{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,8,6]],"date-time":"2024-08-06T03:22:51Z","timestamp":1722914571384},"reference-count":17,"publisher":"Oxford University Press (OUP)","issue":"4","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":2482,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/2.0\/uk\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2010,2,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: The small number of samples in many microarray experiments is a challenge for the correct identification of differentially expressed gens (DEGs) by conventional statistical means. Information from public microarray databases can help more efficient identification of DEGs. To model various experimental conditions of a public microarray database, we applied Gaussian mixture model and extracted bi- or tri-modal distributions of gene expression. Prior variance of Baldi's Bayesian framework was estimate for the analysis of the small sample-sized datasets.<\/jats:p>\n               <jats:p>Results: First, we estimated the prior variance of a gene expression by pooling variances obtained from mixture modeling of large samples in the public microarray database. Then, using the prior variance, we identified DEGs in small sample-sized test datasets using the Baldi's framework. For benchmark study, we generated test datasets having several samples from relatively large datasets. Our proposed method outperformed other benchmark methods in terms of detecting gold-standard DEGs from the test datasets. The results may be a challenging evidence for usage of public microarray databases in microarray data analysis.<\/jats:p>\n               <jats:p>Availability: \u00a0Supplementary data are available at http:\/\/www.snubi.org\/publication\/MixBayes<\/jats:p>\n               <jats:p>Contact: \u00a0juhan@snu.ac.kr<\/jats:p>","DOI":"10.1093\/bioinformatics\/btp685","type":"journal-article","created":{"date-parts":[[2009,12,17]],"date-time":"2009-12-17T03:52:01Z","timestamp":1261021921000},"page":"486-492","source":"Crossref","is-referenced-by-count":11,"title":["Mixture-model based estimation of gene expression variance from public database improves identification of differentially expressed genes in small sized microarray data"],"prefix":"10.1093","volume":"26","author":[{"given":"Mingoo","family":"Kim","sequence":"first","affiliation":[{"name":"1 Seoul National University Biomedical Informatics (SNUBI) and 2 Division of Biomedical Informatics, Seoul National University College of Medicine, Seoul 110-799, Korea"},{"name":"1 Seoul National University Biomedical Informatics (SNUBI) and 2 Division of Biomedical Informatics, Seoul National University College of Medicine, Seoul 110-799, Korea"}]},{"given":"Sung Bum","family":"Cho","sequence":"additional","affiliation":[{"name":"1 Seoul National University Biomedical Informatics (SNUBI) and 2 Division of Biomedical Informatics, Seoul National University College of Medicine, Seoul 110-799, Korea"},{"name":"1 Seoul National University Biomedical Informatics (SNUBI) and 2 Division of Biomedical Informatics, Seoul National University College of Medicine, Seoul 110-799, Korea"}]},{"given":"Ju Han","family":"Kim","sequence":"additional","affiliation":[{"name":"1 Seoul National University Biomedical Informatics (SNUBI) and 2 Division of Biomedical Informatics, Seoul National University College of Medicine, Seoul 110-799, Korea"},{"name":"1 Seoul National University Biomedical Informatics (SNUBI) and 2 Division of Biomedical Informatics, Seoul National University College of Medicine, Seoul 110-799, Korea"}]}],"member":"286","published-online":{"date-parts":[[2009,12,16]]},"reference":[{"key":"2023012508023939900_B1","doi-asserted-by":"crossref","first-page":"509","DOI":"10.1093\/bioinformatics\/17.6.509","article-title":"A Bayesian framework for the analysis of microarray expression data: regularized t -test and statistical inferences of gene changes","volume":"17","author":"Baldi","year":"2001","journal-title":"Bioinformatics"},{"key":"2023012508023939900_B2","doi-asserted-by":"crossref","first-page":"185","DOI":"10.1093\/bioinformatics\/19.2.185","article-title":"A comparison of normalization methods for high density oligonucleotide array data based on bias and variance","volume":"19","author":"Bolstad","year":"2003","journal-title":"Bioinformatics"},{"key":"2023012508023939900_B3","doi-asserted-by":"crossref","first-page":"68","DOI":"10.1093\/nar\/gkg091","article-title":"ArrayExpress\u2013a public repository for microarray gene expression data at the EBI","volume":"31","author":"Brazma","year":"2003","journal-title":"Nucleic Acids Res."},{"key":"2023012508023939900_B4","doi-asserted-by":"crossref","first-page":"207","DOI":"10.1093\/nar\/30.1.207","article-title":"Gene Expression Omnibus: NCBI gene expression and hybridization array data repository","volume":"30","author":"Edgar","year":"2002","journal-title":"Nucleic Acids Res."},{"key":"2023012508023939900_B5","doi-asserted-by":"crossref","first-page":"70","DOI":"10.1002\/gepi.1124","article-title":"Empirical bayes methods and false discovery rates for microarrays","volume":"23","author":"Efron","year":"2002","journal-title":"Genet. 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