Table 1.
Selection of 10 top scoring putative miRNA regulations in PTC, fvPTC, and tcPTC. Selected Spearman correlations of mRNAs and miRNAs were calculated independently in cPTC (321 samples), fvPTC (99 samples), and tcPTC (35 samples) datasets. All shown correlations were predicted by two used prediction tools: miRanda and TargetScan as putative miRNA regulations. Top 10 from each type of thyroid cancer (cPTC, fvPTC, and tcPTC) were ranked by correlation coefficient value and 10 lowest correlations are shown for each dataset (cPTC, fvPTC, and tcPTC). In columns from left, “regulation name,” assigned name of correlation; “correlation r,” correlation coefficient value (Spearman); “Correlation FDR,” DR corrected p value of correlation; “mature miRNA,” mature miRNA name; “confirmed by TargetRank,” stating that if regulation is confirmed by TargetRank (rank and score in the parenthesis); “gene symbol,” HGNC symbol of gene in correlation; and “gene name,” HGNC official full name.
| Regulation name | Correlation r | Correlation FDR | Mature miR | Confirmed by TargetRank | Gene symbol | Gene name |
|---|---|---|---|---|---|---|
| PTC_1 | −0.750 | <1e − 12 | hsa-miR-146b-5p | YES (19, 0.48) | PHKB | Phosphorylase kinase, beta |
| PTC_2 | −0.681 | <1e − 12 | hsa-miR-146b-5p | NO | TMEM164 | Transmembrane protein 164 |
| PTC_3 | −0.675 | <1e − 12 | hsa-miR-204-5p | NO | LAD1 | Ladinin 1 |
| PTC_4 | −0.670 | <1e − 12 | hsa-miR-21-5p | NO | BTBD11 | BTB (POZ) domain containing 11 |
| PTC_5 | −0.662 | <1e − 12 | hsa-miR-874-3p | YES (36, 0.39) | ITGB4 | Integrin, beta 4 |
| PTC_6 | −0.657 | <1e − 12 | hsa-miR-204-5p | NO | ERBB3 | v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 3 |
| PTC_7 | −0.657 | <1e − 12 | hsa-miR-30c-2-3p | NO | EHBP1L1 | EH domain binding protein 1-like 1 |
| PTC_8 | −0.655 | <1e − 12 | hsa-miR-146b-5p | YES (44, 0.41) | IRAK1 | Interleukin-1 receptor-associated kinase 1 |
| PTC_9 | −0.655 | <1e − 12 | hsa-miR-30a-3p | NO | TNFSF11 | Tumor necrosis factor (ligand) superfamily, member 11 |
| PTC_10 | −0.653 | <1e − 12 | hsa-miR-30c-2-3p | NO | RAP2B | RAP2B, member of RAS oncogene family |
| PTC_11 | −0.653 | <1e − 12 | hsa-miR-146b-5p | NO | DNTT | DNA nucleotidylexotransferase |
| PTC_12 | −0.653 | <1e − 12 | hsa-miR-146b-5p | NO | FHOD3 | Formin homology 2 domain containing 3 |
| PTC_13 | −0.652 | <1e − 12 | hsa-miR-204-5p | NO | POU2F3 | POU class 2 homeobox 3 |
| fvPTC_1 | −0.786 | <1e − 12 | hsa-miR-874-3p | NO | LASP1 | LIM and SH3 protein 1 |
| fvPTC_2 | −0.729 | <1e − 12 | hsa-miR-484 | NO | MET | met protooncogene |
| fvPTC_3 | −0.724 | <1e − 12 | hsa-miR-152-3p | NO | LIPH | Lipase, member H |
| fvPTC_4 | −0.714 | <1e − 12 | hsa-miR-874-3p | NO | SHF | Src homology 2 domain containing F |
| fvPTC_5 | −0.714 | <1e − 12 | hsa-miR-874-3p | NO | LMNA | Lamin A/C |
| fvPTC_6 | −0.709 | 3.89e – 12 | hsa-miR-152-3p | NO | QSOX1 | Quiescin Q6 sulfhydryl oxidase 1 |
| fvPTC_7 | −0.708 | 3.89e − 12 | hsa-miR-152-3p | NO | PRR15 | Proline rich 15 |
| fvPTC_8 | −0.707 | 6.83e − 12 | hsa-miR-148b-3p | NO | CD276 | CD276 molecule |
| fvPTC_9 | −0.706 | 6.83e − 12 | hsa-miR-874-3p | NO | PTK7 | Protein tyrosine kinase 7 |
| fvPTC_10 | −0.704 | 6.83e − 12 | hsa-miR-152-3p | NO | CORO2A | Coronin, actin binding protein, 2A |
| fvPTC_11 | −0.704 | 6.83e − 12 | hsa-miR-874-3p | NO | GNAI2 | Guanine nucleotide binding protein (G protein), alpha inhibiting activity polypeptide 2 |
| fvPTC_12 | −0.703 | 6.83e − 12 | hsa-miR-152-3p | YES (79, 0.38) | TGFA | Transforming growth factor, alpha |
| tcPTC_1 | −0.874 | 1.02e − 05 | hsa-miR-342-5p | NO | KCNG3 | Potassium voltage-gated channel, subfamily G, member 3 |
| tcPTC_2 | −0.833 | 0.00018 | hsa-miR-7-2-3p | NO | SDC3 | Syndecan 3 |
| tcPTC_3 | −0.831 | 0.00020 | hsa-miR-454-3p | NO | TBX10 | T-box 10 |