Skip to main content

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