{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,12,2]],"date-time":"2025-12-02T15:15:51Z","timestamp":1764688551728},"reference-count":19,"publisher":"Oxford University Press (OUP)","issue":"18","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2006,9,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: mRNA expression data obtained from high-throughput DNA microarrays exhibit strong departures from homogeneity of variances. Often a complex relationship between mean expression value and variance is seen. Variance stabilization of such data is crucial for many types of statistical analyses, while regularization of variances (pooling of information) can greatly improve overall accuracy of test statistics.<\/jats:p>\n               <jats:p>Results: A Classification and Regression Tree (CART) procedure is introduced for variance stabilization as well as regularization. The CART procedure adaptively clusters genes by variances. Using both local and cluster wide information leads to improved estimation of population variances which improves test statistics. Whereas making use of cluster wide information allows for variance stabilization of data.<\/jats:p>\n               <jats:p>Availability: Sufficient details for our CART procedure are given so that the interested reader can program the method for themselves. The algorithm is also accessible within the Java software package BAMarrayTM, which is freely available to non-commercial users at<\/jats:p>\n               <jats:p>Contact: \u00a0hemant.ishwaran@gmail.com<\/jats:p>","DOI":"10.1093\/bioinformatics\/btl384","type":"journal-article","created":{"date-parts":[[2006,7,15]],"date-time":"2006-07-15T01:51:27Z","timestamp":1152928287000},"page":"2254-2261","source":"Crossref","is-referenced-by-count":6,"title":["CART variance stabilization and regularization for high-throughput genomic data"],"prefix":"10.1093","volume":"22","author":[{"given":"Ariadni","family":"Papana","sequence":"first","affiliation":[{"name":"Department of Statistics, Case University, 10900 Euclid Avenue 1 \u00a0 1 \u00a0 \u00a0 Cleveland OH 44106, USA"}]},{"given":"Hemant","family":"Ishwaran","sequence":"additional","affiliation":[{"name":"Department of Quantitative Health Sciences, Cleveland Clinic, 9500 Euclid Avenue 2 \u00a0 2 \u00a0 \u00a0 Cleveland OH 44195, USA"}]}],"member":"286","published-online":{"date-parts":[[2006,7,14]]},"reference":[{"key":"2023012409205401400_b1","volume-title":"Version 5.0, Affymetrix","author":"Affymetrix Microarray Suite User Guide","year":"2001"},{"key":"2023012409205401400_b2","doi-asserted-by":"crossref","first-page":"509","DOI":"10.1093\/bioinformatics\/17.6.509","article-title":"A Bayesian framework for the analysis of microarray data: regularized t-test and statistical inferences of gene changes","volume":"17","author":"Baldi","year":"2001","journal-title":"Bioinformatics"},{"key":"2023012409205401400_b3","doi-asserted-by":"crossref","first-page":"3807","DOI":"10.1523\/JNEUROSCI.23-09-03807.2003","article-title":"Gene microarrays in hippocampal aging: statistical profiling identifies novel process correlated with cognitive impairment","volume":"23","author":"Blalock","year":"2003","journal-title":"J. Neuroscience"},{"key":"2023012409205401400_b4","volume-title":"Classification and Regression Trees","author":"Breiman","year":"1984"},{"key":"2023012409205401400_b5","doi-asserted-by":"crossref","first-page":"R16","DOI":"10.1186\/gb-2005-6-2-r16","article-title":"Preferred analysis methods for Affymetrix GeneChips revealed by a wholly defined control dataset","volume":"6","author":"Choe","year":"2005","journal-title":"Genome Biology"},{"key":"2023012409205401400_b6","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1093\/biostatistics\/kxh018","article-title":"Improved statistical tests for differential gene expression by shrinking variance components estimates","volume":"6","author":"Cui","year":"2005","journal-title":"Biostatistics"},{"key":"2023012409205401400_b7","doi-asserted-by":"crossref","first-page":"S105","DOI":"10.1093\/bioinformatics\/18.suppl_1.S105","article-title":"A variance-stabilizing transformation for gene-expression microarray data","volume":"18","author":"Durbin","year":"2002","journal-title":"Bioinformatics"},{"key":"2023012409205401400_b8","doi-asserted-by":"crossref","first-page":"1151","DOI":"10.1198\/016214501753382129","article-title":"Empirical Bayes analysis of a microarray experiment","volume":"96","author":"Efron","year":"2001","journal-title":"J. Am. Stat. Assoc."},{"key":"2023012409205401400_b9","doi-asserted-by":"crossref","DOI":"10.1007\/0-387-29362-0","volume-title":"Bioinformatics and Computational Biology Solutions using R and Bioconductor","author":"Gentleman","year":"2005"},{"key":"2023012409205401400_b10","doi-asserted-by":"crossref","first-page":"S96","DOI":"10.1093\/bioinformatics\/18.suppl_1.S96","article-title":"Variance stabilization applied to microarray data calibration and to the quantification of differential expression","volume":"18","author":"Huber","year":"2002","journal-title":"Bioinformatics"},{"key":"2023012409205401400_b11","doi-asserted-by":"crossref","first-page":"249","DOI":"10.1093\/biostatistics\/4.2.249","article-title":"Exploration, normalization, and summaries of high density oligonucleotide array probe level data","volume":"4","author":"Irizarry","year":"2003","journal-title":"Biostatistics"},{"key":"2023012409205401400_b12","doi-asserted-by":"crossref","first-page":"438","DOI":"10.1198\/016214503000224","article-title":"Detecting differentially expressed genes in microarrays using Bayesian model selection","volume":"98","author":"Ishwaran","year":"2003","journal-title":"J. Am. Stat. Assoc."},{"key":"2023012409205401400_b13","doi-asserted-by":"crossref","first-page":"764","DOI":"10.1198\/016214505000000051","article-title":"Spike and slab gene selection for multigroup microarray data","volume":"100","author":"Ishwaran","year":"2005","journal-title":"J. Amer. Stat. Assoc."},{"key":"2023012409205401400_b14","doi-asserted-by":"crossref","first-page":"3629","DOI":"10.1093\/bioinformatics\/bti593","article-title":"TileMAp: create chromosomal map tiling array hybridizations","volume":"21","author":"Ji","year":"2005","journal-title":"Bioinformatics"},{"key":"2023012409205401400_b15","doi-asserted-by":"crossref","first-page":"436","DOI":"10.1038\/415436a","article-title":"Prediction of central nervous system embryonal tumour outcome based on gene expression","volume":"415","author":"Pomeroy","year":"2001","journal-title":"Nature"},{"key":"2023012409205401400_b16","doi-asserted-by":"crossref","DOI":"10.2202\/1544-6115.1027","article-title":"Linear models and empirical Bayes methods for assessing differential expression in microarray experiments","volume":"3","author":"Smyth","year":"2004","journal-title":"Stat. Appl. Genet. Mol. Biol."},{"key":"2023012409205401400_b17","doi-asserted-by":"crossref","first-page":"1","DOI":"10.2307\/2331554","article-title":"The probable error of a mean","volume":"6","author":"Student","year":"1908","journal-title":"Biometrika"},{"key":"2023012409205401400_b18","doi-asserted-by":"crossref","first-page":"5116","DOI":"10.1073\/pnas.091062498","article-title":"Significance analysis of microarrays applied to the ionizing radiation response","volume":"98","author":"Tusher","year":"2001","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023012409205401400_b19","doi-asserted-by":"crossref","first-page":"2448","DOI":"10.1093\/bioinformatics\/btg345","article-title":"A random variance model for detection of differential gene expression in small microarray experiments","volume":"19","author":"Wright","year":"2003","journal-title":"Bioinformatics"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/22\/18\/2254\/48840075\/bioinformatics_22_18_2254.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/22\/18\/2254\/48840075\/bioinformatics_22_18_2254.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,24]],"date-time":"2023-01-24T09:57:37Z","timestamp":1674554257000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/22\/18\/2254\/317902"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2006,7,14]]},"references-count":19,"journal-issue":{"issue":"18","published-print":{"date-parts":[[2006,9,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btl384","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2006,9,15]]},"published":{"date-parts":[[2006,7,14]]}}}