Open Access Highly Accessed Research article

Protein expression based multimarker analysis of breast cancer samples

Angela P Presson12*, Nam K Yoon3, Lora Bagryanova3, Vei Mah3, Mohammad Alavi3, Erin L Maresh3, Ayyappan K Rajasekaran6, Lee Goodglick35, David Chia35 and Steve Horvath145*

Author Affiliations

1 Department of Biostatistics, UCLA, Los Angeles, CA, 90095, USA

2 Department of Pediatrics, David Geffen School of Medicine, UCLA, Los Angeles, CA, 90095, USA

3 Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, 90095, USA

4 Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, 90095, USA

5 Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA

6 Nemours Center for Childhood Cancer Research, Wilmington, DE, USA

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BMC Cancer 2011, 11:230  doi:10.1186/1471-2407-11-230

Published: 8 June 2011



Tissue microarray (TMA) data are commonly used to validate the prognostic accuracy of tumor markers. For example, breast cancer TMA data have led to the identification of several promising prognostic markers of survival time. Several studies have shown that TMA data can also be used to cluster patients into clinically distinct groups. Here we use breast cancer TMA data to cluster patients into distinct prognostic groups.


We apply weighted correlation network analysis (WGCNA) to TMA data consisting of 26 putative tumor biomarkers measured on 82 breast cancer patients. Based on this analysis we identify three groups of patients with low (5.4%), moderate (22%) and high (50%) mortality rates, respectively. We then develop a simple threshold rule using a subset of three markers (p53, Na-KATPase-β1, and TGF β receptor II) that can approximately define these mortality groups. We compare the results of this correlation network analysis with results from a standard Cox regression analysis.


We find that the rule-based grouping variable (referred to as WGCNA*) is an independent predictor of survival time. While WGCNA* is based on protein measurements (TMA data), it validated in two independent Affymetrix microarray gene expression data (which measure mRNA abundance). We find that the WGCNA patient groups differed by 35% from mortality groups defined by a more conventional stepwise Cox regression analysis approach.


We show that correlation network methods, which are primarily used to analyze the relationships between gene products, are also useful for analyzing the relationships between patients and for defining distinct patient groups based on TMA data. We identify a rule based on three tumor markers for predicting breast cancer survival outcomes.

Tissue microarray; breast cancer; tumor marker; prognostic marker; WGCNA