UNDO: A Bioconductor R package for unsupervised deconvolution of mixed gene expressions in tumor samples Journal Article


Authors: Wang, N.; Gong, T.; Clarke, R.; Chen, L.; Shih, I. M.; Zhang, Z.; Levine, D. A.; Xuan, J.; Wang, Y.
Article Title: UNDO: A Bioconductor R package for unsupervised deconvolution of mixed gene expressions in tumor samples
Abstract: 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-stroma 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's 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. Availability and implementation: UNDO is available at http://bioconductor.org/packages. Contact: Supplementary information: Supplementary data are available at Bioinformatics online.
Journal Title: Bioinformatics
Volume: 31
Issue: 1
ISSN: 1367-4803
Publisher: Oxford University Press  
Date Published: 2015-01-01
Start Page: 137
End Page: 139
Language: English
DOI: 10.1093/bioinformatics/btu607
PROVIDER: scopus
PMCID: PMC4271149
PUBMED: 25212756
DOI/URL:
Notes: Export Date: 2 March 2015 -- Source: Scopus
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  1. Douglas A Levine
    369 Levine