{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,9]],"date-time":"2026-01-09T12:27:55Z","timestamp":1767961675396,"version":"3.49.0"},"reference-count":32,"publisher":"Oxford University Press (OUP)","issue":"8","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":2404,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/2.0\/uk\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2010,4,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Global expression patterns within cells are used for purposes ranging from the identification of disease biomarkers to basic understanding of cellular processes. Unfortunately, tissue samples used in cancer studies are usually composed of multiple cell types and the non-cancerous portions can significantly affect expression profiles. This severely limits the conclusions that can be made about the specificity of gene expression in the cell-type of interest. However, statistical analysis can be used to identify differentially expressed genes that are related to the biological question being studied.<\/jats:p>\n               <jats:p>Results: We propose a statistical approach to expression deconvolution from mixed tissue samples in which the proportion of each component cell type is unknown. Our method estimates the proportion of each component in a mixed tissue sample; this estimate can be used to provide estimates of gene expression from each component. We demonstrate our technique on xenograft samples from breast cancer research and publicly available experimental datasets found in the National Center for Biotechnology Information Gene Expression Omnibus repository.<\/jats:p>\n               <jats:p>Availability: R code (http:\/\/www.r-project.org\/) for estimating sample proportions is freely available to non-commercial users and available at http:\/\/www.med.miami.edu\/medicine\/x2691.xml<\/jats:p>\n               <jats:p>Contact: \u00a0jclarke@med.miami.edu<\/jats:p>","DOI":"10.1093\/bioinformatics\/btq097","type":"journal-article","created":{"date-parts":[[2010,3,5]],"date-time":"2010-03-05T01:30:02Z","timestamp":1267752602000},"page":"1043-1049","source":"Crossref","is-referenced-by-count":57,"title":["Statistical expression deconvolution from mixed tissue samples"],"prefix":"10.1093","volume":"26","author":[{"given":"Jennifer","family":"Clarke","sequence":"first","affiliation":[{"name":"1 Department of Medicine, University of Miami, 1120 NW 14th St, Suite 611, Miami, FL 33136, 2 Department of Epidemiology and Public Health, University of Miami, 1120 NW 14th St, Suite 1005, Miami, FL 33136 and 3 Center for Computational Science, University of Miami, 1120 NW 14th St, Suite 619, Miami, FL 33136, USA"},{"name":"1 Department of Medicine, University of Miami, 1120 NW 14th St, Suite 611, Miami, FL 33136, 2 Department of Epidemiology and Public Health, University of Miami, 1120 NW 14th St, Suite 1005, Miami, FL 33136 and 3 Center for Computational Science, University of Miami, 1120 NW 14th St, Suite 619, Miami, FL 33136, USA"}]},{"given":"Pearl","family":"Seo","sequence":"additional","affiliation":[{"name":"1 Department of Medicine, University of Miami, 1120 NW 14th St, Suite 611, Miami, FL 33136, 2 Department of Epidemiology and Public Health, University of Miami, 1120 NW 14th St, Suite 1005, Miami, FL 33136 and 3 Center for Computational Science, University of Miami, 1120 NW 14th St, Suite 619, Miami, FL 33136, USA"}]},{"given":"Bertrand","family":"Clarke","sequence":"additional","affiliation":[{"name":"1 Department of Medicine, University of Miami, 1120 NW 14th St, Suite 611, Miami, FL 33136, 2 Department of Epidemiology and Public Health, University of Miami, 1120 NW 14th St, Suite 1005, Miami, FL 33136 and 3 Center for Computational Science, University of Miami, 1120 NW 14th St, Suite 619, Miami, FL 33136, USA"},{"name":"1 Department of Medicine, University of Miami, 1120 NW 14th St, Suite 611, Miami, FL 33136, 2 Department of Epidemiology and Public Health, University of Miami, 1120 NW 14th St, Suite 1005, Miami, FL 33136 and 3 Center for Computational Science, University of Miami, 1120 NW 14th St, Suite 619, Miami, FL 33136, USA"},{"name":"1 Department of Medicine, University of Miami, 1120 NW 14th St, Suite 611, Miami, FL 33136, 2 Department of Epidemiology and Public Health, University of Miami, 1120 NW 14th St, Suite 1005, Miami, FL 33136 and 3 Center for Computational Science, University of Miami, 1120 NW 14th St, Suite 619, Miami, FL 33136, USA"}]}],"member":"286","published-online":{"date-parts":[[2010,3,4]]},"reference":[{"key":"2023012508083038100_B1","volume-title":"Affymetrix Expression Console Software Version 1.0 \u2014 User Guide.","author":"Affymetrix Inc.","year":"2009"},{"key":"2023012508083038100_B2","volume-title":"Numerical Methods for Partial Differential Equations.","author":"Ames","year":"1977"},{"key":"2023012508083038100_B3","doi-asserted-by":"crossref","first-page":"D760","DOI":"10.1093\/nar\/gkl887","article-title":"NCBI GEO: mining tens of millions of expression profiles\u2014database and tools","volume":"35","author":"Barrett","year":"2006","journal-title":"Nucleic Acids Res."},{"key":"2023012508083038100_B4","doi-asserted-by":"crossref","first-page":"5","DOI":"10.1002\/cjs.5550340103","article-title":"Bootstrap diagnostics and remedies","volume":"34","author":"Canty","year":"2002","journal-title":"Can. J. Stat."},{"key":"2023012508083038100_B5","volume-title":"Microarray gene expression data analysis: A beginner's guide.","author":"Causton","year":"2003"},{"key":"2023012508083038100_B6","doi-asserted-by":"crossref","first-page":"R32","DOI":"10.1186\/bcr1506","article-title":"The effect of the stromal component of breast tumours on prediction of clinical outcome using gene expression microarray analysis","volume":"8","author":"Cleator","year":"2006","journal-title":"Breast Cancer Res."},{"key":"2023012508083038100_B7","doi-asserted-by":"crossref","first-page":"2183","DOI":"10.1093\/bioinformatics\/btm311","article-title":"beadarray: R classes and methods for illumina bead-based data","volume":"23","author":"Dunning","year":"2008","journal-title":"Bioinformatics"},{"key":"2023012508083038100_B8","doi-asserted-by":"crossref","first-page":"85","DOI":"10.1186\/1471-2105-9-85","article-title":"Statistical issues in the analysis of illumina data","volume":"9","author":"Dunning","year":"2008","journal-title":"BMC Bioinformatics"},{"key":"2023012508083038100_B9","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1214\/aos\/1176344552","article-title":"Bootstrap methods: Another look at the jackknife","volume":"7","author":"Efron","year":"1979","journal-title":"Ann. Stat."},{"key":"2023012508083038100_B10","doi-asserted-by":"crossref","first-page":"666","DOI":"10.1136\/jcp.53.9.666","article-title":"Laser capture microdissection in pathology","volume":"53","author":"Fend","year":"2000","journal-title":"J. Clin. Pathol."},{"key":"2023012508083038100_B11","doi-asserted-by":"crossref","first-page":"1663","DOI":"10.1093\/bioinformatics\/bth139","article-title":"Mixture models for assessing differential expression in complex tissues using microarray data","volume":"20","author":"Ghosh","year":"2004","journal-title":"Bioinformatics"},{"key":"2023012508083038100_B12","doi-asserted-by":"crossref","first-page":"3328","DOI":"10.1093\/bioinformatics\/btm508","article-title":"Electronically subtracting expression patterns from a mixed cell population","volume":"23","author":"Gosink","year":"2007","journal-title":"Bioinformatics"},{"key":"2023012508083038100_B13","volume-title":"BeadStudio Gene Expression Module v3.4 User Guide (11317265 Rev A).","author":"Illumina Inc.","year":"2009"},{"key":"2023012508083038100_B14","article-title":"Effects of different normalisation and analysis procedures on illumina gene expression microarray data","volume-title":"Proceedings of the 19th International Conference on Genome Informatics (GIW 2008)","author":"Johnstone","year":"2008"},{"key":"2023012508083038100_B15","volume-title":"Principal components analysis","author":"Jolliffe","year":"2002","edition":"2nd"},{"key":"2023012508083038100_B16","doi-asserted-by":"crossref","first-page":"2395","DOI":"10.1093\/nar\/gkn087","article-title":"Specificity of DNA microarray hybridization: characterization, effectors, and approaches for data correction","volume":"36","author":"Koltai","year":"2008","journal-title":"Nucleic Acids Res."},{"key":"2023012508083038100_B17","doi-asserted-by":"crossref","first-page":"54","DOI":"10.1186\/1471-2105-6-54","article-title":"In silico microdissection of microarray data from heterogeneous cell populations","volume":"6","author":"Lahdesmaki","year":"2005","journal-title":"BMC Bioinformatics"},{"key":"2023012508083038100_B18","doi-asserted-by":"crossref","first-page":"2838","DOI":"10.1214\/08-AOS660","article-title":"Conditional predictive inference post model selection","volume":"37","author":"Leeb","year":"2009","journal-title":"Ann. Stat."},{"key":"2023012508083038100_B19","volume-title":"Schaum's outline of theory and problems of differential geometry.","author":"Lipschutz","year":"1969"},{"key":"2023012508083038100_B20","doi-asserted-by":"crossref","first-page":"10370","DOI":"10.1073\/pnas.1832361100","article-title":"Expression deconvolution: A reinterpretation of DNA microarray data reveals dynamic changes in cell populations","volume":"100","author":"Lu","year":"2003","journal-title":"Proc. Nat. Acad. Sci. USA"},{"key":"2023012508083038100_B21","doi-asserted-by":"crossref","first-page":"1151","DOI":"10.1038\/nbt1239","article-title":"The microarray quality control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements","volume":"24","author":"MAQC Consortium","year":"2006","journal-title":"Nat. Biotechnol."},{"key":"2023012508083038100_B22","doi-asserted-by":"crossref","first-page":"488","DOI":"10.1016\/S0140-6736(05)17866-0","article-title":"Prediction of cancer outcome with microarrays: a multiple random validation strategy","volume":"365","author":"Michiels","year":"2005","journal-title":"Lancet"},{"key":"2023012508083038100_B23","doi-asserted-by":"crossref","first-page":"8431","DOI":"10.1073\/pnas.0401736101","article-title":"Clinico-genomic models for personalized prediction of disease outcomes","volume":"101","author":"Pittman","year":"2004","journal-title":"Proc. Nat. Acad. Sci. USA"},{"key":"2023012508083038100_B24","volume-title":"R: A Language and Environment for Statistical Computing.","author":"R Development Core Team","year":"2009"},{"key":"2023012508083038100_B25","doi-asserted-by":"crossref","first-page":"111","DOI":"10.1016\/j.ygeno.2006.03.004","article-title":"Accurate and precise transcriptional profiles from 50 pg of total RNA or 100 flow-sorted primary lymphocytes","volume":"88","author":"Shearstone","year":"2006","journal-title":"Genomics"},{"key":"2023012508083038100_B26","doi-asserted-by":"crossref","first-page":"751","DOI":"10.1198\/016214504000001097","article-title":"Inference after model selection","volume":"99","author":"Shen","year":"2004","journal-title":"J. Am. Stat. Assoc."},{"key":"2023012508083038100_B27","doi-asserted-by":"crossref","first-page":"615","DOI":"10.1073\/pnas.2536479100","article-title":"In silico dissection of cell-type-associated patterns of gene expression in prostate cancer","volume":"101","author":"Stuart","year":"2004","journal-title":"Proc. Nat. Acad. Sci. USA"},{"key":"2023012508083038100_B28","doi-asserted-by":"crossref","first-page":"530","DOI":"10.1038\/415530a","article-title":"Gene expression profiling predicts clinical outcome of breast cancer","volume":"415","author":"van't Veer","year":"2002","journal-title":"Nature"},{"key":"2023012508083038100_B29","doi-asserted-by":"crossref","first-page":"S279","DOI":"10.1093\/bioinformatics\/17.suppl_1.S279","article-title":"Separation of samples into their constituents using gene expression data","volume":"17","author":"Venet","year":"2001","journal-title":"Bioinformatics"},{"key":"2023012508083038100_B30","doi-asserted-by":"crossref","first-page":"328","DOI":"10.1186\/1471-2105-7-328","article-title":"Computational expresssion deconvolution in a complex mammalian organ","volume":"7","author":"Wang","year":"2006","journal-title":"BMC Bioinformatics"},{"key":"2023012508083038100_B31","doi-asserted-by":"crossref","first-page":"726","DOI":"10.1039\/b706237k","article-title":"The incredible shrinking world of DNA microarrays","volume":"4","author":"Wheelan","year":"2008","journal-title":"Mol. Biosyst."},{"key":"2023012508083038100_B32","doi-asserted-by":"crossref","first-page":"918","DOI":"10.1016\/j.csda.2005.09.010","article-title":"Automatic dimensionality selection from the scree plot via the use of profile likelihood","volume":"51","author":"Zhu","year":"2006","journal-title":"Comput. Stat. Data Anal."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/26\/8\/1043\/48857435\/bioinformatics_26_8_1043.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/26\/8\/1043\/48857435\/bioinformatics_26_8_1043.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,25]],"date-time":"2023-01-25T08:13:02Z","timestamp":1674634382000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/26\/8\/1043\/208640"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2010,3,4]]},"references-count":32,"journal-issue":{"issue":"8","published-print":{"date-parts":[[2010,4,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btq097","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2010,4,15]]},"published":{"date-parts":[[2010,3,4]]}}}