Table 4.
Predicted target genes of miRNAs in the miRNA-target network built by the miRNAtarget software. In the miRTarBase 8.0 column ‘+’ denotes that experimental evidence is available for the miRNA-target interaction in miRTarBase 8.0 database. Target-prediction algorithm scores (miRDB v5.0 score and TargetScan Mouse 7.2 context++ score) for each miRNA are listed if the corresponding threshold criterion (>80 and <−0.2, respectively) is met, otherwise a ‘−’ symbol is shown. (A) The effects of ischemia-reprefusion injury. The miRNA-target network was constructed for mmu-miR-21a-duplex, 142a-duplex, 146a-5p, -199a-duplex, 214-3p and 223-3p. (B) The nephrectomy network was constructed for the same miRs, except miR-21a-duplex, as miR-21a-duplex was not regulated by nephroctomy.
| A | Gene Symbol | NCBI Gene Description | miRNA Target Strength | Associated miRNAs | miRTarBase 8.0 | miRDB v5.0 Score | TargetScan Mouse 7.2 Context++ Score |
|---|---|---|---|---|---|---|---|
| 1 | CD2AP | CD2-associated protein | 4 | mmu-miR-21a-3p | − | 93.3 | - |
| mmu-miR-142a-3p | + | - | - | ||||
| mmu-miR-199a-3p | − | 94.5 | −0.603 | ||||
| mmu-miR-223-3p | − | - | −0.299 | ||||
| 2 | Cdk17 | cyclin-dependent kinase 17 | 4 | mmu-miR-21a-3p | − | 95.4 | −0.210 |
| mmu-miR-142a-5p | − | 93.2 | - | ||||
| mmu-miR-199a-3p | − | 88.3 | −0.342 | ||||
| mmu-miR-223-3p | − | 98.8 | −0.834 | ||||
| 3 | Crebrf | CREB3 regulatory factor | 4 | mmu-miR-21a-3p | − | 90.4 | - |
| mmu-miR-199a-3p | − | - | −0.220 | ||||
| mmu-miR-199a-5p | − | - | −0.213 | ||||
| mmu-miR-223-3p | − | 80.4 | - | ||||
| 4 | PlxnA2 | plexin A2 | 4 | mmu-miR-142a-5p | − | 91.1 | - |
| mmu-miR-199a-5p | − | 95.5 | −0.369 | ||||
| mmu-miR-214-3p | − | 82.4 | - | ||||
| mmu-miR-223-3p | + | - | - | ||||
| 5 | Acvr2a | activin receptor IIA | 3 | mmu-miR-199a-3p | − | 98.6 | −0.614 |
| mmu-miR-199a-5p | − | - | −0.306 | ||||
| mmu-miR-223-3p | − | 94.2 | −0.436 | ||||
| 6 | Celf1 | CUGBP, Elav-like family member 1 | 3 | mmu-miR-199a-3p | − | - | −0.253 |
| mmu-miR-214-3p | − | 81.0 | - | ||||
| mmu-miR-223-3p | + | - | - | ||||
| 7 | Dennd6a | DENN/MADD domain containing 6A | 3 | mmu-miR-21a-3p | − | 94.6 | - |
| mmu-miR-199a-5p | − | - | −0.236 | ||||
| mmu-miR-223-3p | + | - | - | ||||
| 8 | Etv1 | ets variant 1 | 3 | mmu-miR-21a-3p | − | 99.5 | - |
| mmu-miR-21a-5p | − | - | −0.238 | ||||
| mmu-miR-142a-5p | − | 92.8 | - | ||||
| 9 | Fam199x | family with sequence similarity 199, X-linked | 3 | mmu-miR-142a-5p | − | 84.4 | - |
| mmu-miR-199a-3p | − | 96.0 | −0.485 | ||||
| mmu-miR-223-3p | − | 93.5 | - | ||||
| 10 | Fgl2 | fibrinogen-like protein 2 | 3 | mmu-miR-21a-3p | − | 93.8 | - |
| mmu-miR-199a-3p | − | - | −0.208 | ||||
| mmu-miR-199a-5p | + | - | - | ||||
| 11 | Hlf | hepatic leukemia factor | 3 | mmu-miR-21a-3p | − | 99.1 | - |
| mmu-miR-199a-5p | − | - | −0.299 | ||||
| mmu-miR-223-3p | + | - | −0.584 | ||||
| 12 | Il6 | interleukin 6 | 3 | mmu-miR-142a-3p | + | - | - |
| mmu-miR-146a-5p | + | - | - | ||||
| mmu-miR-223-3p | + | - | - | ||||
| 13 | Kras | Kirsten rat sarcoma viral oncogene homolog | 3 | mmu-miR-142a-5p | − | 92.5 | - |
| mmu-miR-146a-5p | − | 88.6 | - | ||||
| mmu-miR-223-3p | + | - | - | ||||
| 14 | Lrrc1 | leucine rich repeat containing 1 | 3 | mmu-miR-142a-3p | − | 92.9 | - |
| mmu-miR-199a-3p | − | - | −0.272 | ||||
| mmu-miR-214-3p | − | 81.7 | - | ||||
| 15 | Luzp2 | leucine zipper protein 2 | 3 | mmu-miR-21a-3p | − | 97.1 | - |
| mmu-miR-142a-5p | − | - | −0.205 | ||||
| mmu-miR-223-3p | + | - | - | ||||
| 16 | Naa50 | N(alpha)-acetyltransferase 50, NatE catalytic subunit | 3 | mmu-miR-21a-3p | − | 99.7 | - |
| mmu-miR-214-3p | − | 94.6 | - | ||||
| mmu-miR-223-3p | − | 86.6 | −0.284 | ||||
| 17 | Nfia | nuclear factor I/A | 3 | mmu-miR-21a-5p | − | - | −0.321 |
| mmu-miR-199a-3p | − | - | −0.268 | ||||
| mmu-miR-223-3p | − | - | −0.296 | ||||
| 18 | Nufip2 | nuclear fragile X mental retardation protein interacting protein 2 | 3 | mmu-miR-21a-3p | − | 83.0 | - |
| mmu-miR-199a-3p | − | 88.6 | −0.330 | ||||
| mmu-miR-214-3p | − | 98.7 | - | ||||
| 19 | Pip5k1b | phosphatidylinositol-4-phosphate 5-kinase, type 1 beta | 3 | mmu-miR-142a-5p | − | - | −0.202 |
| mmu-miR-146a-5p | − | - | −0.236 | ||||
| mmu-miR-199a-3p | − | 88.7 | −0.319 | ||||
| 20 | Ptpn4 | protein tyrosine phosphatase, non-receptor type 4 | 3 | mmu-miR-142a-5p | − | 97.9 | - |
| mmu-miR-199a-3p | − | - | −0.274 | ||||
| mmu-miR-199a-5p | − | - | −0.253 | ||||
| 21 | Qk | quaking | 3 | mmu-miR-21a-3p | − | 84.5 | - |
| mmu-miR-199a-3p | + | - | - | ||||
| mmu-miR-214-3p | − | 82.9 | - | ||||
| 22 | Rc3h1 | RING CCCH (C3H) domains 1 | 3 | mmu-miR-21a-5p | + | - | - |
| mmu-miR-146a-5p | + | - | - | ||||
| mmu-miR-214-3p | − | 86.3 | - | ||||
| 23 | Rimklb | ribosomal modification protein rimK-like family member B | 3 | mmu-miR-21a-3p | − | 98.7 | - |
| mmu-miR-142a-3p | − | 85.7 | - | ||||
| mmu-miR-199a-3p | − | 95.1 | - | ||||
| 24 | Smarcd1 | SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 1 | 3 | mmu-miR-199a-5p | − | - | −0.238 |
| mmu-miR-214-3p | − | 99.1 | - | ||||
| mmu-miR-223-3p | − | - | −0.258 | ||||
| 25 | Srsf6 | serine and arginine-rich splicing factor 6 | 3 | mmu-miR-21a-3p | − | 83.4 | −0.287 |
| mmu-miR-142a-5p | − | 98.7 | - | ||||
| mmu-miR-146a-5p | − | 88.2 | - | ||||
| 26 | Stim2 | stromal interaction molecule 2 | 3 | mmu-miR-199a-3p | − | - | −0.288 |
| mmu-miR-214-3p | − | 80.1 | - | ||||
| mmu-miR-223-3p | − | 95.0 | - | ||||
| 27 | Tm9sf3 | transmembrane 9 superfamily member 3 | 3 | mmu-miR-146a-5p | − | 85.4 | - |
| mmu-miR-199a-5p | − | - | −0.256 | ||||
| mmu-miR-223-3p | + | - | - | ||||
| 28 | Tmem170 | transmembrane protein 170 | 3 | mmu-miR-21a-5p | − | - | −0.492 |
| mmu-miR-199a-3p | − | - | −0.293 | ||||
| mmu-miR-223-3p | − | - | −0.693 | ||||
| B | Gene Symbol | NCBI Gene Description | miRNA Target Strength | Associated miRNAs | miRTarBase 8.0 | miRDB v5.0 Score | TargetScan Mouse 7.2 Context++ Score |
| 1 | PlxnA2 | plexin A2 | 4 | mmu-miR-142a-5p | − | 91.1 | - |
| mmu-miR-199a-5p | − | 95.5 | −0.369 | ||||
| mmu-miR-214-3p | − | 82.4 | - | ||||
| mmu-miR-223-3p | + | - | - | ||||
| 2 | Acvr2a | activin receptor IIA | 3 | mmu-miR-199a-3p | − | 98.6 | −0.614 |
| mmu-miR-199a-5p | − | - | −0.306 | ||||
| mmu-miR-223-3p | − | 94.2 | −0.436 | ||||
| 3 | CD2AP | CD2-associated protein | 3 | mmu-miR-142a-3p | + | - | - |
| mmu-miR-199a-3p | − | 94.5 | −0.603 | ||||
| mmu-miR-223-3p | − | - | −0.299 | ||||
| 4 | Cdk17 | cyclin-dependent kinase 17 | 3 | mmu-miR-142a-5p | − | 93.2 | - |
| mmu-miR-199a-3p | − | 88.3 | −0.342 | ||||
| mmu-miR-223-3p | − | 98.8 | −0.834 | ||||
| 5 | Celf1 | CUGBP, Elav-like family member 1 | 3 | mmu-miR-199a-3p | − | - | −0.253 |
| mmu-miR-214-3p | − | 81.0 | - | ||||
| mmu-miR-223-3p | + | - | - | ||||
| 6 | Crebrf | CREB3 regulatory factor | 3 | mmu-miR-199a-3p | − | - | −0.220 |
| mmu-miR-199a-5p | − | - | −0.213 | ||||
| mmu-miR-223-3p | − | 80.4 | - | ||||
| 7 | Fam199x | family with sequence similarity 199, X-linked | 3 | mmu-miR-142a-5p | − | 84.4 | - |
| mmu-miR-199a-3p | − | 96.0 | −0.485 | ||||
| mmu-miR-223-3p | − | 93.5 | - | ||||
| 8 | Il6 | interleukin 6 | 3 | mmu-miR-142a-3p | + | - | - |
| mmu-miR-146a-5p | + | - | - | ||||
| mmu-miR-223-3p | + | - | - | ||||
| 9 | Kras | Kirsten rat sarcoma viral oncogene homolog | 3 | mmu-miR-142a-5p | − | 92.5 | - |
| mmu-miR-146a-5p | − | 88.6 | - | ||||
| mmu-miR-223-3p | + | - | - | ||||
| 10 | Lrrc1 | leucine rich repeat containing 1 | 3 | mmu-miR-142a-3p | − | 92.9 | - |
| mmu-miR-199a-3p | − | - | −0.272 | ||||
| mmu-miR-214-3p | − | 81.7 | - | ||||
| 11 | Pip5k1b | phosphatidylinositol-4-phosphate 5-kinase, type 1 beta | 3 | mmu-miR-142a-5p | − | - | −0.202 |
| mmu-miR-146a-5p | − | - | −0.236 | ||||
| mmu-miR-199a-3p | − | 88.7 | −0.319 | ||||
| 12 | Ptpn4 | protein tyrosine phosphatase, non-receptor type 4 | 3 | mmu-miR-142a-5p | − | 97.9 | - |
| mmu-miR-199a-3p | − | - | −0.274 | ||||
| mmu-miR-199a-5p | − | - | −0.253 | ||||
| 13 | Smarcd1 | SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 1 | 3 | mmu-miR-199a-5p | − | - | −0.238 |
| mmu-miR-214-3p | − | 99.1 | - | ||||
| mmu-miR-223-3p | − | - | −0.258 | ||||
| 14 | Stim2 | stromal interaction molecule 2 | 3 | mmu-miR-199a-3p | − | - | −0.288 |
| mmu-miR-214-3p | − | 80.1 | - | ||||
| mmu-miR-223-3p | − | 95.0 | - | ||||
| 15 | Tm9sf3 | transmembrane 9 superfamily member 3 | 3 | mmu-miR-146a-5p | − | 85.4 | - |
| mmu-miR-199a-5p | − | - | −0.256 | ||||
| mmu-miR-223-3p | + | - | - |