Confirmation of peptide identity using SID SRM-MS.

<p>List of peptides for which SID SRM-MS was used to confirm their identification. UniProtKB accession number and amino acid sequence are shown.</p><p>SID: Stable isotope dilution.</p><p>SRM-MS: selected reaction monitoring mass spectrometry.</p

Univariate and multivariate analysis of predictors of overall survival.

<p> <b>Univariate and Multivariable Cox proportional hazards regression to determine predictors of overall survival. Note: Molecular subtype was used in place of ER and HER2 status; Decorin Iwavg was used in place of Decorin Iavg.</b></p

Overall survival curves based on DE/HE expression and hormone treatment.

<p>A, Survival curves for cases with high and low DE that did not receive hormone treatment. B, Survival curves for cases with high and low DE that received hormone treatment. C, Survival curves for cases with high and low HE that did not receive hormone treatment. D, Survival curves for cases with high and low HE that received hormone treatment. Univariate Cox regression used to determine HR and 95% CI. DE: Decorin staining in malignant epithelial tissue. HE: HSP90B1 staining in malignant epithelial tissue.</p

Overall survival curves using combinations of DE and HE expression levels.

<p>Univariate Cox regression used to determine HR; logrank p-values reported; Bonferroni multiple testing adjustment for pairwise comparisons p = 0.05/5 = 0.01. DE: Decorin staining in malignant epithelial tissue. HE: HSP90B1 staining in malignant epithelial tissue. HR: Hazard ratio.</p

Scoring system used for DCN and HSP90B1 immunohistochemistry.

<p>A, Strong DCN positivity in stroma (3+) and negative in carcinoma (0) (magnification 200×). B, Strong DCN positivity in carcinoma (3+), weak stromal positivity (1+) (200×). C, Moderate HSP90B1 positivity in carcinoma (1+) (200×). D, Strong HSP90B1 positivity in carcinoma (3+) (200×). Decorin antibody (Sigma-Aldrich, St. Louis, MO) used at a dilution of 1∶400. HSP90B1 antibody (Sigma-Aldrich, St. Louis, MO) used at a dilution of 1∶4000.</p

Antibodies used to validate putative biomarkers.

<p>List of commercially available antibodies purchased, including manufacturing laboratory, used to validate putative biomarkers. Only antibodies designed for use on formalin fixed paraffin embedded tissue were used.</p

Overall survival curves for high and low DE staining based on tumour molecular subtype.

<p>Univariate Cox regression used to determine HR; logrank p-values reported. Molecular subtypes were defined by IHC expression of ER, HER2 and Ki-67 as suggested by Cheang <i>et al.</i> (2009) and Hugh <i>et al.</i> (2009). DE: Decorin staining in malignant epithelial tissue. HR: Hazard ratio.</p

Overall and Disease-free survival based on high and low DCN and HSP90B1 staining.

<p>A, OS curve for DE. B, DFS curve for DE. C, OS curve for HE. D, DFS curve for HE. DE: Decorin staining in malignant epithelial tissue. HE: HSP90B1 staining in malignant epithelial tissue. OS: Time from diagnosis to death from any cause. DFS: Time from diagnosis to any recurrence or death from any cause.</p

Venn diagram of Differentially expressed proteins.

<p>Number of proteins differentially expressed for each comparison group as well as overlapping proteins. Node-negative breast cancer tissue (group A), node positive BC tissue (group B), and normal breast tissue (group N).</p