SF1: Pathway analyses performed using the Reactome dataset through CPDB of the changes occurring during cancer. Many basic cell function processes are upregulated in the tumor cells as expected, with particularly prominent changes in pathways associated with metabolism.

SF2: Induced module analyses of the changes in protein expression between tumor and normal samples. A) Upregulated protein complexes observed in the tumor samples shows a central node that is likely linked in part by known oncogenes such as BRCA1 and PCNA. B) Downregulated protein complexes that are suppressed in the tumor are less coherently observed, with many of the links (factors labeled in purple) being derived from imputation. Both visualizations were drawn from CPDB using a z-cutoff of 40 and only intermediately or highly confident interactions.

SF3: Correlational analysis using Pearson’s R based on subsets of proteins assigned their subcellular distribution according to KEGG GO annotations. One protein may be assigned into multiple organelles for this analysis. A,B)

Proteins localized to the Golgi apparatus and ER both cleanly separate out between tumor and normal samples, demonstrating that key proteins involved in basic protein transport and synthesis are altered during tumor cell development. C,E) The same pattern can also be seen in cytoplasmic and nuclear proteins, as previously reported elsewhere. D) Interestingly, endosome proteins show a much heavier degree of similarity between normal and tumor samples, suggesting that tumor cells may actually share similar capabilities in processing vesicles for recycling. F) Ribosomal proteins expression is highly conserved between normal and tumor cells.

SF4– tSNE visualizations of the TCGA cohort in Fig3. Annotation of the plot using other clinical characteristics demonstrates that the clustering (and consequently SSBP1 expression level) does not appear to be sharply influenced by tumor location, metastasis, cell type of origin, or finer disease stage differences.

SF5– A) Gating strategy implemented for the flow cytometry evaluations of mitochondrial dynamics in Fig 4. B) Distribution mapping shows slight correlation between mitochondrial mass and cellular granularity. C) Representative flow cytometry plots showing mitochondrial mass in the presence of cisplatin or 5-FU following siRNA depletion of SSBP1.