Fig. 1: AMFs are associated with BC.

a Patterns of RiBP dysregulation across 15 different cancer types. Variations in color intensity correspond to the log₂-fold change (log₂FC) in expression levels. The upper bar plot illustrates the frequency with which each RiBP is dysregulated across the cancer types examined. A mutation heatmap reveals the proportion of BC patients with RiBP mutations. b Bar graphs depicting the percentage of significantly up-regulated AMFs (blue) and RPs (red) across 15 cancer types. c Heatmap of RiBPs proteome profiles in BC patients (Tumor n = 133, Normal n = 18, from CPTAC project⁷⁰). d Stacked bar chart showing the counts of up-regulated, unchanged and down-regulated RPs and AMFs as inferred from differential proteomic analysis. e The mutation frequency of core-AMFs (n = 94), known oncogenes (n = 206), tumor suppressor genes (TSGs, n = 220), and transcription factors (TFs, n = 1353) in BC patients. f–g Boxplots illustrating the log₂FC in the mRNA expression level of core-AMFs across different tumor grades (Grade 1, n = 183; Grade 2, n = 632; Grade 3, n = 253) (f) and clinical subtypes (HR, n = 657; HER2, n = 153; TN, n = 170) (g) compared to normal in BC patients. h Kaplan3-Meier survival analysis of TCGA-BC dataset (high n = 546, low n = 540) based on predictive survival using 113 core-AMFs gene signatures as determined by gene expression levels. i Gene silencing effects of 113 core-AMFs using open-source shRNA data in 16 BC cell lines and 200 other cancer cell lines. Distribution of log₂ ratios between final cell populations and initial DNA pool for core-AMFs, known oncogenes, known TSGs, and non-cancer genes. e–g, i, Box plots show the distribution of data across groups. The central line within the box represents the median value. The upper and lower edges of the box represent the 75th and 25th percentiles, respectively (Interquartile Range, IQR). The whiskers extend from the box to the maximum and minimum values within 1.5 times the interquartile range (IQR), with any data points beyond this range considered as outliers. Data shown as mean ± SEM. Statistical analysis between all groups was conducted by two-sided Wilcoxon rank-sum test (e–g, i) or two-sided Log-rank (Mantel-Cox) test (h).