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

Niya Wang, Ting Gong, Robert Clarke, Lulu Chen, Ie Ming Shih, Zhen Zhang, Douglas A. Levine, Jianhua Xuan, Yue Wang

Research output: Contribution to journalArticle

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.

Original languageEnglish (US)
Pages (from-to)137-139
Number of pages3
JournalBioinformatics
Volume31
Issue number1
DOIs
StatePublished - Jan 1 2015

    Fingerprint

ASJC Scopus subject areas

  • Statistics and Probability
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Computational Theory and Mathematics
  • Computational Mathematics

Cite this