Fig. 6: Experimental validation of miRNAs targeted by the vitamin D receptor agonist calcitriol.
From: sChemNET: a deep learning framework for predicting small molecules targeting microRNA function
a Enhanced volcano plot of miRNAs differentially expressed in SH-SY5Y cell lines upon drug treatment. P-value was obtained with two-way ANOVA test and contrasts were determined between control and treated using Fisher’s Least Significant Difference (LSD); (b) sChemNET predicted rank for calcitriol for the group of miRNAs found to be non-significant (NS) vs. the group found to be significant in terms of p-value and log2FC (S) in SH-SY5Y cell lines (\(n=64\) for NS and \(n=6\) for S). For the boxplots the center line represents the median and the lines extending from both ends of the box indicate the quartile (Q) variability outside Q1 and Q3 to the minimum and maximum values; (c) Enhanced volcano plot of miRNAs differentially expressed under treatment with calcitriol on endothelial progenitor cells and control cells derived from the bone marrow of male Sprague-Dawley rats. P-values were obtained with DESeq2 by the Wald test and adjusted for multiple testing using the Benjamini–Hochberg method. d ChemNET predicted rank for calcitriol for the group of miRNAs found to be non-significant (NS) vs. the group found to be significant in terms of p-value and log2FC (S) in miRNAs from Rattus Norvergicus (\(n=7\) for NS and \(n=5\) for S). For the boxplots the center line represents the median and the lines extending from both ends of the box indicate the quartile (Q) variability outside Q1 and Q3 to the minimum and maximum values. e Box plots for the droplet digital PCR (ddPCR) quantification of the copies/ul of miR-181a-5p, miR-181b-5p, miR-181c-5p, and miR-181d-5p in human non-metastatic MCF10CA1a and metastatic MCF10CA1a-ras breast cancer cell line with and without calcitrol treatment determined by ddPCR. The significance between groups is shown by the p-value. There are \(n=3\) replicates for each condition. For the boxplots the center line represents the median and the lines extending from both ends of the box indicate the quartile (Q) variability outside Q1 and Q3 to the minimum and maximum values. The p-values were determined by two-side pairwise comparison.
