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Table 2 Putative microRNA-mRNA regulatory module defined by microRNA down-regulation and mRNA up-regulationa

From: MicroRNA-21 regulates prostaglandin E2 signaling pathway by targeting 15-hydroxyprostaglandin dehydrogenase in tongue squamous cell carcinoma

Putative miR-mRNA regulatory module Bioinformatics Predictionc Correlation (TCGA dataset)d Correlation (HNSCC cell line)e
miR (down)b mRNA (up)b Pearson r p value Pearson r p value
hsa-miR-375 COL4A6 5 −0.3145 0.13511 0.2432  
hsa-miR-375 COL5A1 5 −0.3659 0.079472 −0.2159 0.4585
hsa-miR-125b COL5A1 5 −0.437 0.03274 −0.0325 0.9122
hsa-miR-375 COL5A2 5 −0.3708 0.075136 −0.231 0.426861
hsa-miR-375 CXCL1 4 −0.0864 0.689479 0.7146  
hsa-miR-125b CXCL13 6 −0.3346 0.110688 −0.1736 0.552828
hsa-miR-375 DFNA5 4 −0.4936 0.014374 −0.0855 0.771344
hsa-miR-100 FSTL4 3 −0.0923 0.668975 −0.1796 0.538966
hsa-miR-99a FSTL4 3 −0.1413 0.511067 −0.1847 0.527303
hsa-miR-125b HMGA2 5 −0.4628 0.023036 −0.0557 0.849995
hsa-miR-375 IFI44L 4 −0.1937 0.366226 0.42  
hsa-miR-125b IGFBP3 4 −0.3656 0.079472 −0.2774 0.336959
hsa-miR-125b LAMC2 5 −0.6952 0.000164 0.3459  
hsa-miR-375 LAMC2 3 −0.4309 0.035971 0.4508  
hsa-miR-375 ODC1 3 −0.2375 0.264826 −0.1239 0.673024
  1. aThe putative microRNA-mRNA regulatory module (MRM) was constructed based on microRNA and mRNA expression profiles of OTSCC, as we previously reported in [16] and [15], respectively
  2. bDifferential expression of microRNAs and mRNAs was validated using dataset on 12 OTSCC and paired normal tissue samples that was extracted from TCGA. Genes that show statistically significant differential expression were identified with bold font
  3. cThe candidate targets of a microRNA 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 a microRNA target was presented. The gene/microRNA pairs predicted by at least 3 tools were listed in the table
  4. dCorrelations of microRNA and mRNA levels were assessed using dataset on 12 paired OTSCC and normal controls that was extracted from TCGA Data Portal. Inverted correlation (negative Pearson r value) is expected for a MRM, and p value was calculated
  5. eCorrelations of microRNA and mRNA levels were assessed by quantitative real-time PCR based on 13 HNSCC cell line. Inverted correlation (negative Pearson r value) is expected for a MRM, and p value was calculated