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A method for cell type marker discovery by high-throughput gene expression analysis of mixed cell populations

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Item Type:Article
Title:A method for cell type marker discovery by high-throughput gene expression analysis of mixed cell populations
Creators Name:Andrade-Navarro, M.A. and Kanji, F. and Palii, C.G. and Brand, M. and Atkins, H. and Perez-Iratxeta, C.
Abstract:BACKGROUND: Gene transcripts specifically expressed in a particular cell type (cell-type specific gene markers) are useful for its detection and isolation from a tissue or other cell mixtures. However, finding informative marker genes can be problematic when working with a poorly characterized cell type, as markers can only be unequivocally determined once the cell type has been isolated. We propose a method that could identify marker genes of an uncharacterized cell type within a mixed cell population, provided that the proportion of the cell type of interest in the mixture can be estimated by some indirect method, such as a functional assay. RESULTS: We show that cell-type specific gene markers can be identified from the global gene expression of several cell mixtures that contain the cell type of interest in a known proportion by their high correlation to the concentration of the corresponding cell type across the mixtures. CONCLUSIONS: Genes detected using this high-throughput strategy would be candidate markers that may be useful in detecting or purifying a cell type from a particular biological context. We present an experimental proof-of-concept of this method using cell mixtures of various well-characterized hematopoietic cell types, and we evaluate the performance of the method in a benchmark that explores the requirements and range of validity of the approach.
Keywords:Cell Markers, High-Throughput Gene Expression, Cell Isolation, Proof-of Concept
Source:BMC Biotechnology
Publisher:BioMed Central
Page Range:80
Date:3 October 2013
Official Publication:https://doi.org/10.1186/1472-6750-13-80
PubMed:View item in PubMed

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