Fig. 3: RBM15 gene signatures are associated with cancer metabolism.

a Gene expression signatures specific to the loss of RBM15 expression via shRBM15 in two TNBC cell lines. Genes in the Venn diagram were selected by applying class comparison analysis via the BRB array tool (p < 0.001). The gene expression profiles are presented in matrix format. In this matrix, red and blue indicate relatively high and low expression levels, respectively, as indicated in the scale bar (log₂-transformed scale). Genes associated with oncogenic potential are listed. b Schematic diagram of prediction model generation and evaluation of predicted outcomes based on a differentially expressed gene signature of RBM15 in BC cells. c A differentially expressed gene signature was used to construct a series of classifiers that estimated the probability of how much the expression pattern of BC patients was similar to the shared signature; control signature (CS) vs. knockdown signature (KS). K‒M plots of the OS of breast cancer patients in the TCGA-BRCA cohort were generated using the gene expression signature as a classifier. The differences between groups were significant as indicated (log-rank test). LOOCV leave-one-out cross-validation, CCP compound covariate predictor, 1NN one nearest neighbor, 3NN three nearest neighbors, NC nearest centroid, SVM support vector machine, LDA linear discriminator analysis. d Ingenuity pathway analysis (IPA) of genes differentially expressed after RBM15 silencing. e, f The indicated cells were infected or transfected with the indicated shRNA or siRNA. The cells were used for qRT‒PCR (e) and western blot (f) analyses of RBM15-associated genes in TNBC cells. The data are expressed as the means ± standard deviations (SDs) from three independent replicates. Student’s t test was performed to determine statistical significance (*p < 0.05, **p < 0.01, ***p < 0.005, and ****p < 0.001).