MiRNA-target interactions in osteogenic signaling pathways involving zinc and the metal regulatory element
Description
The miRNA positions taken from microTSS supplementary data was batch converted to hg38. Those miRNAs were then put into a query for TarBase validated target interactions with genes found in the KEGG pathways TGF-beta, MAPK, and Wnt to find which of these miRNAs are involved with osteogenesis processes. The TSSs for 86 pre-miRNA genes were predicted by the microTSS algorithm; 44 of these pre-miRNAs contain an MRE within the range specified, without interruption between the MRE motif and the MIR gene TSS by the presence of another gene. These 44 pre-miRNAs equate to 73 mature miRNAs. Within the TGF-β, MAPK, and Wnt signaling pathways, 65 of the 73 mature miRNAs have Tarbase-verified MTIs (hereafter called “verified MTIs”) with 241 genes. Of the 460 genes in these three signaling pathways, 413 have an MRE in the range specified. Of those 413 genes, 213 have verified MTIs with 64 mature miRNAs which also have MREs. The TGF-β pathway contained MTIs consisting of 39 miRNAs/44 genes, the MAPK pathway contained MTIs consisting of 57 miRNAs/130 genes, and the Wnt pathway contained MTIs consisting of 43 miRNAs/61 genes. MAPK1 exhibited 10 MTIs, the most verified MTIs in the TGF-β and MAPK signaling pathways. CCND2 exhibited 9 MTIs, the most verified MTIs in the Wnt signaling pathway. Hsa-miR-124-3p targeted the most genes in the TGF-β (12 genes) and MAPK (32 genes) signaling pathways. Hsa-miR-20b-5p targeted the most genes, 12, in the Wnt signaling pathway.
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Institutions
- University of Georgia