Table 1.
miR-125b direct targets identified by integration of RIP-seq and T-RNA sequencing differential analysis.
| Gene symbol | Predicted binding-site TargetScan | RNA fold change† | RNA Padj† | RIP fold change‡ | RIP Padj†‡ | RIP to RNA ratio |
|---|---|---|---|---|---|---|
| Taz | Y* | 0.88 | 0.213 | 2.196 | 0 | 2.494 |
| M6pr | Y* | 0.818 | 0.006 | 2.039 | 0 | 2.494 |
| Tor2a | Y* | 0.722 | 0.002 | 1.786 | 0 | 2.476 |
| Mtfp1 | Y* | 0.762 | 0.018 | 1.865 | 0 | 2.449 |
| Tnks1bp1 | 0.927 | 0.607 | 2.194 | 0 | 2.366 | |
| Gnpat | 0.901 | 0.44 | 2.067 | 0 | 2.294 | |
| Gm47356 | 0.869 | 0.602 | 1.965 | 0.002 | 2.262 | |
| Trnp1 | 1.018 | 0.968 | 2.201 | 0 | 2.163 | |
| Rhot2 | Y* | 0.992 | 0.982 | 2.051 | 0 | 2.068 |
| Lsm14b | 0.924 | 0.611 | 1.833 | 0 | 1.985 | |
| Mlxipl | 0.915 | 0.743 | 1.812 | 0 | 1.981 | |
| Lrrc10b | Y* | 0.774 | 0.029 | 1.521 | 0.056 | 1.966 |
| Trabd | 0.867 | 0.416 | 1.697 | 0.001 | 1.957 | |
| Ceacam1 | Y | 0.66 | 0.002 | 1.284 | 0.608 | 1.944 |
| Cpne5 | Y | 0.694 | 0.016 | 1.345 | 0.613 | 1.937 |
| Abtb1 | Y* | 0.814 | 0.242 | 1.576 | 0.025 | 1.935 |
| Nectin2 | 0.821 | 0.114 | 1.572 | 0.05 | 1.915 | |
| Gm10125 | 0.925 | 0.818 | 1.745 | 0.03 | 1.886 | |
| Pex11g | 0.756 | 0.06 | 1.419 | 0.486 | 1.876 | |
| Dusp23 | Y | 0.703 | 0.006 | 1.319 | 0.768 | 1.875 |
| Kcnc2 | Y* | 0.6 | 0 | 1.118 | 0.999 | 1.864 |
| Guk1 | 1.045 | 0.896 | 1.944 | 0 | 1.86 | |
| Mfge8 | Y | 0.712 | 0.013 | 1.32 | 0.771 | 1.853 |
| Rnf113a2 | 1.088 | 0.494 | 1.998 | 0.001 | 1.836 | |
| Stc1 | Y* | 0.785 | 0.142 | 1.44 | 0.406 | 1.833 |
| Src | Y | 0.712 | 0.011 | 1.285 | 0.852 | 1.804 |
| Nrm | Y* | 0.674 | 0 | 1.214 | 0.963 | 1.801 |
| Pgap3 | Y* | 0.698 | 0 | 1.257 | 0.802 | 1.801 |
| Coch | 1.027 | 0.954 | 1.849 | 0.004 | 1.8 | |
| Rabl6 | Y | 0.891 | 0.331 | 1.591 | 0.001 | 1.786 |
| Apoo | 1.059 | 0.689 | 1.886 | 0.004 | 1.781 | |
| Cyth1 | Y* | 0.94 | 0.514 | 1.658 | 0.001 | 1.763 |
| Gm17167 | 0.84 | 0.445 | 1.478 | 0.364 | 1.758 | |
| Cd34 | Y* | 0.764 | 0.123 | 1.34 | 0.662 | 1.753 |
| Cbx7 | Y* | 0.817 | 0.13 | 1.431 | 0.379 | 1.753 |
| Brms1 | Y* | 0.826 | 0.11 | 1.446 | 0.428 | 1.75 |
| Grk4 | 0.914 | 0.787 | 1.597 | 0.175 | 1.746 | |
| Rnf44 | Y* | 0.849 | 0.338 | 1.478 | 0.025 | 1.741 |
| Pstpip2 | 0.691 | 0.002 | 1.203 | 0.999 | 1.74 | |
| Syvn1 | Y* | 0.886 | 0.393 | 1.54 | 0 | 1.738 |
| Agtrap | Y* | 0.891 | 0.601 | 1.547 | 0.258 | 1.737 |
| Fam83h | Y* | 0.738 | 0.001 | 1.278 | 0.543 | 1.732 |
| Them6 | Y* | 0.649 | 0.001 | 1.123 | 0.999 | 1.731 |
| Nudt16 | 0.849 | 0.234 | 1.467 | 0.402 | 1.728 | |
| Vipr1 | Y | 0.893 | 0.499 | 1.541 | 0 | 1.726 |
| Lypla2 | Y* | 0.874 | 0.204 | 1.501 | 0.037 | 1.718 |
| Gm43960 | 1.035 | 0.938 | 1.767 | 0.029 | 1.707 | |
| G6pc3 | 0.9 | 0.517 | 1.532 | 0.114 | 1.703 | |
| Dis3l2 | Y* | 0.805 | 0.012 | 1.367 | 0.64 | 1.699 |
| Ccdc50 | 0.841 | 0.073 | 1.429 | 0.233 | 1.698 | |
| Sirt6 | Y* | 0.82 | 0.019 | 1.386 | 0.607 | 1.692 |
| Dnajc14 | Y* | 0.834 | 0.002 | 1.403 | 0.329 | 1.683 |
| Mlycd | Y* | 0.754 | 0.002 | 1.267 | 0.775 | 1.681 |
| Gm45844 | 0.913 | 0.75 | 1.53 | 0.196 | 1.676 | |
| Aftph | 0.956 | 0.747 | 1.597 | 0.018 | 1.671 | |
| Dph7 | 0.941 | 0.774 | 1.571 | 0.209 | 1.669 | |
| Ptpn5 | 0.706 | 0.011 | 1.176 | 0.999 | 1.666 | |
| Pgp | Y* | 1.01 | 0.98 | 1.682 | 0.004 | 1.665 |
| Car8 | 0.58 | 0 | 0.965 | 0.999 | 1.664 | |
| AU040320 | Y | 0.769 | 0 | 1.274 | 0.533 | 1.656 |
| Rpl35 | 1.06 | 0.839 | 1.75 | 0.003 | 1.651 | |
| Ppp4r3a | Y | 0.95 | 0.789 | 1.564 | 0.003 | 1.646 |
| Ptpn1 | Y* | 0.759 | 0 | 1.248 | 0.805 | 1.645 |
| Sfi1 | 0.984 | 0.954 | 1.615 | 0.146 | 1.642 | |
| P2ry6 | 0.687 | 0 | 1.127 | 0.999 | 1.641 | |
| Impdh1 | 0.785 | 0.003 | 1.286 | 0.379 | 1.639 | |
| St14 | Y | 0.811 | 0.087 | 1.327 | 0.752 | 1.636 |
| Rps6-ps4 | 1.021 | 0.957 | 1.668 | 0.078 | 1.633 | |
| Qsox2 | Y* | 0.832 | 0.026 | 1.357 | 0.096 | 1.632 |
| Gm38025 | 0.957 | 0.89 | 1.561 | 0.243 | 1.631 | |
| Acads | Y* | 0.823 | 0.183 | 1.342 | 0.441 | 1.629 |
| D130040H23Rik | Y | 0.828 | 0.28 | 1.348 | 0.673 | 1.628 |
| Gm47102 | 0.837 | 0.442 | 1.361 | 0.428 | 1.626 | |
| Tlnrd1 | 0.809 | 0.097 | 1.315 | 0.533 | 1.626 | |
| Creld1 | Y | 0.838 | 0.189 | 1.36 | 0.517 | 1.623 |
| Sox12 | Y* | 0.639 | 0 | 1.036 | 0.999 | 1.622 |
| Anp32a | 0.963 | 0.908 | 1.559 | 0.006 | 1.619 | |
| Entpd3 | Y* | 0.903 | 0.604 | 1.456 | 0.078 | 1.613 |
| Lfng | Y* | 0.767 | 0.075 | 1.236 | 0.845 | 1.613 |
| 6030458C11Rik | Y | 0.764 | 0 | 1.228 | 0.684 | 1.608 |
| Klc2 | Y* | 0.903 | 0.536 | 1.45 | 0.11 | 1.606 |
| Igfbp7 | 0.66 | 0.002 | 1.059 | 0.999 | 1.604 | |
| Ppt2 | Y | 0.69 | 0 | 1.106 | 0.999 | 1.603 |
| Zfp111 | Y | 0.958 | 0.842 | 1.534 | 0.111 | 1.601 |
| Phldb2 | Y | 0.86 | 0.455 | 1.377 | 0.375 | 1.6 |
| 4933421O10Rik | 0.818 | 0.035 | 1.307 | 0.8 | 1.598 | |
| Rtn2 | 0.966 | 0.896 | 1.544 | 0.037 | 1.597 | |
| Slc37a1 | 0.702 | 0 | 1.12 | 0.999 | 1.596 | |
| Dedd2 | 0.899 | 0.682 | 1.431 | 0.286 | 1.592 | |
| Lactb | Y | 0.751 | 0.027 | 1.195 | 0.999 | 1.59 |
| Dgcr8 | 0.917 | 0.618 | 1.459 | 0.375 | 1.59 | |
| Dgcr8 | 0.917 | 0.618 | 1.459 | 0.375 | 1.59 | |
| Gm42785 | 0.902 | 0.612 | 1.433 | 0.379 | 1.589 | |
| Gm28756 | 0.955 | 0.912 | 1.515 | 0.303 | 1.587 | |
| Gm21244 | 0.917 | 0.763 | 1.455 | 0.39 | 1.587 | |
| Gm15097 | 0.967 | 0.939 | 1.535 | 0.258 | 1.586 | |
| 4933411E06Rik | 0.876 | 0.62 | 1.389 | 0.502 | 1.585 | |
| Mtus1 | Y* | 0.794 | 0.052 | 1.259 | 0.917 | 1.584 |
| Ppp6r1 | 1.011 | 0.96 | 1.601 | 0.001 | 1.584 | |
| Fen1 | 0.906 | 0.534 | 1.434 | 0.072 | 1.583 | |
| Gm44578 | 0.989 | 0.984 | 1.564 | 0.229 | 1.582 | |
| Gcnt1 | Y* | 0.799 | 0.044 | 1.263 | 0.501 | 1.581 |
| Pop5 | Y | 0.867 | 0.448 | 1.37 | 0.243 | 1.581 |
| Gm5860 | 0.81 | 0.262 | 1.278 | 0.828 | 1.579 | |
| Gm43498 | 1.005 | 0.994 | 1.585 | 0.183 | 1.578 | |
| Ap1s3 | Y* | 0.927 | 0.705 | 1.462 | 0.39 | 1.577 |
| Cdh22 | Y | 0.808 | 0.18 | 1.274 | 0.666 | 1.576 |
| Rce1 | 0.809 | 0.081 | 1.275 | 0.69 | 1.576 | |
| Gm45159 | 0.926 | 0.82 | 1.459 | 0.398 | 1.576 | |
| Klhl21 | Y* | 0.829 | 0.286 | 1.306 | 0.693 | 1.576 |
| Atg4d | Y* | 0.843 | 0.405 | 1.329 | 0.613 | 1.576 |
| Fgfr1 | Y* | 0.747 | 0.012 | 1.175 | 0.999 | 1.574 |
| Zfp488 | Y | 0.924 | 0.734 | 1.454 | 0.428 | 1.574 |
| Olfr1116 | 0.982 | 0.969 | 1.543 | 0.258 | 1.572 | |
| Neurl3 | 0.691 | 0.005 | 1.086 | 0.999 | 1.571 | |
| Ccdc162 | 0.869 | 0.499 | 1.365 | 0.582 | 1.57 | |
| Rabl2 | Y | 0.82 | 0.098 | 1.287 | 0.878 | 1.569 |
| Stk11ip | 0.801 | 0.002 | 1.255 | 0.9 | 1.568 | |
| Mrpl53 | 0.981 | 0.958 | 1.538 | 0.105 | 1.567 | |
| C1qtnf1 | Y | 0.729 | 0.024 | 1.143 | 0.999 | 1.567 |
| Frem2 | 0.739 | 0.05 | 1.159 | 0.999 | 1.567 | |
| Ecd | 0.859 | 0.153 | 1.346 | 0.49 | 1.567 | |
| Zfp385a | Y | 0.735 | 0.01 | 1.15 | 0.999 | 1.565 |
| Vps29 | Y | 1.106 | 0.536 | 1.73 | 0.001 | 1.564 |
| Ano3 | 0.673 | 0.008 | 1.053 | 0.999 | 1.564 | |
| Spata6 | 0.958 | 0.869 | 1.494 | 0.358 | 1.56 | |
| Olfr338 | 0.866 | 0.549 | 1.35 | 0.603 | 1.559 | |
| Efcab14 | Y* | 0.887 | 0.301 | 1.382 | 0.364 | 1.559 |
| Klf16 | Y* | 0.863 | 0.152 | 1.345 | 0.594 | 1.559 |
| Znhit1 | Y | 0.959 | 0.885 | 1.492 | 0.353 | 1.556 |
| Gm48443 | 0.875 | 0.404 | 1.361 | 0.533 | 1.556 | |
| Churc1 | 0.993 | 0.986 | 1.545 | 0.234 | 1.555 | |
| Cep19 | 0.899 | 0.523 | 1.397 | 0.533 | 1.554 | |
| 9930111J21Rik2 | Y | 0.914 | 0.785 | 1.421 | 0.375 | 1.554 |
| Cnot6 | 0.83 | 0.168 | 1.289 | 0.144 | 1.553 | |
| Pgpep1 | Y* | 0.894 | 0.61 | 1.384 | 0.385 | 1.548 |
| Npc1 | 0.771 | 0.001 | 1.193 | 0.977 | 1.547 | |
| Hdac5 | 0.809 | 0.151 | 1.25 | 0.942 | 1.544 | |
| Ctbp1 | Y | 0.848 | 0.005 | 1.303 | 0.43 | 1.537 |
| Olfr365 | 0.979 | 0.954 | 1.505 | 0.353 | 1.537 | |
| Cchcr1 | 0.981 | 0.936 | 1.507 | 0.328 | 1.536 | |
| Olfr552 | 0.967 | 0.94 | 1.485 | 0.345 | 1.536 | |
| Sp110 | 0.871 | 0.609 | 1.337 | 0.648 | 1.535 | |
| Lingo1 | Y | 0.852 | 0.312 | 1.308 | 0.474 | 1.535 |
| Ppp6r3 | Y* | 0.939 | 0.618 | 1.438 | 0.023 | 1.531 |
| Wdr25 | Y | 0.9 | 0.551 | 1.377 | 0.533 | 1.53 |
| Prpf18 | 0.907 | 0.322 | 1.386 | 0.443 | 1.528 | |
| 2810039B14Rik | 0.871 | 0.496 | 1.33 | 0.708 | 1.528 | |
| Rab17 | Y | 0.718 | 0.005 | 1.097 | 0.999 | 1.528 |
| Mob2 | Y | 0.889 | 0.391 | 1.355 | 0.486 | 1.525 |
| 1700082M22Rik | 0.874 | 0.62 | 1.333 | 0.717 | 1.525 | |
| Cadm1 | 0.872 | 0.385 | 1.33 | 0.366 | 1.525 | |
| Triap1 | Y* | 0.923 | 0.687 | 1.408 | 0.382 | 1.524 |
| Olfr1328 | 0.915 | 0.715 | 1.394 | 0.366 | 1.523 | |
| Gm4117 | 0.878 | 0.609 | 1.337 | 0.639 | 1.523 | |
| Nmnat1 | Y | 0.852 | 0.408 | 1.297 | 0.819 | 1.523 |
| Gm43577 | 0.94 | 0.864 | 1.431 | 0.465 | 1.523 | |
| Gm42927 | 0.972 | 0.941 | 1.479 | 0.328 | 1.522 | |
| Zfp697 | Y | 0.888 | 0.597 | 1.35 | 0.689 | 1.519 |
| Bmf | Y* | 0.623 | 0 | 0.946 | 0.999 | 1.519 |
| Gm45038 | 0.93 | 0.795 | 1.412 | 0.401 | 1.518 | |
| C130073E24Rik | 0.979 | 0.963 | 1.487 | 0.36 | 1.518 | |
| E130309D02Rik | Y | 0.924 | 0.716 | 1.4 | 0.366 | 1.516 |
| Coro2a | Y* | 0.656 | 0 | 0.994 | 0.999 | 1.514 |
| Mdga1 | Y* | 0.794 | 0.193 | 1.201 | 0.999 | 1.513 |
| Mogs | 0.772 | 0.05 | 1.167 | 0.857 | 1.512 | |
| 4632415L05Rik | Y | 0.886 | 0.414 | 1.339 | 0.713 | 1.511 |
| Gm43190 | 0.978 | 0.96 | 1.477 | 0.375 | 1.511 | |
| Prdm11 | Y | 0.907 | 0.683 | 1.369 | 0.648 | 1.51 |
| Dhtkd1 | 0.991 | 0.986 | 1.496 | 0.345 | 1.509 | |
| Vps4b | Y* | 0.784 | 0.053 | 1.183 | 0.999 | 1.509 |
| Inpp4b | 0.779 | 0.076 | 1.174 | 0.999 | 1.508 | |
| Oraov1 | Y | 0.898 | 0.369 | 1.354 | 0.637 | 1.508 |
| Gm43660 | 0.916 | 0.76 | 1.382 | 0.419 | 1.508 | |
| Tcp11l2 | 0.711 | 0.019 | 1.072 | 0.999 | 1.508 | |
| Olfr374 | 0.87 | 0.551 | 1.31 | 0.786 | 1.506 | |
| Sned1 | Y* | 0.921 | 0.808 | 1.387 | 0.348 | 1.505 |
| Gm16892 | 0.958 | 0.925 | 1.441 | 0.375 | 1.504 | |
| Akap2 | Y | 0.97 | 0.944 | 1.458 | 0.286 | 1.502 |
| Kcnn2 | 0.734 | 0.052 | 1.102 | 0.999 | 1.501 |
Genes (n = 180) with RIP-seq to T-RNA ratio > 1.5 are shown.
Y indicates the presence of at least one predicted miR-125b binding site by TargetScan mouse, version 7.2.
Y* indicates target conservation in humans;
†
Fold change and adjusted P value of differential analysis of transcripts in MIN6 cells transfected with miR-125b mimics versus controls.
‡
Fold change and adjusted P value of differential analysis of Ago2-immunoprecipitated RNAs in MIN6 cells transfected with miR-125b mimics versus controls.