Open Access Highly Accessed Research article

Correlation of mRNA and protein levels: Cell type-specific gene expression of cluster designation antigens in the prostate

Laura E Pascal123*, Lawrence D True24, David S Campbell3, Eric W Deutsch3, Michael Risk1, Ilsa M Coleman5, Lillian J Eichner13, Peter S Nelson5 and Alvin Y Liu123

Author Affiliations

1 Department of Urology, University of Washington, Seattle WA 98195, USA

2 Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle WA 98195, USA

3 Institute for Systems Biology, Seattle WA 98103, USA

4 Department of Pathology, University of Washington, Seattle WA 98195, USA

5 Fred Hutchinson Cancer Research Center, Seattle WA 98109, USA

For all author emails, please log on.

BMC Genomics 2008, 9:246  doi:10.1186/1471-2164-9-246

Published: 23 May 2008



Expression levels of mRNA and protein by cell types exhibit a range of correlations for different genes. In this study, we compared levels of mRNA abundance for several cluster designation (CD) genes determined by gene arrays using magnetic sorted and laser-capture microdissected human prostate cells with levels of expression of the respective CD proteins determined by immunohistochemical staining in the major cell types of the prostate – basal epithelial, luminal epithelial, stromal fibromuscular, and endothelial – and for prostate precursor/stem cells and prostate carcinoma cells. Immunohistochemical stains of prostate tissues from more than 50 patients were scored for informative CD antigen expression and compared with cell-type specific transcriptomes.


Concordance between gene and protein expression findings based on 'present' vs. 'absent' calls ranged from 46 to 68%. Correlation of expression levels was poor to moderate (Pearson correlations ranged from 0 to 0.63). Divergence between the two data types was most frequently seen for genes whose array signals exceeded background (> 50) but lacked immunoreactivity by immunostaining. This could be due to multiple factors, e.g. low levels of protein expression, technological sensitivities, sample processing, probe set definition or anatomical origin of tissue and actual biological differences between transcript and protein abundance.


Agreement between these two very different methodologies has great implications for their respective use in both molecular studies and clinical trials employing molecular biomarkers.