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

doi:10.1038/nmeth.3337

Robust enumeration of cell subsets from tissue expression profiles

Nat Methods. 2015 May;12(5):453-7. doi: 10.1038/nmeth.3337. Epub 2015 Mar 30.

Authors

Aaron M Newman¹, Chih Long Liu¹, Michael R Green², Andrew J Gentles³, Weiguo Feng⁴, Yue Xu⁵, Chuong D Hoang⁵, Maximilian Diehn⁶, Ash A Alizadeh⁷

Affiliations

¹ 1] Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, California, USA. [2] Department of Medicine, Division of Oncology, Stanford Cancer Institute, Stanford University, Stanford, California, USA.
² 1] Department of Medicine, Division of Oncology, Stanford Cancer Institute, Stanford University, Stanford, California, USA. [2] Center for Cancer Systems Biology, Stanford University, Stanford, California, USA.
³ 1] Center for Cancer Systems Biology, Stanford University, Stanford, California, USA. [2] Department of Radiology, Stanford University, Stanford, California, USA.
⁴ Department of Radiation Oncology, Stanford University, Stanford, California, USA.
⁵ Department of Cardiothoracic Surgery, Division of Thoracic Surgery, Stanford University, Stanford, California, USA.
⁶ 1] Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, California, USA. [2] Department of Radiation Oncology, Stanford University, Stanford, California, USA. [3] Stanford Cancer Institute, Stanford University, Stanford, California, USA.
⁷ 1] Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, California, USA. [2] Department of Medicine, Division of Oncology, Stanford Cancer Institute, Stanford University, Stanford, California, USA. [3] Center for Cancer Systems Biology, Stanford University, Stanford, California, USA. [4] Stanford Cancer Institute, Stanford University, Stanford, California, USA. [5] Department of Medicine, Division of Hematology, Stanford Cancer Institute, Stanford University, Stanford, California, USA.

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/).

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Biomarkers
Gene Expression Regulation / physiology
Humans
Palatine Tonsil / cytology*
Palatine Tonsil / metabolism*
RNA / classification
RNA / genetics
RNA / metabolism
Reproducibility of Results
Software
Tissue Culture Techniques / methods*
Tissue Preservation / methods*
Transcriptome*

Robust enumeration of cell subsets from tissue expression profiles

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