메뉴 건너뛰기




Volumn 6, Issue 9, 2011, Pages 1071-1079

Gene set analysis and network analysis for genome-wide association studies

(2)  Pedroso, Inti a   Breen, Gerome a  

a NONE

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA;

EID: 80052441156     PISSN: None     EISSN: 15596095     Source Type: Journal    
DOI: 10.1101/pdb.top065581     Document Type: Article
Times cited : (21)

References (66)
  • 2
    • 58849112975 scopus 로고    scopus 로고
    • Pathways-based analyses of wholegenome association study data in bipolar disorder reveal genes mediating ion channel activity and synaptic neurotransmission
    • Askland K, Read C, Moore J. 2009. Pathways-based analyses of wholegenome association study data in bipolar disorder reveal genes mediating ion channel activity and synaptic neurotransmission. Hum Genet 125: 63-79.
    • (2009) Hum Genet , vol.125 , pp. 63-79
    • Askland, K.1    Read, C.2    Moore, J.3
  • 3
    • 44149084690 scopus 로고    scopus 로고
    • Using genetic markers to orient the edges in quantitative trait networks: The NEO software
    • doi: 10.1186/1752-0509-2-34
    • Aten JE, Fuller TF, Lusis AJ, Horvath S. 2008. Using genetic markers to orient the edges in quantitative trait networks: The NEO software. BMC Syst Biol 2: 34. doi: 10.1186/1752-0509-2-34.
    • (2008) BMC Syst Biol , vol.2 , pp. 34
    • Aten, J.E.1    Fuller, T.F.2    Lusis, A.J.3    Horvath, S.4
  • 6
    • 58349112341 scopus 로고    scopus 로고
    • Prioritizing risk pathways: A novel association approach to searching for disease pathways fusing SNPs and pathways
    • Chen L, Zhang L, Zhao Y, Xu L, Shang Y, Wang Q, Li W, Wang H, Li X. 2009. Prioritizing risk pathways: A novel association approach to searching for disease pathways fusing SNPs and pathways. Bioinformatics 25: 237-242.
    • (2009) Bioinformatics , vol.25 , pp. 237-242
    • Chen, L.1    Zhang, L.2    Zhao, Y.3    Xu, L.4    Shang, Y.5    Wang, Q.6    Li, W.7    Wang, H.8    Li, X.9
  • 8
    • 35348891430 scopus 로고    scopus 로고
    • Network-based classification of breast cancer metastasis
    • doi: 10.1038/msb4100180
    • Chuang HY, Lee E, Liu YT, Lee D, Ideker T. 2007. Network-based classification of breast cancer metastasis. Mol Syst Biol 3: 140. doi: 10.1038/msb4100180.
    • (2007) Mol Syst Biol , vol.3 , pp. 140
    • Chuang, H.Y.1    Lee, E.2    Liu, Y.T.3    Lee, D.4    Ideker, T.5
  • 11
    • 34249676425 scopus 로고    scopus 로고
    • A pragmatic suggestion for dealing with results for candidate genes obtained from genome wide association studies
    • doi: 10.1186/1471-2156-8-20
    • Curtis D, Vine AE, Knight J. 2007. A pragmatic suggestion for dealing with results for candidate genes obtained from genome wide association studies. BMC Genet 8: 20. doi: 10.1186/1471-2156-8-20.
    • (2007) BMC Genet , vol.8 , pp. 20
    • Curtis, D.1    Vine, A.E.2    Knight, J.3
  • 12
    • 42649086788 scopus 로고    scopus 로고
    • From gene expression to disease risk
    • Dermitzakis ET. 2008. From gene expression to disease risk. Nat Genet 40: 492-493.
    • (2008) Nat Genet , vol.40 , pp. 492-493
    • Dermitzakis, E.T.1
  • 13
    • 46249128543 scopus 로고    scopus 로고
    • Identifying functional modules in protein-protein interaction networks: An integrated exact approach
    • Dittrich MT, Klau GW, Rosenwald A, Dandekar T, Muller T. 2008. Identifying functional modules in protein-protein interaction networks: An integrated exact approach. Bioinformatics 24: 223-i231.
    • (2008) Bioinformatics , vol.24
    • Dittrich, M.T.1    Klau, G.W.2    Rosenwald, A.3    Dandekar, T.4    Muller, T.5
  • 14
    • 42249087793 scopus 로고    scopus 로고
    • Estimation of significance thresholds for genomewide association scans
    • Dudbridge F, Gusnanto A. 2008. Estimation of significance thresholds for genomewide association scans. Genet Epidemiol 32: 227-234.
    • (2008) Genet Epidemiol , vol.32 , pp. 227-234
    • Dudbridge, F.1    Gusnanto, A.2
  • 17
    • 70349629971 scopus 로고    scopus 로고
    • Using biological networks to search for interacting loci in genome-wide association studies
    • Emily M, Mailund T, Hein J, Schauser L, Schierup MH. 2009. Using biological networks to search for interacting loci in genome-wide association studies. Eur J Hum Genet 17: 1231-1240.
    • (2009) Eur J Hum Genet , vol.17 , pp. 1231-1240
    • Emily, M.1    Mailund, T.2    Hein, J.3    Schauser, L.4    Schierup, M.H.5
  • 18
    • 41649101685 scopus 로고    scopus 로고
    • Increasing power in association studies by using linkage disequilibrium structure and molecular function as prior information
    • Eskin E. 2008. Increasing power in association studies by using linkage disequilibrium structure and molecular function as prior information. Genome Res 18: 653-660.
    • (2008) Genome Res , vol.18 , pp. 653-660
    • Eskin, E.1
  • 22
    • 58549096683 scopus 로고    scopus 로고
    • Decanalization and the origin of complex disease
    • Gibson G. 2009. Decanalization and the origin of complex disease. Nat Rev Genet 10: 134-140.
    • (2009) Nat Rev Genet , vol.10 , pp. 134-140
    • Gibson, G.1
  • 24
    • 65949107547 scopus 로고    scopus 로고
    • Common genetic variation and human traits
    • Goldstein DB. 2009. Common genetic variation and human traits. N Engl J Med 360: 1696-1698.
    • (2009) N Engl J Med , vol.360 , pp. 1696-1698
    • Goldstein, D.B.1
  • 25
    • 56649097558 scopus 로고    scopus 로고
    • GSEA-SNP: Applying gene set enrichment analysis to SNP data from genome-wide association studies
    • Holden M, Deng S, Wojnowski L, Kulle B. 2008. GSEA-SNP: Applying gene set enrichment analysis to SNP data from genome-wide association studies. Bioinformatics 24: 2784-2785.
    • (2008) Bioinformatics , vol.24 , pp. 2784-2785
    • Holden, M.1    Deng, S.2    Wojnowski, L.3    Kulle, B.4
  • 26
    • 41649119247 scopus 로고    scopus 로고
    • Protein networks in disease
    • Ideker T, Sharan R. 2008. Protein networks in disease. Genome Res 18: 644-652.
    • (2008) Genome Res , vol.18 , pp. 644-652
    • Ideker, T.1    Sharan, R.2
  • 27
    • 40549109599 scopus 로고    scopus 로고
    • Pathway-based association analysis of genome-wide screening data suggest that genes associated with the gamma-aminobutyric acid receptor signaling pathway are involved in neuroleptic-induced, treatment-resistant tardive dyskinesia
    • Inada T, Koga M, Ishiguro H, Horiuchi Y, Syu A, Yoshio T, Takahashi N, Ozaki N, Arinami T. 2008. Pathway-based association analysis of genome-wide screening data suggest that genes associated with the gamma-aminobutyric acid receptor signaling pathway are involved in neuroleptic-induced, treatment-resistant tardive dyskinesia. Pharmacogenet Genomics 18: 317-323.
    • (2008) Pharmacogenet Genomics , vol.18 , pp. 317-323
    • Inada, T.1    Koga, M.2    Ishiguro, H.3    Horiuchi, Y.4    Syu, A.5    Yoshio, T.6    Takahashi, N.7    Ozaki, N.8    Arinami, T.9
  • 28
    • 46449111382 scopus 로고    scopus 로고
    • Geneticlinkage mapping of complex hereditary disorders to a wholegenome molecular-interaction network
    • Iossifov I, Zheng T, Baron M, Gilliam TC, Rzhetsky A. 2008. Geneticlinkage mapping of complex hereditary disorders to a wholegenome molecular-interaction network. Genome Res 18: 1150-1162.
    • (2008) Genome Res , vol.18 , pp. 1150-1162
    • Iossifov, I.1    Zheng, T.2    Baron, M.3    Gilliam, T.C.4    Rzhetsky, A.5
  • 29
    • 60849093174 scopus 로고    scopus 로고
    • A random forest approach to the detection of epistatic interactions in case-control studies
    • doi: 10.1186/1471-2105-10- S1-S-65
    • Jiang R, Tang W, Wu X, Fu W. 2009. A random forest approach to the detection of epistatic interactions in case-control studies. BMC Bioinformatics 10: doi: 10.1186/1471-2105-10- S1-S-65.
    • (2009) BMC Bioinformatics , vol.10
    • Jiang, R.1    Tang, W.2    Wu, X.3    Fu, W.4
  • 30
    • 48949116612 scopus 로고    scopus 로고
    • Network-guided genetic screening: Building, testing and using gene networks to predict gene function
    • Lehner B, Lee I. 2008. Network-guided genetic screening: Building, testing and using gene networks to predict gene function. Brief Funct Genomics Proteomics 7: 217-227.
    • (2008) Brief Funct Genomics Proteomics , vol.7 , pp. 217-227
    • Lehner, B.1    Lee, I.2
  • 32
    • 37549054343 scopus 로고    scopus 로고
    • A systematic method for mapping multiple loci: An application to construct a genetic network for rheumatoid arthritis
    • Li C, Zhang G, Li X, Rao S, Gong B, Jiang W, Hao D, Wu P, Wu C, Du L, et al. 2008. A systematic method for mapping multiple loci: An application to construct a genetic network for rheumatoid arthritis. Gene 408: 104-111.
    • (2008) Gene , vol.408 , pp. 104-111
    • Li, C.1    Zhang, G.2    Li, X.3    Rao, S.4    Gong, B.5    Jiang, W.6    Hao, D.7    Wu, P.8    Wu, C.9    Du, L.10
  • 33
    • 48249142391 scopus 로고    scopus 로고
    • Estimation and testing for the effect of a genetic pathway on a disease outcome using logistic kernel machine regression via logistic mixed models
    • doi: 10.1186/1471-2105-9-292
    • Liu D, Ghosh D, Lin X. 2008. Estimation and testing for the effect of a genetic pathway on a disease outcome using logistic kernel machine regression via logistic mixed models. BMC Bioinformatics 9: 292. doi: 10.1186/1471-2105-9-292.
    • (2008) BMC Bioinformatics , vol.9 , pp. 292
    • Liu, D.1    Ghosh, D.2    Lin, X.3
  • 34
    • 49049108362 scopus 로고    scopus 로고
    • Parallel and serial computing tools for testing single-locus and epistatic SNP effects of quantitative traits in genome-wide association studies
    • doi: 10.1186/1471-2105-9-315
    • Ma L, Runesha HB, Dvorkin D, Garbe JR, Da Y. 2008. Parallel and serial computing tools for testing single-locus and epistatic SNP effects of quantitative traits in genome-wide association studies. BMC Bioinformatics 9: 315. doi: 10.1186/1471-2105-9-315.
    • (2008) BMC Bioinformatics , vol.9 , pp. 315
    • Ma, L.1    Runesha, H.B.2    Dvorkin, D.3    Garbe, J.R.4    Da, Y.5
  • 35
    • 33745438900 scopus 로고    scopus 로고
    • GAIA: An easy-to-use web-based application for interaction analysis of case-control data
    • doi: 10.1186/1471-2350-7-34
    • Macgregor S, Khan IA. 2006. GAIA: An easy-to-use web-based application for interaction analysis of case-control data. BMC Med Genet 7: 34. doi: 10.1186/1471-2350-7-34.
    • (2006) BMC Med Genet , vol.7 , pp. 34
    • Macgregor, S.1    Khan, I.A.2
  • 36
    • 16844366786 scopus 로고    scopus 로고
    • Genome-wide strategies for detecting multiple loci that influence complex diseases
    • Marchini J, Donnelly P, Cardon LR. 2005. Genome-wide strategies for detecting multiple loci that influence complex diseases. Nat Genet 37: 413-417.
    • (2005) Nat Genet , vol.37 , pp. 413-417
    • Marchini, J.1    Donnelly, P.2    Cardon, L.R.3
  • 37
    • 58149347486 scopus 로고    scopus 로고
    • Genome-wide association studies: Potential next steps on a genetic journey
    • McCarthy MI, Hirschhorn JN. 2008. Genome-wide association studies: Potential next steps on a genetic journey. Hum Mol Genet 17: R156-R165.
    • (2008) Hum Mol Genet , vol.17
    • McCarthy, M.I.1    Hirschhorn, J.N.2
  • 38
    • 42949084703 scopus 로고    scopus 로고
    • Polymorphism interaction analysis (PIA): A method for investigating complex gene-gene interactions
    • doi:10.11861471-2105-9-146
    • Mechanic LE, Luke BT, Goodman JE, Chanock SJ, Harris CC. 2008. Polymorphism interaction analysis (PIA): A method for investigating complex gene-gene interactions. BMC Bioinform 9: 146. doi:10.11861471-2105-9-146.
    • (2008) BMC Bioinform , vol.9 , pp. 146
    • Mechanic, L.E.1    Luke, B.T.2    Goodman, J.E.3    Chanock, S.J.4    Harris, C.C.5
  • 39
    • 60549085927 scopus 로고    scopus 로고
    • Gene-wide analyses of genome-wide association data sets: Evidence for multiple common risk alleles for schizophrenia and bipolar disorder and for overlap in genetic risk
    • Moskvina V, Craddock N, Holmans P, Nikolov I, Pahwa JS, Green E, Owen MJ, O'Donovan MC. 2009. Gene-wide analyses of genome-wide association data sets: Evidence for multiple common risk alleles for schizophrenia and bipolar disorder and for overlap in genetic risk. Mol Psychiatry 14: 252-260.
    • (2009) Mol Psychiatry , vol.14 , pp. 252-260
    • Moskvina, V.1    Craddock, N.2    Holmans, P.3    Nikolov, I.4    Pahwa, J.S.5    Green, E.6    Owen, M.J.7    O'Donovan, M.C.8
  • 40
    • 43149116763 scopus 로고    scopus 로고
    • Gene-set approach for expression pattern analysis
    • Nam D, Kim SY. 2008. Gene-set approach for expression pattern analysis. Brief Bioinform 9: 189-197.
    • (2008) Brief Bioinform , vol.9 , pp. 189-197
    • Nam, D.1    Kim, S.Y.2
  • 41
    • 36949021059 scopus 로고    scopus 로고
    • Detecting high-order interactions of single nucleotide polymorphisms using genetic programming
    • Nunkesser R, Bernholt T, Schwender H, Ickstadt K, Wegener I. 2007. Detecting high-order interactions of single nucleotide polymorphisms using genetic programming. Bioinformatics 23: 3280-3288.
    • (2007) Bioinformatics , vol.23 , pp. 3280-3288
    • Nunkesser, R.1    Bernholt, T.2    Schwender, H.3    Ickstadt, K.4    Wegener, I.5
  • 43
    • 66649104469 scopus 로고    scopus 로고
    • Interrogating type 2 diabetes genome-wide association data using a biological pathway-based approach
    • Perry JR, McCarthy MI, Hattersley AT, Zeggini E, Weedon MN, Frayling TM. 2009. Interrogating type 2 diabetes genome-wide association data using a biological pathway-based approach. Diabetes 58: 1463-1467.
    • (2009) Diabetes , vol.58 , pp. 1463-1467
    • Perry, J.R.1    McCarthy, M.I.2    Hattersley, A.T.3    Zeggini, E.4    Weedon, M.N.5    Frayling, T.M.6
  • 45
    • 33847293352 scopus 로고    scopus 로고
    • Complex disease-associated pharmacogenetics: Drug efficacy, drug safety, and confirmation of a pathogenetic hypothesis (Alzheimer's disease)
    • Roses AD, Saunders AM, Huang Y, Strum J, Weisgraber KH, Mahley RW. 2007. Complex disease-associated pharmacogenetics: Drug efficacy, drug safety, and confirmation of a pathogenetic hypothesis (Alzheimer's disease). Pharmacogenomics J 7: 10-28.
    • (2007) Pharmacogenomics J , vol.7 , pp. 10-28
    • Roses, A.D.1    Saunders, A.M.2    Huang, Y.3    Strum, J.4    Weisgraber, K.H.5    Mahley, R.W.6
  • 46
    • 67349154804 scopus 로고    scopus 로고
    • Advances in systems biology are enhancing our understanding of disease and moving us closer to novel disease treatments
    • Schadt EE, Zhang B, Zhu J. 2009. Advances in systems biology are enhancing our understanding of disease and moving us closer to novel disease treatments. Genetica 136: 259-269.
    • (2009) Genetica , vol.136 , pp. 259-269
    • Schadt, E.E.1    Zhang, B.2    Zhu, J.3
  • 48
    • 0021824223 scopus 로고
    • Role of the apolipoprotein E polymorphism in determining normal plasma lipid and lipoprotein variation
    • Sing CF, Davignon J. 1985. Role of the apolipoprotein E polymorphism in determining normal plasma lipid and lipoprotein variation. Am J Hum Genet 37: 268-285.
    • (1985) Am J Hum Genet , vol.37 , pp. 268-285
    • Sing, C.F.1    Davignon, J.2
  • 52
    • 66649108315 scopus 로고    scopus 로고
    • Epistatic module detection for casecontrol studies: A Bayesian model with a Gibbs sampling strategy
    • doi: 10.1371/journal.pgen.1000464
    • Tang W, Wu X, Jiang R, Li Y. 2009. Epistatic module detection for casecontrol studies: A Bayesian model with a Gibbs sampling strategy. PLoS Genet 5: e1000464. doi: 10.1371/journal.pgen.1000464.
    • (2009) PLoS Genet , vol.5
    • Tang, W.1    Wu, X.2    Jiang, R.3    Li, Y.4
  • 53
    • 53649098737 scopus 로고    scopus 로고
    • Pathway analysis of seven common diseases assessed by genome-wide association
    • Torkamani A, Topol EJ, Schork NJ. 2008. Pathway analysis of seven common diseases assessed by genome-wide association. Genomics 92: 265-272.
    • (2008) Genomics , vol.92 , pp. 265-272
    • Torkamani, A.1    Topol, E.J.2    Schork, N.J.3
  • 57
    • 60849086187 scopus 로고    scopus 로고
    • Mega SNP Hunter: A learning approach to detect disease predisposition SNPs and high level interactions in genome wide association study
    • doi: 10.1186/1471-2105-10-13
    • Wan X, Yang C, Yang Q, Xue H, Tang NL, Yu W. 2009. Mega SNP Hunter: A learning approach to detect disease predisposition SNPs and high level interactions in genome wide association study. BMC Bioinformatics 10: 13. doi: 10.1186/1471-2105-10-13.
    • (2009) BMC Bioinformatics , vol.10 , pp. 13
    • Wan, X.1    Yang, C.2    Yang, Q.3    Xue, H.4    Tang, N.L.5    Yu, W.6
  • 58
    • 36249029788 scopus 로고    scopus 로고
    • Pathway-based approaches for analysis of genomewide association studies
    • Wang K, Li M, Bucan M. 2007. Pathway-based approaches for analysis of genomewide association studies. Am J Hum Genet 81: 1278-1283.
    • (2007) Am J Hum Genet , vol.81 , pp. 1278-1283
    • Wang, K.1    Li, M.2    Bucan, M.3
  • 61
    • 60149109479 scopus 로고    scopus 로고
    • SNPHarvester: A filtering-based approach for detecting epistatic interactions in genome-wide association studies
    • Yang C, He Z, Wan X, Yang Q, Xue H, Yu W. 2009. SNPHarvester: A filtering-based approach for detecting epistatic interactions in genome-wide association studies. Bioinformatics 25: 504-511.
    • (2009) Bioinformatics , vol.25 , pp. 504-511
    • Yang, C.1    He, Z.2    Wan, X.3    Yang, Q.4    Xue, H.5    Yu, W.6
  • 64
    • 0034531149 scopus 로고    scopus 로고
    • Complex adaptive systems and human health: The influence of common genotypes of the apolipoprotein E (ApoE) gene polymorphism and age on the relational order within a field of lipid metabolism traits
    • Zerba KE, Ferrell RE, Sing CF. 2000. Complex adaptive systems and human health: The influence of common genotypes of the apolipoprotein E (ApoE) gene polymorphism and age on the relational order within a field of lipid metabolism traits. Hum Genet 107: 466-475.
    • (2000) Hum Genet , vol.107 , pp. 466-475
    • Zerba, K.E.1    Ferrell, R.E.2    Sing, C.F.3
  • 65
    • 51749106170 scopus 로고    scopus 로고
    • Genetics of inflammatory bowel disease: Clues to pathogenesis
    • Zhang H, Massey D, Tremelling M, Parkes M. 2008. Genetics of inflammatory bowel disease: Clues to pathogenesis. Br Med Bull 87: 17-30.
    • (2008) Br Med Bull , vol.87 , pp. 17-30
    • Zhang, H.1    Massey, D.2    Tremelling, M.3    Parkes, M.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.