miR-100 target genes identified in epithelial cells by microarray analysis and bioinformatics prediction.

aGene names in bold font were genes that down-regulated in 4 out of 5 microRNA transfection experiments, or down-regulated in 3 out of 5 microRNA transfection experiments and predicted to be miR-100 targets by 10 out of 12 bioinformatics tools tested.bHuman skin keratinocyte HaCaT and head and neck squamous cell carcinoma cell 1386Ln were treated with either miR-100 or control mimic and differential expression analysis was carried out using Affymetrix GeneChip HuGene 1.0 ST arrays. The data was processed using Robust Multi-array Analysis (RMA), and the down-regulated gene was defined as a gene with a microRNA-induced expressional change equal or less than the known target gene mTOR (fold difference = 0.88 and 0.67, respectively for HaCaT and 1386Ln cells).cMicroarray data on C4-2 prostate cancer cells treated with either miR-99a or control (GEO accession GSE26332) [7], and processed using Robust Multi-array Analysis (RMA). The down-regulated gene was defined as a gene with a microRNA-induced expressional change equal or less than the known target gene mTOR (fold difference = 0.67).dData from Henson et al 2009 [23].eData from Gebeshuber et al 2012 [24].fThe candidate targets of miR-100 were predicted using a collection of 12 bioinformatics tools, including DIANAmT, miRanda, microCosm, miRDB, miRWalk, RNAhybrid, PicTar (4-way), PicTar (5-way), PITA, RNA22, TargetScan5, and TargetScanHuman 6.2. The number of bioinformatics tools (out of a total of 12 tools tested here) that predict a gene to be miR-100 target was presented.