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

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

Published: 23 May 2008

Additional files

Additional file 1:

Scatter plot of IHC staining intensity and gene expression levels determined by Affymetrix array for MACS-sorted cell populations. Statistical Pearson correlation ranged from -0.01 – 0.55 and Spearman Coefficients ranged from 0.00 – 0.51. There was no positive overall correlation of immunolocalization data with array data for endothelial, stromal or progenitor cells, and moderate positive correlation for luminal, basal and cancer.

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Additional file 2:

Scatter plot using updated probe set definitions. Statistical Pearson correlations ranged from 0.09 – 0.57 and Spearman Coefficients ranged from 0.03 – 0.63 using updated probe set definitions. Updated probe set definitions increased correlation from none to moderate positive correlation for progenitor cells.

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Additional file 3:

Scatter plot of IHC staining intensity and gene expression levels determined by Affymetrix and Agilent array for LCM cells. Statistical Pearson correlation ranged from 0.26 – 0.57 and Spearman Coefficients ranged from 0.25 – 0.43. There was no positive correlation of immunolocalization data with array data for LCM stromal cells assayed by either Agilent or Affymetrix. Pearson correlation for LCM luminal cells was 0.57 and Spearman coefficient was 0.43, which were the same values as that for MACS-sorted luminal cells using updated probe set definitions. Pearson correlation between LCM stromal cell data and MACS-sorted stromal cell data assayed by Affymetrix array was 0.68, Spearman coefficient was 0.78. Pearson correlation between LCM stromal cell data analyzed by Agilent array and Affymetrix MACS-sorted stromal cell data was 0.65, Spearman coefficient was 0.55. Pearson correlation between LCM stromal cell data analyzed by Agilent array and Affymetrix LCM stromal cell data was 0.33, Spearman coefficient was 0.59.

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