{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,11]],"date-time":"2026-03-11T23:29:32Z","timestamp":1773271772582,"version":"3.50.1"},"reference-count":42,"publisher":"Springer Science and Business Media LLC","issue":"S1","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Genomics"],"published-print":{"date-parts":[[2014,1]]},"DOI":"10.1186\/1471-2164-15-s1-s10","type":"journal-article","created":{"date-parts":[[2014,1,24]],"date-time":"2014-01-24T16:36:05Z","timestamp":1390581365000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":5,"title":["Supervised categorical principal component analysis for genome-wide association analyses"],"prefix":"10.1186","volume":"15","author":[{"given":"Meng","family":"Lu","sequence":"first","affiliation":[]},{"given":"Hye-Seung","family":"Lee","sequence":"additional","affiliation":[]},{"given":"David","family":"Hadley","sequence":"additional","affiliation":[]},{"given":"Jianhua Z","family":"Huang","sequence":"additional","affiliation":[]},{"given":"Xiaoning","family":"Qian","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2014,1,24]]},"reference":[{"issue":"2","key":"5683_CR1","doi-asserted-by":"publisher","first-page":"166","DOI":"10.1056\/NEJMra0905980","volume":"363","author":"TA Manolio","year":"2010","unstructured":"Manolio TA: Genomewide association studies and assessment of the risk of disease. N Engl J Med. 2010, 363 (2): 166-176. 10.1056\/NEJMra0905980.","journal-title":"N Engl J Med"},{"key":"5683_CR2","doi-asserted-by":"publisher","first-page":"846","DOI":"10.1093\/jnci\/djq173","volume":"102","author":"J Ioannidis","year":"2010","unstructured":"Ioannidis J, Castaldi P, Evangelou E: A compendium of genome-wide associations for cancer: Critical synopsis and reappraisal. Journal of the National Cancer Institute. 2010, 102: 846-858. 10.1093\/jnci\/djq173.","journal-title":"Journal of the National Cancer Institute"},{"key":"5683_CR3","doi-asserted-by":"publisher","first-page":"45","DOI":"10.1097\/00125817-200203000-00002","volume":"4","author":"JN Hirschhorn","year":"2002","unstructured":"Hirschhorn JN, Lohmueller K, Byrne E, Hirschhorn K: A comprehensive review of genetic association studies. Genet Med. 2002, 4: 45-61. 10.1097\/00125817-200203000-00002.","journal-title":"Genet Med"},{"key":"5683_CR4","volume-title":"Permutation-based Pathway Testing Using the Super Learner Algorithm","author":"P Chaffee","year":"2009","unstructured":"Chaffee P, et al: Permutation-based Pathway Testing Using the Super Learner Algorithm. 2009, University of California, Berkely, Berkely"},{"issue":"12","key":"5683_CR5","doi-asserted-by":"publisher","first-page":"2115","DOI":"10.1101\/gr.204001","volume":"11","author":"J Hoh","year":"2001","unstructured":"Hoh J, Wille A, Ott J: Trimming, weighting, and grouping SNPs in human case-control association studies. Genome Res. 2001, 11 (12): 2115-2119. 10.1101\/gr.204001.","journal-title":"Genome Res"},{"issue":"23","key":"5683_CR6","doi-asserted-by":"publisher","first-page":"2784","DOI":"10.1093\/bioinformatics\/btn516","volume":"24","author":"M Holden","year":"2008","unstructured":"Holden M, Deng S, Wojnowski L, Kulle B: GSEA-SNP: Applying gene set enrichment analysis to SNP data from genome-wide association studies. Bioinformatics. 2008, 24 (23): 2784-2785. 10.1093\/bioinformatics\/btn516.","journal-title":"Bioinformatics"},{"key":"5683_CR7","doi-asserted-by":"publisher","first-page":"1278","DOI":"10.1086\/522374","volume":"81","author":"K Wang","year":"2007","unstructured":"Wang K, Li M, Bucan M: Pathway-based approaches for analysis of genomewide association studies. Am J Hum Genet. 2007, 81: 1278-1283. 10.1086\/522374.","journal-title":"Am J Hum Genet"},{"issue":"2","key":"5683_CR8","first-page":"353","volume":"80","author":"T Wang","year":"2007","unstructured":"Wang T, Elston RC: Improved power by use of a weighted score test for linkage disequilibrium mapping. Bioinformatics. 2007, 80 (2): 353-360.","journal-title":"Bioinformatics"},{"key":"5683_CR9","doi-asserted-by":"publisher","first-page":"111","DOI":"10.1038\/ejhg.2009.115","volume":"18","author":"G Peng","year":"2010","unstructured":"Peng G, et al: Gene and pathway-based analysis: Second wave of genome-wide association studies. Eur J Hum Genet. 2010, 18: 111-117. 10.1038\/ejhg.2009.115.","journal-title":"Eur J Hum Genet"},{"issue":"43","key":"5683_CR10","doi-asserted-by":"publisher","first-page":"15545","DOI":"10.1073\/pnas.0506580102","volume":"102","author":"A Subramanian","year":"2005","unstructured":"Subramanian A, et al: Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acac Sci. 2005, 102 (43): 15545-15550. 10.1073\/pnas.0506580102.","journal-title":"Proc Natl Acac Sci"},{"issue":"2","key":"5683_CR11","doi-asserted-by":"publisher","first-page":"929","DOI":"10.1016\/j.ajhg.2010.05.002","volume":"86","author":"MC Wu","year":"2010","unstructured":"Wu MC, Others: Powerful snp-set analysis for case-control genome-wide association studies. The American Journal of Human Genetics. 2010, 86 (2): 929-942.","journal-title":"The American Journal of Human Genetics"},{"issue":"2","key":"5683_CR12","doi-asserted-by":"publisher","first-page":"386","DOI":"10.1016\/j.ajhg.2007.10.010","volume":"82","author":"LC Kwee","year":"2008","unstructured":"Kwee LC, Liu D, Lin X, Ghosh D, Epstein MP: A powerful and flexible multilocus association test for quantitative traits. The American Journal of Human Genetics. 2008, 82 (2): 386-397. 10.1016\/j.ajhg.2007.10.010.","journal-title":"The American Journal of Human Genetics"},{"key":"5683_CR13","volume-title":"ACM Conference on Bioinformatics, Computational Biology and Biomedicine (ACM BCB)","author":"M Lu","year":"2012","unstructured":"Lu M, Huang J, Qian X: Supervised logistic principal component analysis for pathway based genome-wide association studies. ACM Conference on Bioinformatics, Computational Biology and Biomedicine (ACM BCB). 2012"},{"key":"5683_CR14","doi-asserted-by":"publisher","first-page":"1045","DOI":"10.1038\/ejhg.2010.62","volume":"18","author":"L Luo","year":"2010","unstructured":"Luo L, et al: Genome-wide gene and pathway analysis. Eur J Hum Genet. 2010, 18: 1045-1053. 10.1038\/ejhg.2010.62.","journal-title":"Eur J Hum Genet"},{"key":"5683_CR15","doi-asserted-by":"publisher","first-page":"99","DOI":"10.1186\/1471-2105-12-99","volume":"12","author":"L Weng","year":"2011","unstructured":"Weng L, et al: SNP-based pathway enrichment analysis for genome-wide association studies. BMC Bioinformatics. 2011, 12: 99-10.1186\/1471-2105-12-99.","journal-title":"BMC Bioinformatics"},{"issue":"8","key":"5683_CR16","doi-asserted-by":"publisher","first-page":"700","DOI":"10.1002\/gepi.20422","volume":"33","author":"K Yu","year":"2009","unstructured":"Yu K, et al: Pathway analysis by adaptive combination of p-values. Genet Epidemiol. 2009, 33 (8): 700-709. 10.1002\/gepi.20422.","journal-title":"Genet Epidemiol"},{"issue":"4","key":"5683_CR17","doi-asserted-by":"publisher","first-page":"401","DOI":"10.1093\/bioinformatics\/btl633","volume":"23","author":"S Rivals","year":"2007","unstructured":"Rivals S, et al: Enrichment or depletion of a go category within a class of genes: which test?. Bioinformatics. 2007, 23 (4): 401-407. 10.1093\/bioinformatics\/btl633.","journal-title":"Bioinformatics"},{"issue":"4","key":"5683_CR18","doi-asserted-by":"publisher","first-page":"497","DOI":"10.1093\/bioinformatics\/btn641","volume":"25","author":"M Li","year":"2008","unstructured":"Li M, Wang K, Grant SFA, Hakonarson H, Li C: Atom: a powerful gene-based association test by combining optimally weighted markers. Bioinformatics. 2008, 25 (4): 497-503.","journal-title":"Bioinformatics"},{"key":"5683_CR19","doi-asserted-by":"publisher","first-page":"716","DOI":"10.1002\/gepi.20532","volume":"34","author":"X Chen","year":"2010","unstructured":"Chen X, Wang L, Hu B, Guo M, Barnard J, Zhu X: Pathway-based analysis for genome-wide association studies using supervised principal components. Genetic Epidemiology. 2010, 34: 716-724. 10.1002\/gepi.20532.","journal-title":"Genetic Epidemiology"},{"key":"5683_CR20","doi-asserted-by":"publisher","first-page":"780","DOI":"10.1086\/429838","volume":"76","author":"DJ Schaid","year":"2005","unstructured":"Schaid DJ, et al: Nonparametric tests of association of multiple genes with human disease. The American Journal of Human Genetics. 2005, 76: 780-793. 10.1086\/429838.","journal-title":"The American Journal of Human Genetics"},{"issue":"6","key":"5683_CR21","doi-asserted-by":"publisher","first-page":"446","DOI":"10.1038\/nrg2809","volume":"11","author":"EE Eichler","year":"2010","unstructured":"Eichler EE, et al: Missing heritability and strategies for finding the underlying causes of complex disease. Nat Rev Genet. 2010, 11 (6): 446-450. 10.1038\/nrg2809.","journal-title":"Nat Rev Genet"},{"issue":"12","key":"5683_CR22","doi-asserted-by":"publisher","first-page":"1598","DOI":"10.1093\/bioinformatics\/bts180","volume":"28","author":"TS Shah","year":"2012","unstructured":"Shah TS, Liu JZ, Floyd JAB, Morris JA, Wirth N, Barrett JC, Anderson CA: opticall: a robust genotype-calling algorithm for rare, low-frequency and common variants. Bioinformatics. 2012, 28 (12): 1598-1603. 10.1093\/bioinformatics\/bts180.","journal-title":"Bioinformatics"},{"key":"5683_CR23","doi-asserted-by":"publisher","first-page":"661","DOI":"10.1038\/nature05911","volume":"447","author":"Wellcome Trust Case Control Consortium","year":"2007","unstructured":"Wellcome Trust Case Control Consortium: Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls. Nature. 2007, 447: 661-678. 10.1038\/nature05911.","journal-title":"Nature"},{"issue":"3","key":"5683_CR24","doi-asserted-by":"publisher","first-page":"1579","DOI":"10.1214\/10-AOAS327","volume":"4","author":"S Lee","year":"2010","unstructured":"Lee S, Huang JZ, Hu J: Sparse logistic principal components analysis for binary data. The Annals of Applied Statistics. 2010, 4 (3): 1579-1601. 10.1214\/10-AOAS327.","journal-title":"The Annals of Applied Statistics"},{"issue":"473","key":"5683_CR25","doi-asserted-by":"publisher","first-page":"119","DOI":"10.1198\/016214505000000628","volume":"101","author":"E Bair","year":"2006","unstructured":"Bair E, Hastie T, Paul D, Tibshirani R: Prediction by supervised principal components. Journal of the American Statistical Association. 2006, 101 (473): 119-137. 10.1198\/016214505000000628.","journal-title":"Journal of the American Statistical Association"},{"issue":"2","key":"5683_CR26","doi-asserted-by":"publisher","first-page":"559","DOI":"10.1080\/14786440109462720","volume":"6","author":"K Pearson","year":"1901","unstructured":"Pearson K: On lines and planes of closest fit to systems of points in space. The London, Edinburgh and Dublin Pholosophical Magazine and Journal of Science. 1901, 6 (2): 559-572.","journal-title":"The London, Edinburgh and Dublin Pholosophical Magazine and Journal of Science"},{"key":"5683_CR27","first-page":"617","volume":"14","author":"M Collins","year":"2002","unstructured":"Collins M, Dasgupta S, Schapire R: A generalization of principal component analysis to the exponential family. Advanced in Neural Information Processing System. 2002, 14: 617-642.","journal-title":"Advanced in Neural Information Processing System"},{"key":"5683_CR28","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1561\/2200000001","volume":"1","author":"MJ Wainwright","year":"2008","unstructured":"Wainwright MJ, Jordan MI: Graphical models, exponential families, and variational inference. Foundations and Trends in Machine Learning. 2008, 1: 1-305.","journal-title":"Foundations and Trends in Machine Learning"},{"key":"5683_CR29","volume-title":"Proceedings of Advances in Neural Information Processing Systems","author":"G Gordon","year":"2002","unstructured":"Gordon G: Generalized linear models. Proceedings of Advances in Neural Information Processing Systems. 2002, 15:"},{"issue":"26","key":"5683_CR30","doi-asserted-by":"publisher","first-page":"2304","DOI":"10.1093\/bioinformatics\/btr341","volume":"27","author":"Z Su","year":"2011","unstructured":"Su Z, Marchini J, Donnelly P: Hapgen2: simulation of multiple disease snps. Bioinformatics. 2011, 27 (26): 2304-2305.","journal-title":"Bioinformatics"},{"key":"5683_CR31","doi-asserted-by":"publisher","first-page":"1061","DOI":"10.1038\/nature09534","volume":"467","author":"Consortium TGP","year":"2010","unstructured":"Consortium TGP: A map of human genome variation from population-scale sequencing. Nature. 2010, 467: 1061-1073. 10.1038\/nature09534.","journal-title":"Nature"},{"issue":"19","key":"5683_CR32","doi-asserted-by":"publisher","first-page":"2581","DOI":"10.1093\/bioinformatics\/btm386","volume":"23","author":"FA Wright","year":"2007","unstructured":"Wright FA, et al: Simulating association studies: a data-based resampling method for candidate regions or whole genome scans. Bioinformatics. 2007, 23 (19): 2581-2588. 10.1093\/bioinformatics\/btm386.","journal-title":"Bioinformatics"},{"key":"5683_CR33","doi-asserted-by":"publisher","first-page":"311","DOI":"10.1016\/j.ajhg.2008.06.024","volume":"83","author":"B Li","year":"2008","unstructured":"Li B, Leal SM: Methods for detecting associations with rare variants for common diseases:application to analysis of sequence data. Am J Hum Genet. 2008, 83: 311-321. 10.1016\/j.ajhg.2008.06.024.","journal-title":"Am J Hum Genet"},{"issue":"44","key":"5683_CR34","doi-asserted-by":"crossref","first-page":"7097","DOI":"10.3748\/wjg.v12.i44.7097","volume":"12","author":"G Radford-Smith","year":"2006","unstructured":"Radford-Smith G, Pandeya N: Associations between NOD2\/CARD15 genotype and phenotype in Crohn's disease-Are we there yet?. World Journal of Gastroenterology. 2006, 12 (44): 7097-7103.","journal-title":"World Journal of Gastroenterology"},{"issue":"6","key":"5683_CR35","doi-asserted-by":"publisher","first-page":"637","DOI":"10.1097\/01.mcg.0000278579.81576.18","volume":"41","author":"BS Ryan","year":"2007","unstructured":"Ryan BS: Bacteria in crohn's disease: mechanisms of inflammation and therapeutic implications. J Clin Gastroenterol. 2007, 41 (6): 637-10.1097\/01.mcg.0000278579.81576.18.","journal-title":"J Clin Gastroenterol"},{"key":"5683_CR36","doi-asserted-by":"crossref","unstructured":"Ballard D, Abraham C, Cho J, Zhao H: Pathway analysis comparison using Crohn's disease genome wide association studies. BMC Medical Genomics. 2010, 3 (25):","DOI":"10.1186\/1755-8794-3-25"},{"issue":"5","key":"5683_CR37","doi-asserted-by":"publisher","first-page":"265","DOI":"10.1016\/j.ygeno.2008.07.011","volume":"92","author":"A Torkamani","year":"2008","unstructured":"Torkamani A, Topol EJ, Schork NJ: Pathway analysis of seven common diseases assessed by genome-wide association. Genomics. 2008, 92 (5): 265-272. 10.1016\/j.ygeno.2008.07.011.","journal-title":"Genomics"},{"issue":"2","key":"5683_CR38","doi-asserted-by":"publisher","first-page":"363","DOI":"10.5507\/bp.2006.056","volume":"150","author":"V Hrabovsky","year":"2006","unstructured":"Hrabovsky V, Zadak Z, Blaha V, Hyspler R, Ticha A, Karlik T: Lipid metabolism in active crohn's disease: pre-results. Biomed Pap Med Fac Univ Palacky Olomouc Czech Repub. 2006, 150 (2): 363-366. 10.5507\/bp.2006.056.","journal-title":"Biomed Pap Med Fac Univ Palacky Olomouc Czech Repub"},{"issue":"3","key":"5683_CR39","doi-asserted-by":"publisher","first-page":"272","DOI":"10.1111\/j.1365-2249.2009.04033.x","volume":"158","author":"OJ Broom","year":"2009","unstructured":"Broom OJ, Widjaya B, Troelse J, Olsen J, Nielsen OH: Mitogen activated protein kinases: a role in inflammatory bowel disease?. Clin Exp Immunol. 2009, 158 (3): 272-280. 10.1111\/j.1365-2249.2009.04033.x.","journal-title":"Clin Exp Immunol"},{"issue":"11","key":"5683_CR40","doi-asserted-by":"publisher","first-page":"296","DOI":"10.1097\/01.MIB.0000160810.76729.9c","volume":"2005","author":"JB Wiroth","year":"2005","unstructured":"Wiroth JB, et al: Muscle performance in patients with crohn's disease in clinical remission. Inflamm Bowel Dis. 2005, 2005 (11): 296-303.","journal-title":"Inflamm Bowel Dis"},{"issue":"12","key":"5683_CR41","doi-asserted-by":"publisher","first-page":"1002382","DOI":"10.1371\/journal.pgen.1002382","volume":"7","author":"N Yi","year":"2011","unstructured":"Yi N, Liu N, Zhi D, Li J: Hierarchical generalized linear models for multiple groups of rare and common variants: Jointly estimating group and individual-variant effects. PLOS Genetics. 2011, 7 (12): 1002382-10.1371\/journal.pgen.1002382.","journal-title":"PLOS Genetics"},{"issue":"2","key":"5683_CR42","doi-asserted-by":"publisher","first-page":"231","DOI":"10.1080\/10618600.2012.681250","volume":"22","author":"S Noah","year":"2013","unstructured":"Noah S, Jerome F, Trevor H, Robert T: A sparse-group lasso. Journal of Computational and Graphical Statistics. 2013, 22 (2): 231-245. 10.1080\/10618600.2012.681250.","journal-title":"Journal of Computational and Graphical Statistics"}],"container-title":["BMC Genomics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2164-15-S1-S10.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,9,2]],"date-time":"2021-09-02T02:50:23Z","timestamp":1630551023000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcgenomics.biomedcentral.com\/articles\/10.1186\/1471-2164-15-S1-S10"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2014,1]]},"references-count":42,"journal-issue":{"issue":"S1","published-print":{"date-parts":[[2014,1]]}},"alternative-id":["5683"],"URL":"https:\/\/doi.org\/10.1186\/1471-2164-15-s1-s10","relation":{},"ISSN":["1471-2164"],"issn-type":[{"value":"1471-2164","type":"electronic"}],"subject":[],"published":{"date-parts":[[2014,1]]},"assertion":[{"value":"24 January 2014","order":1,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"S10"}}