References
- P. Y. P. Kao, K. H. Leung, L. W. C. Chan, S. P. Yip, M. K. H. Yap, "Pathway analysis of complex diseases for GWAS, extending to consider rare variants, multi-omics and interactions", Biochimica et Biophysica Acta, Vol. 1861, Issue. 2, pp. 335-353, 2017. https://doi.org/10.1016/j.bbagen.2016.11.030
- S. E. Kim, H. Kim, Y. Yun, S. G. Heo, J. Cho, M. Kwon, Y. Chang, S. Ryu, H. Shin, C. Shin, N. H. Cho, Y. A. Sung, H. Kim, "Meta-analysis of genome-wide SNP- and pathway-based associations for facets of neuroticism", Journal of Human Genetics, Vol. 62, pp. 903-909, 2017. https://doi.org/10.1038/jhg.2017.61
- J. Wu, X. Mao, T. Cai, J. Luo, L. Wei, "KOBAS server: a web-based platform for automated annotation and pathway identification", Nucleic Acids Research, Vol. 34, W720-724, 2006. https://doi.org/10.1093/nar/gkl167
- L. Weng, F. Macciardi, A. Subramanian, G. Guffanti, S. G. Potkin, Z. Yu, X. Xie, "SNP-based pathway enrichment analysis for genome-wide association studies", BMC Bioinformatics, 12:99, 2011. https://doi.org/10.1186/1471-2105-12-99
- I. Medina, D. Montaner, N. Bonifaci, M. A. Pujana, J. Carbonell, J. Tarraga, F. Al-Shahrour, J. Dopazo, "Gene set-based analysis of polymorphisms: finding pathways or biological processes associated to traits in genome-wide association studies", Nucleic Acids Research, Vol. 37, W340-344, 2009. https://doi.org/10.1093/nar/gkp481
- P. Holmans, E. K. Green, J. S. Pahwa, M. A. Ferreira, S. M. Purcell, P. Sklar, Wellcome Trust Case-Control Consortium, M. J. Owen, M. C. O'Donovan, N. Craddock, "Gene ontology analysis of GWA study data sets provides insights into the biology of bipolar disorder", American Journal of Human Genetics, Vol. 85, pp. 13-24, 2009. https://doi.org/10.1016/j.ajhg.2009.05.011
- D. Zamar, B. Tripp, G. Ellis, D. Daley, "Path: a tool to facilitate pathway-based genetic association analysis", Bioinformatics, Vol. 25, pp. 2444-2446, 2009. https://doi.org/10.1093/bioinformatics/btp431
- R. M. Cantor, K. Lange, J. S. Sinsheimer, "Prioritizing GWAS Results: A review of statistical methods and recommendations for their application", American Journal of Human Genetics, Vol. 86, pp. 6-22, 2010. https://doi.org/10.1016/j.ajhg.2009.11.017
- K. Zhang, S. Cui, S. Chang, L. Zhang, J. Wang, "i-GSEA4GWAS: a web server for identification of pathways/gene sets associated with traits by applying an improved gene set enrichment analysis to genome-wide association study", Nucleic Acids Research, Vol. 38, W90-95, 2010. https://doi.org/10.1093/nar/gkq324
- E. Cirillo, M. Kutmon, M. G. Hernandez, T. Hooimeijer, M. E. Adriaens, L. M. T. Eijssen, L. D. Parnell, S. L. Coort, C. T. Evelo, "From SNPs to pathways: Biological interpretation of type 2 diabetes (T2DM) genome wide association study (GWAS) results", PLoS ONE, Vol. 13, No. 4, 2018.
- D. W. Huang, B. T. Sherman, R. A. Lempicki, "Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists", Nucleic Acids Res, Vol. 37, pp. 1-13, 2009. https://doi.org/10.1093/nar/gkn923
- G. Peng, L. Luo, H. Siu, Y. Zhu, P. Hu, S. Hong, J. Zhao, X. Zhou, J. D. Reveille, L. Jin, C. I. Amos, M. Xiong, "Gene and pathway-based second-wave analysis of genome-wide association studies", European Journal of Human Genetics, Vol. 18, pp. 111-117, 2010. https://doi.org/10.1038/ejhg.2009.115
- H. J. Ban, J. Y. Heo, K. S. Oh, K.J. Park, "Identification of type 2 diabetes-associated combination of SNPs using support vector machine", BMC Genetics, Vol. 23, pp. 11-26, 2010.
- K. Zhang, S. Chang, S. Cui, L. Guo, L. Zhang, J. Wang, "ICSNPathway: identify candidate causal SNPs and pathways from genome-wide association study by one analytical framework", Nucleic Acids Research, Vol. 39, W437-443, 2011. https://doi.org/10.1093/nar/gkr391
- D. F. Schwarz, O. Hädicke, J. Erdmann, A. Ziegler, D. Bayer, S. Moller, "SNPtoGO: characterizing SNPs by enriched GO terms", Bioinformatics, Vol. 24, pp. 146-148, 2008. https://doi.org/10.1093/bioinformatics/btm551
- dbSNP : a database of single nucleotide polymorphisms [Internet]. Available: http://www.ncbi.nlm.nih.gov/projects/SNP.
- refGene [Internet]. Available: http://www.ncbi.nlm.nih.gov/RefSeq.
- K. Sidiropoulos, G. Viteri, C. Sevilla, S. Jupe, M. Webber, M. Orlic-Milacic, B. Jassal, B. May, V. Shamovsky, C. Duenas, K. Rothfels, L. Matthews, H. Song, L. Stein, R. Haw, P. D'Eustachio, P. Ping, H. Hermjakob, A. Fabregat, "Reactome enhanced pathway visualization", Bioinformatics, Vol. 33, Issue. 21, pp. 3461-3467, 2017. https://doi.org/10.1093/bioinformatics/btx441
- A. Subramanian, P. Tamayo, V. K. Mootha, S. Mukherjee, B. L. Ebert, M.A. Gillette, A. Paulovich, S. L. Pomeroy, T. R. Golub, E. S. Lander, J. P. Mesirov, "Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles", Proc Natl Acad Sci USA, Vol. 102, pp. 15545-15550, 2005. https://doi.org/10.1073/pnas.0506580102
- Kyoto Encyclopedia of Genes and Genomes (KEGG) [Internet]. Available: http://www.genome.jp/kegg.
- Gene Ontology database [Internet]. Available: http://www.geneontology.org.
- A. Hamosh, A. F. Scott, J. S. Amberger, C. A. Bocchini, V. A. McKusick, "Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders", Nucleic Acids Research, Vol. 33, Issue. supp. l_1, pp. D514-D517, 2005.
- M. A. Garcia-Campos, J. Espinal-Enriquez, E. Hernandez-Lemus, "Pathway Analysis: State of the Art", Frontiers in Physiology, 6:383, 2015.
- S. R. Chowbina, X. Wu, F. Zhang, P. M. Li, R. Pandey, H. N. Kasamsetty, J.Y. Chen, "HPD: an online integrated human pathway database enabling systems biology studies", BMC Bioinformatics, Vol. 10, Suppl 11:S5, 2009.
- S. Purcell, B. Neale, K. Todd-Brown, L. Thomas, M. A. R. Ferreira, D. Bender, J. Maller, P. Sklar, P. I. W. de Bakker, M. J. Daly, P. C. Sham, "PLINK: A Tool Set for Whole-Genome Association and Population-Based Linkage Analyses", The American Journal of Human Genetics, Vol. 81, Issue. 3, pp. 559-575, 2007. https://doi.org/10.1086/519795