메뉴 건너뛰기




Volumn 12, Issue 5, 2014, Pages 210-220

Pathway-based analysis tools for complex diseases: A Review

Author keywords

Algorithms; Complex disease; Pathway based analysis; Software and databases

Indexed keywords

ALGORITHM; ANALYTIC METHOD; BIOMICS; COMPUTER PROGRAM; DATA BASE; GENETIC ANALYSIS; REVIEW; DISEASES; FACTUAL DATABASE; GENE REGULATORY NETWORK; GENETICS; HUMAN; SIGNAL TRANSDUCTION;

EID: 84922526304     PISSN: 16720229     EISSN: 22103244     Source Type: Journal    
DOI: 10.1016/j.gpb.2014.10.002     Document Type: Review
Times cited : (115)

References (63)
  • 1
    • 70350028725 scopus 로고    scopus 로고
    • Finding common susceptibility variants for complex disease: past, present and future
    • Panoutsopoulou K., Zeggini E. Finding common susceptibility variants for complex disease: past, present and future. Brief Funct Genomic Proteomic 2009, 8:345-352.
    • (2009) Brief Funct Genomic Proteomic , vol.8 , pp. 345-352
    • Panoutsopoulou, K.1    Zeggini, E.2
  • 2
    • 36249029788 scopus 로고    scopus 로고
    • Pathway-based approaches for analysis of genomewide association studies
    • Wang K., Li M., Bucan M. Pathway-based approaches for analysis of genomewide association studies. Am J Hum Genet 2007, 81:1278-1283.
    • (2007) Am J Hum Genet , vol.81 , pp. 1278-1283
    • Wang, K.1    Li, M.2    Bucan, M.3
  • 3
    • 35348983887 scopus 로고    scopus 로고
    • A second generation human haplotype map of over 3.1 million SNPs
    • International HapMap Consortium, Frazer KA, Ballinger DG, Cox DR, Hinds DA, Stuve LL, et al. A second generation human haplotype map of over 3.1 million SNPs. Nature 2007;449:851-61.
    • (2007) Nature , vol.449 , pp. 851-861
    • Frazer, K.A.1    Ballinger, D.G.2    Cox, D.R.3    Hinds, D.A.4    Stuve, L.L.5
  • 4
    • 2642583283 scopus 로고    scopus 로고
    • Mapping complex disease loci in whole-genome association studies
    • Carlson C.S., Eberle M.A., Kruglyak L., Nickerson D.A. Mapping complex disease loci in whole-genome association studies. Nature 2004, 429:446-452.
    • (2004) Nature , vol.429 , pp. 446-452
    • Carlson, C.S.1    Eberle, M.A.2    Kruglyak, L.3    Nickerson, D.A.4
  • 5
    • 33847194609 scopus 로고    scopus 로고
    • Human genetics: variants in common diseases
    • Freimer N.B., Sabatti C. Human genetics: variants in common diseases. Nature 2007, 445:828-830.
    • (2007) Nature , vol.445 , pp. 828-830
    • Freimer, N.B.1    Sabatti, C.2
  • 6
    • 67349166946 scopus 로고    scopus 로고
    • Detecting gene-gene interactions that underlie human diseases
    • Cordell H.J. Detecting gene-gene interactions that underlie human diseases. Nat Rev Genet 2009, 10:392-404.
    • (2009) Nat Rev Genet , vol.10 , pp. 392-404
    • Cordell, H.J.1
  • 7
    • 77949772292 scopus 로고    scopus 로고
    • Gene-environment-wide association studies: emerging approaches
    • Thomas D. Gene-environment-wide association studies: emerging approaches. Nat Rev Genet 2010, 11:259-272.
    • (2010) Nat Rev Genet , vol.11 , pp. 259-272
    • Thomas, D.1
  • 8
    • 69449103972 scopus 로고    scopus 로고
    • Epistasis and its implications for personal genetics
    • Moore J.H., Williams S.M. Epistasis and its implications for personal genetics. Am J Hum Genet 2009, 85:309-320.
    • (2009) Am J Hum Genet , vol.85 , pp. 309-320
    • Moore, J.H.1    Williams, S.M.2
  • 9
    • 67649584052 scopus 로고    scopus 로고
    • Gene ontology analysis of GWA study data sets provides insights into the biology of bipolar disorder
    • Holmans P., Green E.K., Pahwa J.S., Ferreira M.A., Purcell S.M., Sklar P., et al. Gene ontology analysis of GWA study data sets provides insights into the biology of bipolar disorder. Am J Hum Genet 2009, 85:13-24.
    • (2009) Am J Hum Genet , vol.85 , pp. 13-24
    • Holmans, P.1    Green, E.K.2    Pahwa, J.S.3    Ferreira, M.A.4    Purcell, S.M.5    Sklar, P.6
  • 12
    • 27344435774 scopus 로고    scopus 로고
    • Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles
    • Subramanian A., Tamayo P., Mootha V.K., Mukherjee S., Ebert B.L., Gillette M.A., et al. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci U S A 2005, 102:15545-15550.
    • (2005) Proc Natl Acad Sci U S A , vol.102 , pp. 15545-15550
    • Subramanian, A.1    Tamayo, P.2    Mootha, V.K.3    Mukherjee, S.4    Ebert, B.L.5    Gillette, M.A.6
  • 13
    • 77956192274 scopus 로고    scopus 로고
    • Common variants conferring risk of schizophrenia: a pathway analysis of GWAS data
    • Jia P., Wang L., Meltzer H.Y., Zhao Z. Common variants conferring risk of schizophrenia: a pathway analysis of GWAS data. Schizophr Res 2010, 122:38-42.
    • (2010) Schizophr Res , vol.122 , pp. 38-42
    • Jia, P.1    Wang, L.2    Meltzer, H.Y.3    Zhao, Z.4
  • 15
    • 67849101185 scopus 로고    scopus 로고
    • Gene set-based analysis of polymorphisms: finding pathways or biological processes associated to traits in genome-wide association studies
    • Medina I., Montaner D., Bonifaci N., Pujana M.A., Carbonell J., Tarraga J., et al. Gene set-based analysis of polymorphisms: finding pathways or biological processes associated to traits in genome-wide association studies. Nucleic Acids Res 2009, 37:W340-W344.
    • (2009) Nucleic Acids Res , vol.37 , pp. W340-W344
    • Medina, I.1    Montaner, D.2    Bonifaci, N.3    Pujana, M.A.4    Carbonell, J.5    Tarraga, J.6
  • 17
    • 58349105009 scopus 로고    scopus 로고
    • LRpath: a logistic regression approach for identifying enriched biological groups in gene expression data
    • Sartor M.A., Leikauf G.D., Medvedovic M. LRpath: a logistic regression approach for identifying enriched biological groups in gene expression data. Bioinformatics 2009, 25:211-217.
    • (2009) Bioinformatics , vol.25 , pp. 211-217
    • Sartor, M.A.1    Leikauf, G.D.2    Medvedovic, M.3
  • 19
    • 77958611364 scopus 로고    scopus 로고
    • Pathway-based analysis for genome-wide association studies using supervised principal components
    • Chen X., Wang L., Hu B., Guo M., Barnard J., Zhu X. Pathway-based analysis for genome-wide association studies using supervised principal components. Genet Epidemiol 2010, 34:716-724.
    • (2010) Genet Epidemiol , vol.34 , pp. 716-724
    • Chen, X.1    Wang, L.2    Hu, B.3    Guo, M.4    Barnard, J.5    Zhu, X.6
  • 21
    • 84871799820 scopus 로고    scopus 로고
    • Along signal paths: an empirical gene set approach exploiting pathway topology
    • Martini P., Sales G., Massa M.S., Chiogna M., Romualdi C. Along signal paths: an empirical gene set approach exploiting pathway topology. Nucleic Acids Res 2013, 41:e19.
    • (2013) Nucleic Acids Res , vol.41 , pp. e19
    • Martini, P.1    Sales, G.2    Massa, M.S.3    Chiogna, M.4    Romualdi, C.5
  • 22
    • 84861123691 scopus 로고    scopus 로고
    • Ten years of pathway analysis: current approaches and outstanding challenges
    • Khatri P., Sirota M., Butte A.J. Ten years of pathway analysis: current approaches and outstanding challenges. PLoS Comput Biol 2012, 8:e1002375.
    • (2012) PLoS Comput Biol , vol.8 , pp. e1002375
    • Khatri, P.1    Sirota, M.2    Butte, A.J.3
  • 23
    • 56149105091 scopus 로고    scopus 로고
    • The pathway less traveled: moving from candidate genes to candidate pathways in the analysis of genome-wide data from large scale pharmacogenetic association studies
    • Wilke R.A., Mareedu R.K., Moore J.H. The pathway less traveled: moving from candidate genes to candidate pathways in the analysis of genome-wide data from large scale pharmacogenetic association studies. Curr Pharmacogenomics Person Med 2008, 6:150-159.
    • (2008) Curr Pharmacogenomics Person Med , vol.6 , pp. 150-159
    • Wilke, R.A.1    Mareedu, R.K.2    Moore, J.H.3
  • 24
    • 84857797202 scopus 로고    scopus 로고
    • Bioinformatics and data mining studies in oral genomics and proteomics: new trends and challenges
    • Giacomelli L., Covani U. Bioinformatics and data mining studies in oral genomics and proteomics: new trends and challenges. Open Dent J 2010, 4:67-71.
    • (2010) Open Dent J , vol.4 , pp. 67-71
    • Giacomelli, L.1    Covani, U.2
  • 27
    • 85027954669 scopus 로고    scopus 로고
    • Genome-wide pathway analysis of genome-wide association studies on systemic lupus erythematosus and rheumatoid arthritis
    • Lee Y.H., Bae S.C., Choi S.J., Ji J.D., Song G.G. Genome-wide pathway analysis of genome-wide association studies on systemic lupus erythematosus and rheumatoid arthritis. Mol Biol Rep 2012, 39:10627-10635.
    • (2012) Mol Biol Rep , vol.39 , pp. 10627-10635
    • Lee, Y.H.1    Bae, S.C.2    Choi, S.J.3    Ji, J.D.4    Song, G.G.5
  • 28
    • 84872897224 scopus 로고    scopus 로고
    • Exploring the pathogenetic association between schizophrenia and type 2 diabetes mellitus diseases based on pathway analysis
    • Liu Y., Li Z., Zhang M., Deng Y., Yi Z., Shi T. Exploring the pathogenetic association between schizophrenia and type 2 diabetes mellitus diseases based on pathway analysis. BMC Med Genomics 2013, 6:S17.
    • (2013) BMC Med Genomics , vol.6 , pp. S17
    • Liu, Y.1    Li, Z.2    Zhang, M.3    Deng, Y.4    Yi, Z.5    Shi, T.6
  • 29
    • 77449140764 scopus 로고    scopus 로고
    • Gene and pathway-based second-wave analysis of genome-wide association studies
    • 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 2010, 18:111-117.
    • (2010) Eur J Hum Genet , vol.18 , pp. 111-117
    • Peng, G.1    Luo, L.2    Siu, H.3    Zhu, Y.4    Hu, P.5    Hong, S.6
  • 30
    • 77953920566 scopus 로고    scopus 로고
    • Pathway analysis comparison using Crohn's disease genome wide association studies
    • Ballard D., Abraham C., Cho J., Zhao H. Pathway analysis comparison using Crohn's disease genome wide association studies. BMC Med Genomics 2010, 3:25.
    • (2010) BMC Med Genomics , vol.3 , pp. 25
    • Ballard, D.1    Abraham, C.2    Cho, J.3    Zhao, H.4
  • 31
    • 73449129315 scopus 로고    scopus 로고
    • Prior biological knowledge-based approaches for the analysis of genome-wide expression profiles using gene sets and pathways
    • Wu M.C., Lin X. Prior biological knowledge-based approaches for the analysis of genome-wide expression profiles using gene sets and pathways. Stat Methods Med Res 2009, 18:577-593.
    • (2009) Stat Methods Med Res , vol.18 , pp. 577-593
    • Wu, M.C.1    Lin, X.2
  • 32
    • 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., et al. Prioritizing risk pathways: a novel association approach to searching for disease pathways fusing SNPs and pathways. Bioinformatics 2009, 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
  • 33
    • 18744389489 scopus 로고    scopus 로고
    • Significance analysis of functional categories in gene expression studies: a structured permutation approach
    • Barry W.T., Nobel A.B., Wright F.A. Significance analysis of functional categories in gene expression studies: a structured permutation approach. Bioinformatics 2005, 21:1943-1949.
    • (2005) Bioinformatics , vol.21 , pp. 1943-1949
    • Barry, W.T.1    Nobel, A.B.2    Wright, F.A.3
  • 34
    • 0035829361 scopus 로고    scopus 로고
    • Controlling the false discovery rate in behavior genetics research
    • Benjamini Y., Drai D., Elmer G., Kafkafi N., Golani I. Controlling the false discovery rate in behavior genetics research. Behav Brain Res 2001, 125:279-284.
    • (2001) Behav Brain Res , vol.125 , pp. 279-284
    • Benjamini, Y.1    Drai, D.2    Elmer, G.3    Kafkafi, N.4    Golani, I.5
  • 35
    • 77949853541 scopus 로고    scopus 로고
    • Gene, region and pathway level analyses in whole-genome studies
    • De la Cruz O., Wen X., Ke B., Song M., Nicolae D.L. Gene, region and pathway level analyses in whole-genome studies. Genet Epidemiol 2010, 34:222-231.
    • (2010) Genet Epidemiol , vol.34 , pp. 222-231
    • De la Cruz, O.1    Wen, X.2    Ke, B.3    Song, M.4    Nicolae, D.L.5
  • 36
    • 68949204302 scopus 로고    scopus 로고
    • Strategies and issues in the detection of pathway enrichment in genome-wide association studies
    • Hong M.G., Pawitan Y., Magnusson P.K., Prince J.A. Strategies and issues in the detection of pathway enrichment in genome-wide association studies. Hum Genet 2009, 126:289-301.
    • (2009) Hum Genet , vol.126 , pp. 289-301
    • Hong, M.G.1    Pawitan, Y.2    Magnusson, P.K.3    Prince, J.A.4
  • 38
    • 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
    • Liu D., Ghosh D., Lin X. 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 2008, 9:292.
    • (2008) BMC Bioinformatics , vol.9 , pp. 292
    • Liu, D.1    Ghosh, D.2    Lin, X.3
  • 40
    • 0033982936 scopus 로고    scopus 로고
    • KEGG: Kyoto encyclopedia of genes and genomes
    • Kanehisa M., Goto S. KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res 2000, 28:27-30.
    • (2000) Nucleic Acids Res , vol.28 , pp. 27-30
    • Kanehisa, M.1    Goto, S.2
  • 43
  • 44
    • 0141742293 scopus 로고    scopus 로고
    • PANTHER: a library of protein families and subfamilies indexed by function
    • Thomas P.D., Campbell M.J., Kejariwal A., Mi H., Karlak B., Daverman R., et al. PANTHER: a library of protein families and subfamilies indexed by function. Genome Res 2003, 13:2129-2141.
    • (2003) Genome Res , vol.13 , pp. 2129-2141
    • Thomas, P.D.1    Campbell, M.J.2    Kejariwal, A.3    Mi, H.4    Karlak, B.5    Daverman, R.6
  • 45
    • 77956482678 scopus 로고    scopus 로고
    • Gene set analysis exploiting the topology of a pathway
    • Massa M.S., Chiogna M., Romualdi C. Gene set analysis exploiting the topology of a pathway. BMC Syst Biol 2010, 4:121.
    • (2010) BMC Syst Biol , vol.4 , pp. 121
    • Massa, M.S.1    Chiogna, M.2    Romualdi, C.3
  • 47
    • 84856327481 scopus 로고    scopus 로고
    • Graphite - a Bioconductor package to convert pathway topology to gene network
    • Sales G., Calura E., Cavalieri D., Romualdi C. Graphite - a Bioconductor package to convert pathway topology to gene network. BMC Bioinformatics 2012, 13:20.
    • (2012) BMC Bioinformatics , vol.13 , pp. 20
    • Sales, G.1    Calura, E.2    Cavalieri, D.3    Romualdi, C.4
  • 48
    • 84883595410 scopus 로고    scopus 로고
    • Graphite web: web tool for gene set analysis exploiting pathway topology
    • Sales G., Calura E., Martini P., Romualdi C. Graphite web: web tool for gene set analysis exploiting pathway topology. Nucleic Acids Res 2013, 41:W89-W97.
    • (2013) Nucleic Acids Res , vol.41 , pp. W89-W97
    • Sales, G.1    Calura, E.2    Martini, P.3    Romualdi, C.4
  • 50
    • 77949497074 scopus 로고    scopus 로고
    • Bioinformatics challenges for genome-wide association studies
    • Moore J.H., Asselbergs F.W., Williams S.M. Bioinformatics challenges for genome-wide association studies. Bioinformatics 2010, 26:445-455.
    • (2010) Bioinformatics , vol.26 , pp. 445-455
    • Moore, J.H.1    Asselbergs, F.W.2    Williams, S.M.3
  • 51
    • 77951646119 scopus 로고    scopus 로고
    • Functional genomics and networks: new approaches in the extraction of complex gene modules
    • Minguez P., Dopazo J. Functional genomics and networks: new approaches in the extraction of complex gene modules. Expert Rev Proteomics 2010, 7:55-63.
    • (2010) Expert Rev Proteomics , vol.7 , pp. 55-63
    • Minguez, P.1    Dopazo, J.2
  • 52
    • 33745427131 scopus 로고    scopus 로고
    • Tracking the epidemiology of human genes in the literature: the HuGE Published Literature database
    • Lin B.K., Clyne M., Walsh M., Gomez O., Yu W., Gwinn M., et al. Tracking the epidemiology of human genes in the literature: the HuGE Published Literature database. Am J Epidemiol 2006, 164:1-4.
    • (2006) Am J Epidemiol , vol.164 , pp. 1-4
    • Lin, B.K.1    Clyne, M.2    Walsh, M.3    Gomez, O.4    Yu, W.5    Gwinn, M.6
  • 53
    • 78549251736 scopus 로고    scopus 로고
    • Analysing biological pathways in genome-wide association studies
    • Wang K., Li M., Hakonarson H. Analysing biological pathways in genome-wide association studies. Nat Rev Genet 2010, 11:843-854.
    • (2010) Nat Rev Genet , vol.11 , pp. 843-854
    • Wang, K.1    Li, M.2    Hakonarson, H.3
  • 54
    • 79959735144 scopus 로고    scopus 로고
    • Gene set analysis of genome-wide association studies: methodological issues and perspectives
    • Wang L., Jia P., Wolfinger R.D., Chen X., Zhao Z. Gene set analysis of genome-wide association studies: methodological issues and perspectives. Genomics 2011, 98:1-8.
    • (2011) Genomics , vol.98 , pp. 1-8
    • Wang, L.1    Jia, P.2    Wolfinger, R.D.3    Chen, X.4    Zhao, Z.5
  • 55
    • 84862499271 scopus 로고    scopus 로고
    • Pathway analysis of genomic data: concepts, methods, and prospects for future development
    • Ramanan V.K., Shen L., Moore J.H., Saykin A.J. Pathway analysis of genomic data: concepts, methods, and prospects for future development. Trends Genet 2012, 28:323-332.
    • (2012) Trends Genet , vol.28 , pp. 323-332
    • Ramanan, V.K.1    Shen, L.2    Moore, J.H.3    Saykin, A.J.4
  • 56
    • 77954300600 scopus 로고    scopus 로고
    • GSA-SNP: a general approach for gene set analysis of polymorphisms
    • Nam D., Kim J., Kim S.Y., Kim S. GSA-SNP: a general approach for gene set analysis of polymorphisms. Nucleic Acids Res 2010, 38:W749-W754.
    • (2010) Nucleic Acids Res , vol.38 , pp. W749-W754
    • Nam, D.1    Kim, J.2    Kim, S.Y.3    Kim, S.4
  • 57
    • 75149134369 scopus 로고    scopus 로고
    • A new permutation strategy of pathway-based approach for genome-wide association study
    • Guo Y.F., Li J., Chen Y., Zhang L.S., Deng H.W. A new permutation strategy of pathway-based approach for genome-wide association study. BMC Bioinformatics 2009, 10:429.
    • (2009) BMC Bioinformatics , vol.10 , pp. 429
    • Guo, Y.F.1    Li, J.2    Chen, Y.3    Zhang, L.S.4    Deng, H.W.5
  • 59
    • 53649106195 scopus 로고    scopus 로고
    • Next-generation DNA sequencing
    • Shendure J., Ji H. Next-generation DNA sequencing. Nat Biotechnol 2008, 26:1135-1145.
    • (2008) Nat Biotechnol , vol.26 , pp. 1135-1145
    • Shendure, J.1    Ji, H.2
  • 60
    • 77951642029 scopus 로고    scopus 로고
    • Selection and mutation in the "new" genetics: an emerging hypothesis
    • Gottlieb B., Beitel L.K., Alvarado C., Trifiro M.A. Selection and mutation in the "new" genetics: an emerging hypothesis. Hum Genet 2010, 127:491-501.
    • (2010) Hum Genet , vol.127 , pp. 491-501
    • Gottlieb, B.1    Beitel, L.K.2    Alvarado, C.3    Trifiro, M.A.4
  • 61
    • 46649099510 scopus 로고    scopus 로고
    • 1000 Genomes project
    • Siva N. 1000 Genomes project. Nat Biotechnol 2008, 26:256.
    • (2008) Nat Biotechnol , vol.26 , pp. 256
    • Siva, N.1
  • 62
    • 84924753131 scopus 로고    scopus 로고
    • Pathway analysis with next-generation sequencing data
    • Zhao J, Zhu Y, Boerwinkle E, Xiong M. Pathway analysis with next-generation sequencing data. Eur J Hum Genet 2014. http://dx.doi.org/10.1038/ejhg.2014.121.
    • (2014) Eur J Hum Genet
    • Zhao, J.1    Zhu, Y.2    Boerwinkle, E.3    Xiong, M.4
  • 63
    • 84880798154 scopus 로고    scopus 로고
    • Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data
    • Chin C.S., Alexander D.H., Marks P., Klammer A.A., Drake J., Heiner C., et al. Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat Methods 2013, 10:563-569.
    • (2013) Nat Methods , vol.10 , pp. 563-569
    • Chin, C.S.1    Alexander, D.H.2    Marks, P.3    Klammer, A.A.4    Drake, J.5    Heiner, C.6


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.