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1 publications mentioning dre-mir-2189

Open access articles that are associated with the species Danio rerio and mention the gene name mir-2189. Click the [+] symbols to view sentences that include the gene name, or the word cloud on the right for a summary.

[+] score: 63
Other miRNAs from this paper: hsa-mir-23a, hsa-mir-29a, hsa-mir-29b-1, hsa-mir-29b-2, hsa-mir-107, hsa-mir-205, hsa-mir-214, hsa-mir-221, hsa-mir-1-2, hsa-mir-122, hsa-mir-133a-1, hsa-mir-133a-2, hsa-mir-184, hsa-mir-193a, hsa-mir-1-1, hsa-mir-29c, hsa-mir-133b, dre-mir-205, dre-mir-214, dre-mir-221, dre-mir-430a-1, dre-mir-430b-1, dre-mir-430c-1, dre-mir-1-2, dre-mir-1-1, dre-mir-23a-1, dre-mir-23a-2, dre-mir-23a-3, dre-mir-29b-1, dre-mir-29b-2, dre-mir-29a, dre-mir-107a, dre-mir-122, dre-mir-133a-2, dre-mir-133a-1, dre-mir-133b, dre-mir-133c, dre-mir-184-1, dre-mir-193a-1, dre-mir-193a-2, dre-mir-202, dre-mir-430c-2, dre-mir-430c-3, dre-mir-430c-4, dre-mir-430c-5, dre-mir-430c-6, dre-mir-430c-7, dre-mir-430c-8, dre-mir-430c-9, dre-mir-430c-10, dre-mir-430c-11, dre-mir-430c-12, dre-mir-430c-13, dre-mir-430c-14, dre-mir-430c-15, dre-mir-430c-16, dre-mir-430c-17, dre-mir-430c-18, dre-mir-430a-2, dre-mir-430a-3, dre-mir-430a-4, dre-mir-430a-5, dre-mir-430a-6, dre-mir-430a-7, dre-mir-430a-8, dre-mir-430a-9, dre-mir-430a-10, dre-mir-430a-11, dre-mir-430a-12, dre-mir-430a-13, dre-mir-430a-14, dre-mir-430a-15, dre-mir-430a-16, dre-mir-430a-17, dre-mir-430a-18, dre-mir-430i-1, dre-mir-430i-2, dre-mir-430i-3, dre-mir-430b-2, dre-mir-430b-3, dre-mir-430b-4, dre-mir-430b-6, dre-mir-430b-7, dre-mir-430b-8, dre-mir-430b-9, dre-mir-430b-10, dre-mir-430b-11, dre-mir-430b-12, dre-mir-430b-13, dre-mir-430b-14, dre-mir-430b-15, dre-mir-430b-16, dre-mir-430b-17, dre-mir-430b-18, dre-mir-430b-5, dre-mir-430b-19, dre-mir-430b-20, hsa-mir-202, hsa-mir-499a, dre-mir-184-2, dre-mir-499, dre-mir-724, dre-mir-725, dre-mir-107b, hsa-mir-499b, dre-mir-29b3
This network visualization shows that (1) all modules contain at least 2 genes that are predicted targets of a deregulated miRNA identified in this study, except the module “Apoptosis and NAFLD”; (2) dre-miR-2189, the only DE miRNA that was downregulated, targets many genes in modules that are predominantly upregulated such as Cell cycle (4 target mRNAs), Apoptosis and Autophagy (19 targets), Epigenetics and Apoptosis/Autophagy (2 targets) and Receptors (4 targets); (3) certain miRNAs have only 1 target gene in the selected modules, including dre-miR-184 (“Oxidative phosphorylation”), dre-miR-430a and dre-miR-430b (“Apoptosis and Autophagy”); (4) while other miRNAs have common target genes in the same modules, i. e., dre-miR-725/dre-miR-724/dre-miR-193a, dre-miR-202, dre-miR-205 and dre-miR-133a that have several common target genes in modules “Oxidative phosphorylation and NAFLD”, “Apoptosis/Autophagy”, “NAFLD” and “Cell cycle”. [score:26]
Once we applied a fold change (FC) selection (for upregulated miRNAs, only predicted targets with a negative FC were considered, and for miR-2189, the only downregulated miRNA we identified, targets with positive FC were selected), we determined that 24.3% of the DE genes in the mRNA-Seq data were predicted to be regulated by the miRNAs of interest in this study. [score:11]
Subsequently, for each of the DE miRNAs identified in Table 1, the sum of the predicted gene targets found within the mRNA-Seq dataset was calculated as well the percentage of targets (relative to the 1491 target genes identified) and the percentage of DE transcripts (relative to the sum of all transcripts called as significant in the RNA-Seq dataset with q ≤ 0.1) (Figure 2B,C): we noted that miR-2189, the only miRNA that was downregulated in the dataset, targets approximately 680 mRNAs present in the mRNA-Seq data (q ≤ 0.1), which represents ~45.7% of the 1,491 mRNAs identified after the FC selection criterion was applied and 10.8% of all the significant DE genes in the dataset (q ≤ 0.1). [score:10]
Dre-miR-2189 was the only downregulated miRNA identified in this study after BPA exposure, yet alone this miRNA has numerous targets in apoptosis, autophagy, cell cycle and receptor modules. [score:6]
Because dre-miR-2189 is the only downregulated miRNA and only mRNAs with positive FC were selected as its predicted targets, its score is equal to 1, showing that it behaves very differently from all other miRNAs. [score:6]
Next, for all the upregulated miRNAs, we selected only those with negative fold change (FC) values and for miR-2189 we selected only those with positive FC values. [score:4]
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