{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,10,8]],"date-time":"2024-10-08T04:15:24Z","timestamp":1728360924000},"reference-count":27,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2004,12,16]],"date-time":"2004-12-16T00:00:00Z","timestamp":1103155200000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/2.0\/"},{"start":{"date-parts":[[2004,12,16]],"date-time":"2004-12-16T00:00:00Z","timestamp":1103155200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/2.0\/"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"abstract":"<jats:title>Abstract<\/jats:title><jats:sec>\n                        <jats:title>Background<\/jats:title>\n                        <jats:p>The main goal in analyzing microarray data is to determine the genes that are differentially expressed across two types of tissue samples or samples obtained under two experimental conditions. Mixture model method (MMM hereafter) is a nonparametric statistical method often used for microarray processing applications, but is known to over-fit the data if the number of replicates is small. In addition, the results of the MMM may not be repeatable when dealing with a small number of replicates. In this paper, we propose a new version of MMM to ensure the repeatability of the results in different runs, and reduce the sensitivity of the results on the parameters.<\/jats:p>\n                     <\/jats:sec><jats:sec>\n                        <jats:title>Results<\/jats:title>\n                        <jats:p>The proposed technique is applied to the two different data sets: Leukaemia data set and a data set that examines the effects of low phosphate diet on regular and <jats:italic>Hyp<\/jats:italic> mice. In each study, the proposed algorithm successfully selects genes closely related to the disease state that are verified by biological information.<\/jats:p>\n                     <\/jats:sec><jats:sec>\n                        <jats:title>Conclusion<\/jats:title>\n                        <jats:p>The results indicate 100% repeatability in all runs, and exhibit very little sensitivity on the choice of parameters. In addition, the evaluation of the applied method on the Leukaemia data set shows 12% improvement compared to the MMM in detecting the biologically-identified 50 expressed genes by Thomas et al. The results witness to the successful performance of the proposed algorithm in quantitative pathogenesis of diseases and comparative evaluation of treatment methods.<\/jats:p>\n                     <\/jats:sec>","DOI":"10.1186\/1471-2105-5-201","type":"journal-article","created":{"date-parts":[[2005,1,12]],"date-time":"2005-01-12T17:25:38Z","timestamp":1105550738000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":10,"title":["A novel Mixture Model Method for identification of differentially expressed genes from DNA microarray data"],"prefix":"10.1186","volume":"5","author":[{"given":"Kayvan","family":"Najarian","sequence":"first","affiliation":[]},{"given":"Maryam","family":"Zaheri","sequence":"additional","affiliation":[]},{"given":"Ali","family":"A Rad","sequence":"additional","affiliation":[]},{"given":"Siamak","family":"Najarian","sequence":"additional","affiliation":[]},{"given":"Javad","family":"Dargahi","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2004,12,16]]},"reference":[{"key":"317_CR1","doi-asserted-by":"publisher","first-page":"364","DOI":"10.1117\/12.281504","volume":"2","author":"Y Chen","year":"1997","unstructured":"Chen Y, Dougherty E, Bittner M: Ratio-based decisions and the quantitative analysis of cDNA microarrays images.\n                           J Biomedical Optics 1997, 2: 364\u2013367. 10.1117\/1.429838","journal-title":"J Biomedical Optics"},{"key":"317_CR2","volume-title":"Statistics: the Exploration and Analysis of Data","author":"J Devore","year":"1997","unstructured":"Devore J, Peck R: Statistics: the Exploration and Analysis of Data. 3rd edition. Pacific Grove, CA: Duxbury Press; 1997.","edition":"3"},{"key":"317_CR3","doi-asserted-by":"publisher","first-page":"1151","DOI":"10.1198\/016214501753382129","volume":"96","author":"B Efron","year":"2001","unstructured":"Efron B, Tibshirani R, Storey J, Tusher V: Empirical Bayes analysis of a microarray experiment.\n                           Journal of the American Statistical Association 2001, 96: 1151\u20131160. 10.1198\/016214501753382129","journal-title":"Journal of the American Statistical Association"},{"key":"317_CR4","doi-asserted-by":"publisher","first-page":"5116","DOI":"10.1073\/pnas.091062498","volume":"98","author":"V Tusher","year":"2001","unstructured":"Tusher V, Tibshirani R, Chu G: Significance analysis of microarrays applied to the ionizing radiation response.\n                           Proc Nat Acad Sci 2001, 98: 5116\u20135121. 10.1073\/pnas.091062498","journal-title":"Proc Nat Acad Sci"},{"key":"317_CR5","first-page":"117","volume":"3","author":"Pan","year":"2001","unstructured":"Pan , Wei , Lin J, Le C: A Mixture Model Approach to Detecting Differentially Expressed Genes with Microarray Data.\n                           Functional & Integrative Genomics 2001, 3: 117\u2013124.","journal-title":"Functional & Integrative Genomics"},{"key":"317_CR6","doi-asserted-by":"publisher","first-page":"1046","DOI":"10.1093\/bioinformatics\/btf879","volume":"19","author":"Y Zhao","year":"2003","unstructured":"Zhao Y, Pan W: Modified nonparametric approaches to detecting differentially expressed genes in replicated microarray experiments.\n                           Bioinformatics 2003, 19: 1046\u20131054. (Also Report 2002\u2013018, Division of Biostatistics, University of Minnesota, 2002) 10.1093\/bioinformatics\/btf879","journal-title":"Bioinformatics"},{"key":"317_CR7","doi-asserted-by":"publisher","first-page":"531","DOI":"10.1126\/science.286.5439.531","volume":"285","author":"T Golub","year":"1999","unstructured":"Golub T, Slonim DK, Tamayo P, Huard C, Gaasenbeek M, Mesirov JP, Coller H, Loh ML, Downing JR, Caligiuri MA, et al.: Molecular classification of cancer: class discovery and class predication by gene expression monitoring.\n                           Science 1999, 285: 531\u2013537. 10.1126\/science.286.5439.531","journal-title":"Science"},{"key":"317_CR8","doi-asserted-by":"publisher","first-page":"81","DOI":"10.1385\/ENDO:13:1:81","volume":"13","author":"M Meyer","year":"2000","unstructured":"Meyer M, Meyer R: mRNA expression of\n                           Phex\n                           in mice and rats: The effect of low phosphate diet.\n                           Endocrine 2000, 13: 81\u201387. 10.1385\/ENDO:13:1:81","journal-title":"Endocrine"},{"key":"317_CR9","doi-asserted-by":"publisher","first-page":"1577","DOI":"10.1210\/endo-107-5-1577","volume":"107","author":"R Meyer","year":"1980","unstructured":"Meyer R, Gray R, Meyer M: Abnormal vitamin D metabolism in the X-linked hypophosphatemic mouse.\n                           Endocrinology 1980, 107: 1577\u20131581.","journal-title":"Endocrinology"},{"key":"317_CR10","first-page":"F309","volume":"266","author":"S Thornton","year":"1994","unstructured":"Thornton S, Tenenhouse H, Martel J, Bockian R, Meyer M, Meyer R: X-linked hypophosphatemic\n                           Gy\n                           mice: renal tubular maximum for phosphate vs. brush-border transport after low-P diet.\n                           Am J Physiol 1994, 266: F309\u2013315.","journal-title":"Am J Physiol"},{"key":"317_CR11","doi-asserted-by":"publisher","first-page":"51","DOI":"10.1210\/en.131.1.51","volume":"131","author":"H Tenenhouse","year":"1992","unstructured":"Tenenhouse H, Meyer R, Mandla S, Meyer M, Gray R: Renal phosphate transport and vitamin D metabolism in X-linked hypophosphatemic\n                           Gy\n                           mice: Response to phosphate deprivation.\n                           Endocrinology 1992, 131: 51\u201356. 10.1210\/en.131.1.51","journal-title":"Endocrinology"},{"key":"317_CR12","doi-asserted-by":"publisher","first-page":"423","DOI":"10.1007\/BF02553713","volume":"37","author":"CE Brown","year":"1985","unstructured":"Brown CE, Wilkie CA, Meyer MH, Meyer RA Jr: Response of tissue phosphate content to acute dietary phosphate deprivation in the X-linked hypophosphatemic mouse.\n                           Calcif Tissue Int 1985, 37: 423\u2013430.","journal-title":"Calcif Tissue Int"},{"key":"317_CR13","first-page":"903","volume-title":"In: Vitamin D: Gene Regulation, Structure-Function Analysis and Clinical Application","author":"R Meyer","year":"1991","unstructured":"Meyer R, Gray R, Meyer M: Abnormal regulation of plasma 1, 25- dihydroxyvitamin D in gyro (\n                           Gy\n                           , X-linked hypophosphatemic) mice. In Vitamin D: Gene Regulation, Structure-Function Analysis and Clinical Application. Edited by: Norman A, Bouillon R, Thomasset M. Walter de Gruyter, New York; 1991:903\u2013904."},{"issue":"1","key":"317_CR14","doi-asserted-by":"publisher","first-page":"23","DOI":"10.1016\/8756-3282(95)00420-3","volume":"18","author":"RA Meyer","year":"1996","unstructured":"Meyer RA, Meyer MH, Morgan PL: Effect of altered diet on serum levels of 1,25- dihydroxyvitamin- D and parathyroid hormone in X-linked hypophasphatemic mice (Hyp and Gy) mice.\n                           Bone 1996, 18(1):23\u201328. 10.1016\/8756-3282(95)00420-3","journal-title":"Bone"},{"key":"317_CR15","doi-asserted-by":"publisher","first-page":"936","DOI":"10.1007\/s004240050088","volume":"431","author":"L Beck","year":"1996","unstructured":"Beck L, Tenenhouse HS, Meyer RA, Meyer MH, Biber J, Murer H: Renal expression of Na+-phosphate cotransporter mRNA and protein: Effect of the Gy mutation and low phosphate diet.\n                           Pflugers Arch 1996, 431: 936\u2013941. 10.1007\/s004240050088","journal-title":"Pflugers Arch"},{"key":"317_CR16","doi-asserted-by":"publisher","first-page":"578","DOI":"10.1093\/comjnl\/41.8.578","volume":"41","author":"C Fraley","year":"1998","unstructured":"Fraley C, Raftery E: How many clusters? Which clustering methods? Answer via model-based cluster analysis.\n                           The Computer Journal 1998, 41: 578\u2013588.","journal-title":"The Computer Journal"},{"key":"317_CR17","volume-title":"Numerical Recipes in C, The Art of Scientific Computing","author":"W Press","year":"1992","unstructured":"Press W, Teukolsky S, Vetterling W, Flannery B: Numerical Recipes in C, The Art of Scientific Computing. 2nd edition. New York: Cambridge University Press; 1992.","edition":"2"},{"key":"317_CR18","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1111\/j.2517-6161.1995.tb02031.x","volume":"57","author":"Y Benjamini","year":"1995","unstructured":"Benjamini Y, Hochberg Y: Controlling the false discovery rate: a practical and powerful approach to multiple testing.\n                           Journal of the Royal Statistical Society, Series B 1995, 57: 289\u2013300.","journal-title":"Journal of the Royal Statistical Society, Series B"},{"key":"317_CR19","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1111\/j.2517-6161.1977.tb01600.x","volume":"39","author":"A Dempster","year":"1977","unstructured":"Dempster A, Laird N, Rubin D: Maximum likelihood estimation from incomplete data via the EM algorithm (with discussion).\n                           J R Statist Soc 1977, 39: 1\u201338.","journal-title":"J R Statist Soc"},{"issue":"2","key":"317_CR20","doi-asserted-by":"publisher","first-page":"137","DOI":"10.1023\/A:1019999408474","volume":"16","author":"K Najarian","year":"2002","unstructured":"Najarian K: Learning-Based Complexity Evaluation of Radial Basis Function Networks.\n                           Neural Processing Letters 2002, 16(2):137\u2013150. 10.1023\/A:1019999408474","journal-title":"Neural Processing Letters"},{"issue":"4","key":"317_CR21","doi-asserted-by":"publisher","first-page":"546","DOI":"10.1093\/bioinformatics\/18.4.546","volume":"18","author":"Pan","year":"2002","unstructured":"Pan , Wei : A comparative review of statistical methods for discovering differentially expressed genes in replicated microarray experiments.\".\n                           Bioinformatics 2002, 18(4):546\u2013554.1. 10.1093\/bioinformatics\/18.4.546","journal-title":"Bioinformatics"},{"key":"317_CR22","doi-asserted-by":"publisher","first-page":"1227","DOI":"10.1101\/gr.165101","volume":"11","author":"J Thomas","year":"2001","unstructured":"Thomas J, Olson J, Tapscott J, Zhao L: An Efficient and Robust statistical modelling approach to discover differentially expressed genes using genomics expression profile.\n                           Genome Research 2001, 11: 1227\u20131236. 10.1101\/gr.165101","journal-title":"Genome Research"},{"key":"317_CR23","doi-asserted-by":"publisher","first-page":"938","DOI":"10.1139\/o79-114","volume":"57","author":"H Tenenhouse","year":"1979","unstructured":"Tenenhouse H, Scriver C: Renal adaptation to phosphate deprivation in the\n                           Hyp\n                           mouse with X-linked hypophosphatemia.\n                           Can J Biochem 1979, 57: 938\u2013944.","journal-title":"Can J Biochem"},{"key":"317_CR24","doi-asserted-by":"publisher","first-page":"671","DOI":"10.1172\/JCI117019","volume":"93","author":"H Tenenhouse","year":"1994","unstructured":"Tenenhouse H, Werner A, Biber J, Ma S, Martel J, Roy S, Murer H: Renal Na(+)-phosphate cotransport in murine X-linked hypophosphatemic rickets. Molecular characterization.\n                           J Clin Invest 1994, 93: 671\u2013676.","journal-title":"J Clin Invest"},{"key":"317_CR25","doi-asserted-by":"publisher","first-page":"19","DOI":"10.1007\/BF02441156","volume":"27","author":"R Meyer","year":"1979","unstructured":"Meyer R, Jowsey J, Meyer M: Osteomalacia and altered magnesium metabolism in the X-linked hypophosphatemic mouse.\n                           Calcif Tissue Int 1979, 27: 19\u201326.","journal-title":"Calcif Tissue Int"},{"key":"317_CR26","doi-asserted-by":"publisher","first-page":"461","DOI":"10.1214\/aos\/1176344136","volume":"6","author":"G Schwartz","year":"1978","unstructured":"Schwartz G: Estimating the dimentions of a model.\n                           Annals of Statistics 1978, 6: 461\u2013464.","journal-title":"Annals of Statistics"},{"unstructured":"National Center for Biotechnology Information[http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi]","key":"317_CR27"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-5-201.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1186\/1471-2105-5-201\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-5-201.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,10,7]],"date-time":"2024-10-07T12:22:31Z","timestamp":1728303751000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-5-201"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2004,12,16]]},"references-count":27,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2004,12]]}},"alternative-id":["317"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-5-201","relation":{},"ISSN":["1471-2105"],"issn-type":[{"type":"electronic","value":"1471-2105"}],"subject":[],"published":{"date-parts":[[2004,12,16]]},"assertion":[{"value":"24 March 2004","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"16 December 2004","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"16 December 2004","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"201"}}