Statistical expression deconvolution from mixed tissue samples

Jennifer Clarke, Pearl H Seo, Bertrand Clarke

Research output: Contribution to journalArticle

43 Citations (Scopus)

Abstract

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. 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 amixed 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. 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. Contact: jclarke@med.miami.edu.

Original languageEnglish
Article numberbtq097
Pages (from-to)1043-1049
Number of pages7
JournalBioinformatics
Volume26
Issue number8
DOIs
StatePublished - Mar 4 2010

Fingerprint

Deconvolution
Gene expression
Tissue
Gene Expression
Proportion
Cell
Information Centers
Biomarkers
Cellular Structures
Biotechnology
Heterografts
Medicine
Estimate
Statistical methods
Genes
Availability
Breast Neoplasms
Breast Cancer
Repository
Specificity

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology
  • Computational Theory and Mathematics
  • Computer Science Applications
  • Computational Mathematics
  • Statistics and Probability
  • Medicine(all)

Cite this

Statistical expression deconvolution from mixed tissue samples. / Clarke, Jennifer; Seo, Pearl H; Clarke, Bertrand.

In: Bioinformatics, Vol. 26, No. 8, btq097, 04.03.2010, p. 1043-1049.

Research output: Contribution to journalArticle

Clarke, Jennifer ; Seo, Pearl H ; Clarke, Bertrand. / Statistical expression deconvolution from mixed tissue samples. In: Bioinformatics. 2010 ; Vol. 26, No. 8. pp. 1043-1049.
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