Fig. 5: The expression of miRNA families across cell lines and tissues.

A Expression patterns of the top 30 miRNA families in cell lines based on our datasets and the DIANA-miTED database. Circle size represents the proportion of miRNA family expression relative to total miRNA families. B The representative miRNA families whose expression was underestimated (up) or overrepresented (bottom) in the DIANA-miTED database compared to our datasets. Each box plot summarizes data from the 17 shared cell lines common to both datasets. C Expression patterns of the top 30 miRNA families in mouse and monkey tissues. Circle size represents the quantification of each miRNA family. Data in (A) and (C) are presented as mean values and their biological replicates: n = 2 (for mouse ovary and testis) or n = 3 (for Caco-2, mouse-breast, monkey-rectum, and monkey-stomach) or n = 4 (for the remaining samples). D Confusion matrix of miRNA families with a tissue-specificity index (TSI) greater than 0.85. Numbers within the bubbles indicate the number of overlapping tissue-specific miRNA families between our datasets and MirGeneDB across various species. Numbers in parentheses on the axes denote the total number of tissue-specific miRNA families identified in each tissue using our datasets (x-axis) and MirGeneDB (y-axis). E The quantification of tissue-specific miRNA families uniquely identified by MirGeneDB (MirGeneDB unique) or common by MirGeneDB and our datasets (Shared). Each box plot summarizes data from the 10 shared tissues common to both datasets. F Expression levels of tissue-specific miRNA families uniquely identified by our datasets in the MirGeneDB and our datasets. Each box plot summarizes data from the 10 shared tissues common to both datasets. Statistical significance was assessed using two-tailed Student’s t-tests. Box plots in (B, E, and F) depict the median (center line), interquartile range (box), and min-max range (whiskers). Source data are provided as a Source Data file.