Commun 2002; 295: 678–681.
  Article CAS Google Scholar
• Divers J, Freedman BI . Susceptibility genes in common complex kidney disease. Curr Opin Nephrol Hypertens 2010; 19: 79–84.
  Article CAS Google Scholar
• Mhatre AN, Janssens S, Nardi MA, Li Y, Lalwani AK . Clinical and molecular genetic analysis of a family with macrothrombocytopenia and early onset sensorineural hearing loss. Eur J Med Genet 2009; 52: 185–190.
  Article Google Scholar
• Geguchadze R, Zhi G, Lau KS, Isotani E, Persechini A, Kamm KE et al. Quantitative measurements of Ca(2+)/calmodulin binding and activation of myosin light chain kinase in cells. FEBS Lett 2004; 557: 121–124.
  Article CAS Google Scholar
• De KJ, Wilczak N, Leta R, Streetland C . Astrocytes in multiple sclerosis lack beta-2 adrenergic receptors. Neurology 1999; 53: 1628–1633.
  Article Google Scholar
• Nizri E, Hamra-Amitay Y, Sicsic C, Lavon I, Brenner T . Anti-inflammatory properties of cholinergic up-regulation: a new role for acetylcholinesterase inhibitors. Neuropharmacology 2006; 50: 540–547.
  Article CAS Google Scholar
• Jian X, Szaro BG, Schmidt JT . Myosin light chain kinase: expression in neurons and upregulation during axon regeneration. J Neurobiol 1996; 31: 379–391.
  Article CAS Google Scholar
• Gallo G . Myosin II activity is required for severing-induced axon retraction in vitro. Exp Neurol 2004; 189: 112–121.
  Article CAS Google Scholar
• Lukas TJ, Miao H, Chen L, Riordan SM, Li W, Crabb AM et al. Susceptibility to glaucoma: differential comparison of the astrocyte transcriptome from glaucomatous African American and Caucasian American donors. Genome Biol 2008; 9: R111.
  Article Google Scholar
• Akkad DA, Hoffjan S, Petrasch-Parwez E, Beygo J, Gold R, Epplen JT . Variation in the IL7RA and IL2RA genes in German multiple sclerosis patients. J Autoimmun 2009; 32: 110–115.
  Article CAS Google Scholar
• Alcina A, Fedetz M, Ndagire D, Fernandez O, Leyva L, Guerrero M et al. IL2RA/CD25 gene polymorphisms: uneven association with multiple sclerosis (MS) and type 1 diabetes (T1D). PLoS One 2009; 4: e4137.
  Article Google Scholar
• Rubio JP, Stankovich J, Field J, Tubridy N, Marriott M, Chapman C et al. Replication of KIAA0350, IL2RA, RPL5 and CD58 as multiple sclerosis susceptibility genes in Australians. Genes Immun 2008; 9: 624–630.
  Article CAS Google Scholar
• Mills GB, Cheung RK, Grinstein S, Gelfand EW . Increase in cytosolic free calcium concentration is an intracellular messenger for the production of interleukin 2 but not for expression of the interleukin 2 receptor. J Immunol 1985; 134: 1640–1643.
  CAS PubMed Google Scholar
• Suh PG, Park JI, Manzoli L, Cocco L, Peak JC, Katan M et al. Multiple roles of phosphoinositide-specific phospholipase C isozymes. BMB Rep 2008; 41: 415–434.
  Article CAS Google Scholar
• Adamski FM, Timms KM, Shieh BH . A unique isoform of phospholipase Cbeta4 highly expressed in the cerebellum and eye. Biochim Biophys Acta 1999; 1444: 55–60.
  Article CAS Google Scholar
• Homma Y, Takenawa T, Emori Y, Sorimachi H, Suzuki K . Tissue- and cell type-specific expression of mRNAs for four types of inositol phospholipid-specific phospholipase C. Biochem Biophys Res Commun 1989; 164: 406–412.
  Article CAS Google Scholar
• Kim D, Jun KS, Lee SB, Kang NG, Min DS, Kim YH et al. Phospholipase C isozymes selectively couple to specific neurotransmitter receptors. Nature 1997; 389: 290–293.
  Article CAS Google Scholar
• Ban M, Goris A, Lorentzen AR, Baker A, Mihalova T, Ingram G et al. Replication analysis identifies TYK2 as a multiple sclerosis susceptibility factor. Eur J Hum Genet 2009; 17: 1309–1313.
  Article CAS Google Scholar
• De Jager PL, Jia X, Wang J, de Bakker PI, Ottoboni L, Aggarwal NT et al. Meta-analysis of genome scans and replication identify CD6, IRF8 and TNFRSF1A as new multiple sclerosis susceptibility loci. Nat Genet 2009; 41: 776–782.
  Article CAS Google Scholar
• Gregory SG, Schmidt S, Seth P, Oksenberg JR, Hart J, prokop A et al. Interleukin 7 receptor alpha chain (IL7R) shows allelic and functional association with multiple sclerosis. Nat Genet 2007; 39: 1083–1091.
  Article CAS Google Scholar
• The International Multiple Sclerosis Genetics Consortium. Risk alleles for multiple sclerosis identified by a genomewide study. N Engl J Med 2007; 357: 851–862.
  Article Google Scholar
• Baranzini SE, Galwey NW, Wang J, Khankhanian P, Lindberg R, Pelletier D et al. Pathway and network-based analysis of genome-wide association studies in multiple sclerosis. Hum Mol Genet 2009; 18: 2078–2090.
  Article CAS Google Scholar
• Elbers CC, van Eijk KR, Franke L, Mulder F, van der Schouw YT, Wijmenga C et al. Using genome-wide pathway analysis to unravel the etiology of complex diseases. Genet Epidemiol 2009; 33: 419–431.
  Article Google Scholar
• O’Dushlaine C, Kenny E, Heron EA, Segurado R, Gill M, Morris DW et al. The SNP ratio test: pathway analysis of genome-wide association datasets. Bioinformatics 2009; 25: 2762–2763.
  Article Google Scholar
• Peng G, Luo L, Siu H, Zhu Y, Hu P, Hong S et al. Gene and pathway-based second-wave analysis of genome-wide association studies. Eur J Hum Genet 2009; 18: 111–117.
  Article Google Scholar
• Saccone SF, Saccone NL, Swan GE, Madden PA, Goate AM, Rice JP et al. Systematic biological prioritization after a genome-wide association study: an application to nicotine dependence. Bioinformatics 2008; 24: 1805–1811.
  Article CAS Google Scholar
• Torkamani A, Topol EJ, Schork NJ . Pathway analysis of seven common diseases assessed by genome-wide association. Genomics 2008; 92: 265–272.
  Article CAS Google Scholar
• Bush WS, Dudek SM, Ritchie MD . Biofilter: a knowledge-integration system for the multi-locus analysis of genome-wide association studies. Pac Symp Biocomput 2009; 14: 368–379.
  Google Scholar
• Cordell HJ, Barratt BJ, Clayton DG . Case/pseudocontrol analysis in genetic association studies: a unified framework for detection of genotype and haplotype associations, gene-gene and gene-environment interactions, and parent-of-origin effects. Genet Epidemiol 2004; 26: 167–185.
  Article Google Scholar
• Fisher RA . The correlation between relatives on the supposition of mendelian inheritance. Trans R Soc Edinburgh 1918; 52: 399–433.
  Article Google Scholar