Additional file 1 of In silico analysis of differentially expressed genesets in metastatic breast cancer identifies potential prognostic biomarkers

Additional file 1: Supplementary Figure S1. KIF2C and ESR1 are hub genes the most significantly co-expressed with the potential biomarker candidate genes. (A and B) Shown are Pearson's pairwise correlation plots of RNA-seq gene expression between four DOE-A (A) or three DUE-A genes (B) and their most significantly co-expressed hub genes identified from PPI networks. Statistical analyses were performed by the pre-set analytic method of bc-GenExMiner. Supplementary Figure S2. Comparison of mRNA expression of the two most significantly co-expressed hub genes (KIF2C and ESR1) between basal-like or triple-negative breast cancer and other subtypes of breast cancer. (A and B) RNA-seq data of KIF2C and ESR1 were obtained from the Cancer Cell Line Encyclopedia (CCLE) and analyzed. N = 31 in BL/TNBC and N = 26 in luminal type cell lines. (C and D) RNA-seq data of KIF2C and ESR1 from The Cancer Genome Atlas (TCGA) [58] were analyzed at bc-GenExMiner v4.3. N = 97 in BL/TNBC and N = 736 in non-BL/TNBC type breast cancer patient samples. Statistical significance in A and B was determined by unpaired t-tests and those in C and D were determined by the pre-set analytic method of bc-GenExMiner. Supplementary Figure S3. Correlation between the expression levels of two co-expressed hub genes (KIF2C and ESR1) and patient survivals. (A and B) Relapse-free, overall, distant metastasis-free, and post-progression survival of two co-expressed hub genes (KIF2C in (A); ESR1 in (B)) were stratified by the expression levels of each gene (low or high). Expression data were analyzed by KM plotter ( http://kmplot.com/ ). JetSet best probes were selected and patients (for KIF2C, N = 3951 in RFS, = 1402 in OS, = 1746 in DMFS and = 414 in PPS; for ESR1, N = 3951 in RFS, = 1402 in OS, = 1746 in DMFS and = 414 in PPS) were split by median expression. (C) Metastatic relapse-free survival of KIF2C and ESR1 was stratified by the expression levels of each gene (low or high). Microarray expression data were analyzed by bc-GenExMiner v4.3 ( http://bcgenex.centregauducheau.fr/ ). Patients (KIF2C, N = 4533; ESR1, N = 4785) were split by median expression. Statistical analyses were performed by pre-set analytic methods. HRs (hazardous ratios) and 95% CIs (confidence intervals) are indicated.