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Figure S1. A) A heatmap of unsupervised hierarchical clustering analysis of z-score normalized protein secretion by one non-malignant control (MCF10A), two basal breast cancer (MDA-231 and HCC1806), and two luminal breast cancer (MCF7 and T47D) cell lines highlights intra-subtype heterogeneity. Each cell line is represented by 3 biological replicates and 2 technical replicates. Red indicates higher secretion, green indicates lower secretion, and white indicates mean secretion. Profile plots of 4 representative clusters are shown which demonstrate proteins B) higher in BLBC, C) lower in luminal BC, D) lower in BLBC, and E) higher in luminal BC. Each line represents one protein and the color indicates the density of proteins with similar expression levels. (PPTX 170 kb)

Figure S8. Correlation between Kaplan-Meier survival plots of the clinical outcomes and mRNA co-overexpression of indicated SeCEP genes based on patient data. “N” refers to “Number of patients,” and “NE” refers to “Number of Events (Overall Survival status = DECEASED)”. Each plot shows the log-rank p-value and Hazard Ratio (HR) with 95% Confidence Interval (CI) between the two groups. The red line designates the patient subpopulation showing statistically significant overexpression of the indicated genes (“altered”). The blue line designates the group of patients not showing statistically significant overexpression of the indicated genes (“not altered”). (PDF 121 kb)

Figure S3. A) Over-represented biological processes in the basal-like and luminal BC subtypes. Bars representing the negative log p-values of BLBC process enrichment are displayed in orange and luminal values are in blue. B) Biological functions activated (positive z-score) or suppressed (negative z-score) in the BLBC (orange) and luminal (blue) PAM50 subtypes. C) Pathway activation analysis of PAM50 subtypes. Orange bars represent BLBC values and blue bars represent luminal values. Positive z-scores indicate pathway activation; negative z-scores indicate pathway suppression. (PPTX 53 kb)

Figure S4. Protein-protein interaction analysis of A) basal-specific and B) luminal-specific secreted proteins. (PDF 6934 kb)

Figure S6. Correlation between Kaplan-Meier survival plots of the clinical outcomes and mRNA co-overexpression of indicated luminal SeCEP genes based on TCGA (left column) and METABRIC (right column) patient data. “N” refers to “Number of patients,” and “NE” refers to “Number of Events (Overall Survival status = DECEASED)”. Each plot shows the log-rank p-value and Hazard Ratio (HR) with 95% Confidence Interval (CI) between the two groups. The red line designates the patient subpopulation showing statistically significant overexpression of the indicated luminal-specific genes (“altered”). The blue line designates the group of patients not showing statistically significant overexpression of the indicated luminal-specific genes (“not altered”). Co-overexpression of distinct sets of genes correlate with statistically significant changes in overall survival in Luminal B patients but not Luminal A or other BC subtypes. (PDF 144 kb)

Figure S4. Protein-protein interaction analysis of A) basal-specific and B) luminal-specific secreted proteins. (PDF 6934 kb)

Figure S2. Western blot validation of LFQ data. (PPTX 1693 kb)

Figure S5. Correlation between Kaplan-Meier survival plots of the clinical outcomes and mRNA co-overexpression of indicated luminal SeCEP genes based on TCGA (left column) and METABRIC (right column) patient data. “N” refers to “Number of patients,” and “NE” refers to “Number of Events (Overall Survival status = DECEASED)”. Each plot shows the log-rank p-value and Hazard Ratio (HR) with 95% Confidence Interval (CI) between the two groups. The red line designates the patient subpopulation showing statistically significant overexpression of the indicated luminal-specific genes (“altered”). The blue line designates the group of patients not showing statistically significant overexpression of the indicated luminal-specific genes (“not altered”). Co-overexpression of distinct sets of genes correlate with statistically significant changes in overall survival in Luminal A patients but not Luminal B or other BC subtypes. (PDF 153 kb)

Figure S7. Correlation between Kaplan-Meier survival plots of the clinical outcomes and mRNA co-overexpression of indicated SeCEP genes based on patient data. “N” refers to “Number of patients,” and “NE” refers to “Number of Events (Overall Survival status = DECEASED)”. Each plot shows the log-rank p-value and Hazard Ratio (HR) with 95% Confidence Interval (CI) between the two groups. The red line designates the patient subpopulation showing statistically significant overexpression of the indicated luminal-specific genes (“altered”). The blue line designates the group of patients not showing statistically significant overexpression of the indicated luminal-specific genes (“not altered”). (PDF 792 kb)

Figure S5. Correlation between Kaplan-Meier survival plots of the clinical outcomes and mRNA co-overexpression of indicated luminal SeCEP genes based on TCGA (left column) and METABRIC (right column) patient data. “N” refers to “Number of patients,” and “NE” refers to “Number of Events (Overall Survival status = DECEASED)”. Each plot shows the log-rank p-value and Hazard Ratio (HR) with 95% Confidence Interval (CI) between the two groups. The red line designates the patient subpopulation showing statistically significant overexpression of the indicated luminal-specific genes (“altered”). The blue line designates the group of patients not showing statistically significant overexpression of the indicated luminal-specific genes (“not altered”). Co-overexpression of distinct sets of genes correlate with statistically significant changes in overall survival in Luminal A patients but not Luminal B or other BC subtypes. (PDF 153 kb)

Figure S2. Western blot validation of LFQ data. (PPTX 1693 kb)

Figure S7. Correlation between Kaplan-Meier survival plots of the clinical outcomes and mRNA co-overexpression of indicated SeCEP genes based on patient data. “N” refers to “Number of patients,” and “NE” refers to “Number of Events (Overall Survival status = DECEASED)”. Each plot shows the log-rank p-value and Hazard Ratio (HR) with 95% Confidence Interval (CI) between the two groups. The red line designates the patient subpopulation showing statistically significant overexpression of the indicated luminal-specific genes (“altered”). The blue line designates the group of patients not showing statistically significant overexpression of the indicated luminal-specific genes (“not altered”). (PDF 792 kb)

Figure S6. Correlation between Kaplan-Meier survival plots of the clinical outcomes and mRNA co-overexpression of indicated luminal SeCEP genes based on TCGA (left column) and METABRIC (right column) patient data. “N” refers to “Number of patients,” and “NE” refers to “Number of Events (Overall Survival status = DECEASED)”. Each plot shows the log-rank p-value and Hazard Ratio (HR) with 95% Confidence Interval (CI) between the two groups. The red line designates the patient subpopulation showing statistically significant overexpression of the indicated luminal-specific genes (“altered”). The blue line designates the group of patients not showing statistically significant overexpression of the indicated luminal-specific genes (“not altered”). Co-overexpression of distinct sets of genes correlate with statistically significant changes in overall survival in Luminal B patients but not Luminal A or other BC subtypes. (PDF 144 kb)

Figure S8. Correlation between Kaplan-Meier survival plots of the clinical outcomes and mRNA co-overexpression of indicated SeCEP genes based on patient data. “N” refers to “Number of patients,” and “NE” refers to “Number of Events (Overall Survival status = DECEASED)”. Each plot shows the log-rank p-value and Hazard Ratio (HR) with 95% Confidence Interval (CI) between the two groups. The red line designates the patient subpopulation showing statistically significant overexpression of the indicated genes (“altered”). The blue line designates the group of patients not showing statistically significant overexpression of the indicated genes (“not altered”). (PDF 121 kb)

Figure S3. A) Over-represented biological processes in the basal-like and luminal BC subtypes. Bars representing the negative log p-values of BLBC process enrichment are displayed in orange and luminal values are in blue. B) Biological functions activated (positive z-score) or suppressed (negative z-score) in the BLBC (orange) and luminal (blue) PAM50 subtypes. C) Pathway activation analysis of PAM50 subtypes. Orange bars represent BLBC values and blue bars represent luminal values. Positive z-scores indicate pathway activation; negative z-scores indicate pathway suppression. (PPTX 53 kb)