{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,28]],"date-time":"2026-01-28T20:58:22Z","timestamp":1769633902449,"version":"3.49.0"},"reference-count":11,"publisher":"Oxford University Press (OUP)","issue":"1","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2015,1,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: We develop a novel unsupervised deconvolution method, within a well-grounded mathematical framework, to dissect mixed gene expressions in heterogeneous tumor samples. We implement an R package, UNsupervised DecOnvolution (UNDO), that can be used to automatically detect cell-specific marker genes (MGs) located on the scatter radii of mixed gene expressions, estimate cellular proportions in each sample and deconvolute mixed expressions into cell-specific expression profiles. We demonstrate the performance of UNDO over a wide range of tumor\u2013stroma mixing proportions, validate UNDO on various biologically mixed benchmark gene expression datasets and further estimate tumor purity in TCGA\/CPTAC datasets. The highly accurate deconvolution results obtained suggest not only the existence of cell-specific MGs but also UNDO\u2019s ability to detect them blindly and correctly. Although the principal application here involves microarray gene expressions, our methodology can be readily applied to other types of quantitative molecular profiling data.<\/jats:p>\n               <jats:p>Availability and implementation: UNDO is available at http:\/\/bioconductor.org\/packages .<\/jats:p>\n               <jats:p>Contact: \u00a0yuewang@vt.edu<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btu607","type":"journal-article","created":{"date-parts":[[2014,9,12]],"date-time":"2014-09-12T02:13:15Z","timestamp":1410487995000},"page":"137-139","source":"Crossref","is-referenced-by-count":50,"title":["UNDO: a Bioconductor R package for unsupervised deconvolution of mixed gene expressions in tumor samples"],"prefix":"10.1093","volume":"31","author":[{"given":"Niya","family":"Wang","sequence":"first","affiliation":[{"name":"1 Department of Electrical and Computer Engineering, Virginia Polytechnic Institute and State University, Arlington, VA 22203, 2 Department of Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, 3 Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC 20057, 4 Departments of Pathology and Oncology, Johns Hopkins University, Baltimore, MD 21231 and 5 Department of Surgery, Memorial Sloan-Kettering Cancer Center, New York, NY 10021, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ting","family":"Gong","sequence":"additional","affiliation":[{"name":"1 Department of Electrical and Computer Engineering, Virginia Polytechnic Institute and State University, Arlington, VA 22203, 2 Department of Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, 3 Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC 20057, 4 Departments of Pathology and Oncology, Johns Hopkins University, Baltimore, MD 21231 and 5 Department of Surgery, Memorial Sloan-Kettering Cancer Center, New York, NY 10021, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Robert","family":"Clarke","sequence":"additional","affiliation":[{"name":"1 Department of Electrical and Computer Engineering, Virginia Polytechnic Institute and State University, Arlington, VA 22203, 2 Department of Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, 3 Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC 20057, 4 Departments of Pathology and Oncology, Johns Hopkins University, Baltimore, MD 21231 and 5 Department of Surgery, Memorial Sloan-Kettering Cancer Center, New York, NY 10021, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lulu","family":"Chen","sequence":"additional","affiliation":[{"name":"1 Department of Electrical and Computer Engineering, Virginia Polytechnic Institute and State University, Arlington, VA 22203, 2 Department of Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, 3 Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC 20057, 4 Departments of Pathology and Oncology, Johns Hopkins University, Baltimore, MD 21231 and 5 Department of Surgery, Memorial Sloan-Kettering Cancer Center, New York, NY 10021, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ie-Ming","family":"Shih","sequence":"additional","affiliation":[{"name":"1 Department of Electrical and Computer Engineering, Virginia Polytechnic Institute and State University, Arlington, VA 22203, 2 Department of Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, 3 Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC 20057, 4 Departments of Pathology and Oncology, Johns Hopkins University, Baltimore, MD 21231 and 5 Department of Surgery, Memorial Sloan-Kettering Cancer Center, New York, NY 10021, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zhen","family":"Zhang","sequence":"additional","affiliation":[{"name":"1 Department of Electrical and Computer Engineering, Virginia Polytechnic Institute and State University, Arlington, VA 22203, 2 Department of Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, 3 Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC 20057, 4 Departments of Pathology and Oncology, Johns Hopkins University, Baltimore, MD 21231 and 5 Department of Surgery, Memorial Sloan-Kettering Cancer Center, New York, NY 10021, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Douglas A.","family":"Levine","sequence":"additional","affiliation":[{"name":"1 Department of Electrical and Computer Engineering, Virginia Polytechnic Institute and State University, Arlington, VA 22203, 2 Department of Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, 3 Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC 20057, 4 Departments of Pathology and Oncology, Johns Hopkins University, Baltimore, MD 21231 and 5 Department of Surgery, Memorial Sloan-Kettering Cancer Center, New York, NY 10021, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jianhua","family":"Xuan","sequence":"additional","affiliation":[{"name":"1 Department of Electrical and Computer Engineering, Virginia Polytechnic Institute and State University, Arlington, VA 22203, 2 Department of Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, 3 Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC 20057, 4 Departments of Pathology and Oncology, Johns Hopkins University, Baltimore, MD 21231 and 5 Department of Surgery, Memorial Sloan-Kettering Cancer Center, New York, NY 10021, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yue","family":"Wang","sequence":"additional","affiliation":[{"name":"1 Department of Electrical and Computer Engineering, Virginia Polytechnic Institute and State University, Arlington, VA 22203, 2 Department of Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, 3 Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC 20057, 4 Departments of Pathology and Oncology, Johns Hopkins University, Baltimore, MD 21231 and 5 Department of Surgery, Memorial Sloan-Kettering Cancer Center, New York, NY 10021, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2014,9,30]]},"reference":[{"key":"2023020116152626000_btu607-B1","doi-asserted-by":"crossref","first-page":"1865","DOI":"10.1093\/bioinformatics\/btt301","article-title":"DeMix: deconvolution for mixed cancer transcriptomes using raw measured data","volume":"29","author":"Ahn","year":"2013","journal-title":"Bioinformatics"},{"key":"2023020116152626000_btu607-B2","doi-asserted-by":"crossref","first-page":"413","DOI":"10.1038\/nbt.2203","article-title":"Absolute quantification of somatic DNA alterations in human cancer","volume":"30","author":"Carter","year":"2012","journal-title":"Nat. Biotechnol."},{"key":"2023020116152626000_btu607-B3","doi-asserted-by":"crossref","first-page":"2044","DOI":"10.1109\/TMI.2011.2160276","article-title":"Tissue-specific compartmental analysis for dynamic contrast-enhanced MR imaging of complex tumors","volume":"30","author":"Chen","year":"2011","journal-title":"IEEE Trans. Med. Imaging"},{"key":"2023020116152626000_btu607-B4","doi-asserted-by":"crossref","first-page":"1043","DOI":"10.1093\/bioinformatics\/btq097","article-title":"Statistical expression deconvolution from mixed tissue samples","volume":"26","author":"Clarke","year":"2010","journal-title":"Bioinformatics"},{"key":"2023020116152626000_btu607-B5","doi-asserted-by":"crossref","first-page":"37","DOI":"10.1038\/nrc2294","article-title":"The properties of high-dimensional data spaces: implications for exploring gene and protein expression data","volume":"8","author":"Clarke","year":"2008","journal-title":"Nat. Rev. Cancer"},{"key":"2023020116152626000_btu607-B6","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":"2023020116152626000_btu607-B7","doi-asserted-by":"crossref","first-page":"229","DOI":"10.1038\/nrg1297","article-title":"Expression profiling-best practices for data generation and interpretation in clinical trials","volume":"5","author":"Hoffman","year":"2004","journal-title":"Nat. Rev. Genet."},{"key":"2023020116152626000_btu607-B8","doi-asserted-by":"crossref","first-page":"346","DOI":"10.1038\/nature12626","article-title":"Influence of tumour micro-environment heterogeneity on therapeutic response","volume":"501","author":"Junttila","year":"2013","journal-title":"Nature"},{"key":"2023020116152626000_btu607-B9","doi-asserted-by":"crossref","first-page":"530","DOI":"10.1109\/78.905873","article-title":"A generalization of joint-diagonalization criteria for source separation","volume":"49","author":"Moreau","year":"2001","journal-title":"IEEE Trans. Signal Process."},{"key":"2023020116152626000_btu607-B10","doi-asserted-by":"crossref","first-page":"2612","DOI":"10.1038\/ncomms3612","article-title":"Inferring tumour purity and stromal and immune cell admixture from expression data","volume":"4","author":"Yoshihara","year":"2013","journal-title":"Nat. Commun."},{"key":"2023020116152626000_btu607-B11","doi-asserted-by":"crossref","first-page":"1473","DOI":"10.1093\/bioinformatics\/btr183","article-title":"BACOM: in silico detection of genomic deletion types and correction of normal cell contamination in copy number data","volume":"27","author":"Yu","year":"2011","journal-title":"Bioinformatics"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/31\/1\/137\/49011292\/bioinformatics_31_1_137.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/31\/1\/137\/49011292\/bioinformatics_31_1_137.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,2]],"date-time":"2023-02-02T00:25:14Z","timestamp":1675297514000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/31\/1\/137\/2366216"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2014,9,30]]},"references-count":11,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2015,1,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btu607","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2015,1,1]]},"published":{"date-parts":[[2014,9,30]]}}}