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Table 1 Putative microRNA-mRNA regulatory module defined by microRNA up-regulation and mRNA down-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 Correlation (patient sample)f
miR (up)b mRNA (down)b Pearson r p value Pearson r p value Pearson r p value
hsa-miR-155 ADH1B 6 −0.3263 0.120034 −0.0317 0.914331   
hsa-miR-31 ADH1B 3 −0.3651 0.079472 0.3863    
hsa-miR-223 ADIPOQ 5 −0.3104 0.140425 0.476    
hsa-miR-130b ADIPOQ 3 −0.3612 0.083075 0.2356    
hsa-miR-223 ALOX12 5 −0.2752 0.193414 0.5856    
hsa-miR-130b ATP1A2 6 −0.4324 0.035023 −0.1899 0.515529   
hsa-miR-31 ATP1A2 3 −0.3265 0.120034 0.2494    
hsa-miR-223 CEACAM5 6 −0.0421 0.845504 −0.1689 0.563792   
hsa-miR-21 CEACAM5 5 −0.107 0.618738 −0.0834 0.776829   
hsa-miR-130b CEACAM5 4 −0.1968 0.358677 −0.2497 0.389269   
hsa-miR-223 CEACAM7 6 −0.111 0.605605 −0.1364 0.641958   
hsa-miR-21 CILP 5 −0.4095 0.047201 −0.1815 0.534608   
hsa-miR-21 CLU 3 −0.4126 0.045447 −0.1612 0.581947   
hsa-miR-31 EMP1 5 −0.1491 0.487134 −0.0997 0.7345   
hsa-miR-130b EMP1 4 −0.5049 0.012034 0.0951    
hsa-miR-21 GPD1L 5 −0.6784 0.000269 −0.4509 0.105628 −0.9536 0.00001
hsa-miR-155 GPD1L 5 −0.3008 0.154363 0.208    
hsa-miR-223 HLF 7 −0.5536 0.005067 0.0789    
hsa-miR-31 HLF 6 −0.5107 0.010896 0.2482    
hsa-miR-130b HLF 6 −0.62 0.001231 0.067    
hsa-miR-21 HLF 3 −0.7801 <0.00001 −0.5774 0.0307 −0.6707 0.048
hsa-miR-31 HPGD 6 −0.2577 0.225391 0.0659    
hsa-miR-21 HPGD 6 −0.55 0.005363 −0.5841 0.0283 −0.7972 0.0011
hsa-miR-130b HPGD 3 −0.4602 0.023715 −0.3617 0.203821   
hsa-miR-21 ID4 5 −0.5229 0.008886 −0.1121 0.702802   
hsa-miR-31 KRT15 3 −0.1438 0.505031 −0.0053 0.985653   
hsa-miR-21 LEPR 5 −0.2902 0.169251 0.6053    
hsa-miR-223 LEPR 4 −0.1443 0.502026 −0.3246 0.257504   
hsa-miR-130b MGLL 4 −0.6913 0.000183 −0.5158 0.05903 −0.1864 0.542035
hsa-miR-223 NEBL 6 −0.518 0.009519 −0.0598 0.8391   
hsa-miR-130b NEBL 5 −0.5237 0.008733 0.091    
hsa-miR-21 NEBL 3 −0.5582 0.004605 −0.1793 0.539655   
hsa-miR-223 NMU 5 −0.2119 0.322319 0.6125    
hsa-miR-31 PPP1R3C 4 −0.2695 0.203707 0.5588    
hsa-miR-155 PTN 6 0.1331   −0.1157 0.693673   
hsa-miR-130b TGM1 7 −0.5858 0.002676 0.0162    
hsa-miR-155 ZNF185 6 −0.0065 0.977802 −0.2152 0.46   
hsa-miR-21 ZNF185 5 −0.3451 0.098725 −0.0739 0.8018   
  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 were 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 OTSCC and paired normal controls that were extracted from TCGA. 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
  6. fCorrelations of 4 pairs of microRNA and mRNA levels were assessed by quantitative real-time PCR based on 13 OTSCC patient oral cytology samples. Inverted correlation (negative Pearson r value) is expected for a MRM, and p value was calculated