Fig. 4

E74-like factor 5 (ELF5) expression is altered in breast cancer in a subtype-specific manner. a ELF5 gene (left) and isoform (right) expression (quantile-normalized counts) for normal breast and breast cancer subtypes. Plotted values are for The Cancer Genome Atlas RNA-sequencing (RNA-seq) samples, and error bars represent the mean with 95 % confidence interval. Fold change (FC) and false discovery rate (FDR) from Limma voom analysis are shown for ELF5 gene data, with green values in bold indicating a significant downregulation and red values in bold a significant upregulation compared with normal (FDR < 0.05). Nonbold green or red values indicate FDR of 0.05–0.10. b Mean ELF5 levels in transcripts per million (TPM) in normal breast and breast cancer, excluding normal-like, with 95 % confidence interval. Relative isoform contributions shown within each bar. Numbers in parentheses indicate samples per group. c Mean ELF5 expression values at the gene and isoform levels (columns 1–6), isoform fold changes in cancer compared with normal (columns 7–11), and isoform ratios (columns 12 and 13). All values are TPM, except for column 1, which is the quantile-normalized count. Ratios were calculated using mean TPM values. d Box-and-whisker plot representing isoform percentage of total ELF5 in normal breast and cancer. Box 25–75th percentile, horizontal line median, error bars 10th–90th percentile, circles outliers. e Mean (left) and median (right) isoform percentage values for normal breast and cancer. f ELF5 levels (quantile-normalized count) for patients with matched normal and cancer samples, categorized according to tumor molecular subtype. Six extra matched normal samples were included, for a total of 65 pairs. Plotted values represent individual samples, with samples from the same patient connected with a line. FC and FDR from paired Limma voom analysis are shown, with green values indicating a significant downregulation compared with normal (FDR < 0.05). Numbers in parentheses indicate sample pairs per group