Figure 4

Characteristics of 31 unique regulations in TNBC identified by DERA.A) Differentially expressed regulations specific for TNBC. Green and red colors indicate under- and over-expression compared to median of normal breast tissues. Direction indicates gene regulation. B) Expression of TNBC specific regulations in terms of the signed fold-changes for the 31 regulations. Expression of a regulation is represented sum of two genes. C) Boxplot of log2 gene expression values of CCNE1 and SKP2. TCGA_Array dataset was used to compare expression of CCNE1 and SKP2 in the different breast cancer subtypes. Grouping into subtypes, including TNBC (n=55), Luminal 1 (n=219), Luminal 2 (n=69) and Non-luminal HER2+ (n=23) is based on immunohistochemistry (IHC) staining. Two sided t-test was used and significance is noted by *** (P<1.0×10⁻¹⁰). D) Kaplan-Meier survival plot of FOXA1-XBP1 regulation. Comparing patients with over-expression, neutral expression and under-expression of FOXA1-XBP1 regulation in the TCGA (left) and GSE3494 (right) datasets. Vertical ticks represent censoring events. The X and Y axes represent follow-up time in days and the percentage of survival, respectively. The associated log-rank p-value is 0.02 in TCGA and 2.15×10⁻³ in GSE3494.