Robust enumeration of cell subsets from tissue expression profiles

Aaron M. Newman, Chih Long Liu, Michael R. Green, Andrew J. Gentles, Weiguo Feng, Yue Xu, Chuong D. Hoang, Maximilian Diehn, Ash A. Alizadeh

Research output: Contribution to journalArticle

628 Citations (Scopus)

Abstract

We introduce CIBERSORT, a method for characterizing cell composition of complex tissues from their gene expression profiles. When applied to enumeration of hematopoietic subsets in RNA mixtures from fresh, frozen and fixed tissues, including solid tumors, CIBERSORT outperformed other methods with respect to noise, unknown mixture content and closely related cell types. CIBERSORT should enable large-scale analysis of RNA mixtures for cellular biomarkers and therapeutic targets (http://cibersort.stanford.edu/).

Original languageEnglish (US)
Pages (from-to)453-457
Number of pages5
JournalNature Methods
Volume12
Issue number5
DOIs
StatePublished - Apr 29 2015

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RNA
Tissue
Transcriptome
Noise
Biomarkers
Gene expression
Tumors
Neoplasms
Chemical analysis
Therapeutics

ASJC Scopus subject areas

  • Biotechnology
  • Molecular Biology
  • Biochemistry
  • Cell Biology

Cite this

Newman, A. M., Liu, C. L., Green, M. R., Gentles, A. J., Feng, W., Xu, Y., ... Alizadeh, A. A. (2015). Robust enumeration of cell subsets from tissue expression profiles. Nature Methods, 12(5), 453-457. https://doi.org/10.1038/nmeth.3337

Robust enumeration of cell subsets from tissue expression profiles. / Newman, Aaron M.; Liu, Chih Long; Green, Michael R.; Gentles, Andrew J.; Feng, Weiguo; Xu, Yue; Hoang, Chuong D.; Diehn, Maximilian; Alizadeh, Ash A.

In: Nature Methods, Vol. 12, No. 5, 29.04.2015, p. 453-457.

Research output: Contribution to journalArticle

Newman, AM, Liu, CL, Green, MR, Gentles, AJ, Feng, W, Xu, Y, Hoang, CD, Diehn, M & Alizadeh, AA 2015, 'Robust enumeration of cell subsets from tissue expression profiles', Nature Methods, vol. 12, no. 5, pp. 453-457. https://doi.org/10.1038/nmeth.3337
Newman AM, Liu CL, Green MR, Gentles AJ, Feng W, Xu Y et al. Robust enumeration of cell subsets from tissue expression profiles. Nature Methods. 2015 Apr 29;12(5):453-457. https://doi.org/10.1038/nmeth.3337
Newman, Aaron M. ; Liu, Chih Long ; Green, Michael R. ; Gentles, Andrew J. ; Feng, Weiguo ; Xu, Yue ; Hoang, Chuong D. ; Diehn, Maximilian ; Alizadeh, Ash A. / Robust enumeration of cell subsets from tissue expression profiles. In: Nature Methods. 2015 ; Vol. 12, No. 5. pp. 453-457.
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