TargetScan

[…] two relatively closely related species: d. simulans and d. yakuba. mir310s cds targets are conserved between d.melanogaster and d.simulans. transcripts targeted by mir310s were identified using the targetscan algorithm [7, 47, 87, 88]. 3’utr annotation was extracted from bdgp6.83. the whole genome alignments were dm6, drosim1, and droyak3 available at the ucsc genome browser. mirna expression […]

[…] p value and the fdr value for each differentially expressed mirna was calculated by using the formula as previously described48., to predict the genes targeted by differentially expressed mirnas, targetscan 50 and miranda 3.3a were used to identify mirna binding sites. the overlaps predicted by both algorithms were used as predicted target genes. functional annotation of predicted mirna […]

[…] (anders et al., 2015). genes with low read count (<10) were filtered out to minimize false positives resulting from amplification. remaining genes were scanned for mirna target sites against the targetscan database (release 6.1). downstream analyses were performed in excel, and final gene lists underwent functional analysis using the gather (chang and nevins, 2006) the david fac tool (huang […]

[…] korea (nrf), funded by the ministry of science, ict and future planning (nrf-2015r1c1a1a02036313)., 1 https://www.ncbi.nlm.nih.gov/geo/ , 2 http://hannonlab.cshl.edu/fastx_toolkit/ , 3 http://www.targetscan.org , 4 http://software.broadinstitute.org/gsea/msigdb , the supplementary material for this article can be found online at: […]

[…] predicted sets of 3’-utrs were termed “orthologous 3’-utrs”, even though orthology is based on the underlying gene product to which they correspond. alignments of orthologous 3’-utr sets for the targetscan predictions were produced with muscle v3.8.31 [58], with default parameters. assemblies and gene sets of the three species used for accessing conservation of mirna target predictions […]