Bioinformatics Analysis

We further analyzed significantly associated genes (mRNA) with a more meaningful FC for seed-region matches with miRNAs by examining the mRNA 3’ UTR FASTA with the seed region sequence of the associated miRNA. MiRNA seed regions (seeds of 6–8 nucleotides in length) were calculated as described in our previous work (15). We believe that a seed match would increase the likelihood that an identified miRNA:mRNA interaction indicates a greater likelihood of a direct biological effect on expression given a higher propensity for binding, especially when a negative beta coefficient was observed. This implies that as the differential expression in the miRNA increased, the differential expressed in the mRNA decreased. Since miRTarBase (16) uses findings from many different investigations and alignments, we used FASTA sequences generated from both GRCh37 and GRCh38 Homo sapiens, using UCSC Table Browser (https://genome.ucsc.edu/cgi-bin/hgTables) (17). FASTA sequences that matched our Ensembl IDs and had a consensus coding sequences (CCDS) available were downloaded. Scripts in R 3.2.3 and in perl 5.018002 were used to conduct the analysis.