A Tale of Three Proteomes: Visualizing Protein and Transcript Abundance Relationships in the Breast Cancer Proteome Portal.

Molecular characterization is transforming research on novel therapeutics in breast cancer. High-throughput methodologies are unbiased to hypotheses; thus, data produced are relevant to address unlimited questions and provide resources for the experimental design process. However, the opportunity is often overlooked because data are not readily accessed or analyzed. Herein, the Breast Cancer Proteome Portal, the only online tool for analyzing protein and transcript abundances across the three breast cancer proteomics studies, is presented. The tool is applied to demonstrate that cofunctioning protein abundances are highly correlated and, conversely, high abundance correlation may be an indicator of cofunction. Furthermore, the cofunction-correlation relationship is less resolved at the transcript level. By applying analysis and visualization tools within the Breast Cancer Proteome Portal, insights are garnered about serine synthesis and the compartmentalization of one-carbon metabolism in breast cancer, and a transcription factor tumorigenic regulatory network of glutamine deamination and oxidation is proposed, illustrating that the Breast Cancer Proteome Portal provides an interface for garnering insights from the information-rich studies of the breast cancer proteome.