Introduction

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.UNDO is available at http://bioconductor.org/packages.

Publications

  1. UNDO: a Bioconductor R package for unsupervised deconvolution of mixed gene expressions in tumor samples.
    Cite this
    Wang N, Gong T, Clarke R, Chen L, Shih IeM, Zhang Z, Levine DA, Xuan J, Wang Y, 2015-01-01 - Bioinformatics (Oxford, England)

Credits

  1. Niya Wang
    Developer

    Department of Electrical and Computer Engineering, Virginia Polytechnic Institute and State University, United States of America

  2. Ting Gong
    Developer

    Department of Electrical and Computer Engineering, Virginia Polytechnic Institute and State University, United States of America

  3. Robert Clarke
    Developer

    Department of Electrical and Computer Engineering, Virginia Polytechnic Institute and State University, United States of America

  4. Lulu Chen
    Developer

    Department of Electrical and Computer Engineering, Virginia Polytechnic Institute and State University, United States of America

  5. Ie-Ming Shih
    Developer

    Department of Electrical and Computer Engineering, Virginia Polytechnic Institute and State University, United States of America

  6. Zhen Zhang
    Developer

    Department of Electrical and Computer Engineering, Virginia Polytechnic Institute and State University, United States of America

  7. Douglas A Levine
    Developer

    Department of Electrical and Computer Engineering, Virginia Polytechnic Institute and State University, United States of America

  8. Jianhua Xuan
    Developer

    Department of Electrical and Computer Engineering, Virginia Polytechnic Institute and State University, United States of America

  9. Yue Wang
    Investigator

    Department of Electrical and Computer Engineering, Virginia Polytechnic Institute and State University, United States of America

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Summary
AccessionBT001601
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesR
User InterfaceTerminal Command Line
Download Count0
Country/RegionUnited States of America
Submitted ByYue Wang