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Estimation of STromal and Immune cells in MAlignant Tumors using Expression data ESTIMATE


Uses gene expression signature to infer the fraction of stromal and immune cells in tumor tissues. ESTIMATE scores correlate with DNA copy number-based tumour purity across samples from 11 different tumour types, profiled on Agilent, Affymetrix platforms or based on RNA sequencing and available through The Cancer Genome Atlas. The prediction accuracy is further corroborated using 3,809 transcriptional profiles available elsewhere in the public domain. The ESTIMATE method allows consideration of tumour-associated normal cells in genomic and transcriptomic studies.

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ESTIMATE classification

ESTIMATE specifications

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Command line interface
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GNU General Public License version 2.0

ESTIMATE distribution


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ESTIMATE support



  • Roel Verhaak <>


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Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Centre, Houston, TX, USA; Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan; Department of Systems Biology, The University of Texas MD Anderson Cancer Centre, Houston, TX, USA; Catedra de Bioinformatica, Tecnologico de Monterrey, Campus Monterrey, Monterrey, Nuevo Leon, Mexico; USC Epigenome Centre, University of Southern California, Los Angeles, CA, USA; Gynecology Service, Department of Surgery, Memorial Sloan-Kettering Cancer Centre, New York, NY, USA; The Broad Institute of Harvard and MIT, Cambridge, MA, USA

Funding source(s)

This work was supported by the U.S. National Cancer Institute (grant n°CA143883 to The University of Texas MD Anderson Genome Data Analysis Centre).

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