miRTarBase - #MIRT501725


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pre-miRNA Information
pre-miRNA hsa-mir-516b-1   
Genomic Coordinates chr19: 53736845 - 53736934
Synonyms MIRN516-4, MIRN516B-1, MIRN516B1, MIR516B1
Description Homo sapiens miR-516b-1 stem-loop
Comment None
RNA Secondary Structure
Associated Diseases
pre-miRNA hsa-mir-516b-2   
Genomic Coordinates chr19: 53725442 - 53725526
Synonyms MIRN516-3, MIRN516B-2, MIRN516B2, MIR516B2
Description Homo sapiens miR-516b-2 stem-loop
Comment None
RNA Secondary Structure
Associated Diseases

Mature miRNA Information
Mature miRNA hsa-miR-516b-3p
Sequence 56| UGCUUCCUUUCAGAGGGU |73
Evidence Experimental
Experiments Array-cloned
SNPs in miRNA
Mutant ID Mutant Position Mutant Source
rs1413434631 1 dbSNP
rs746170707 2 dbSNP
rs1312744198 2 dbSNP
rs752101959 3 dbSNP
rs770077784 4 dbSNP
rs1193425541 6 dbSNP
rs953142850 7 dbSNP
rs1020245150 7 dbSNP
rs775845942 11 dbSNP
rs1402471980 11 dbSNP
rs760158839 15 dbSNP
rs78861479 16 dbSNP
rs765933705 16 dbSNP
Putative Targets

Gene Information
Gene Symbol OVOL1   
Synonyms HOVO1
Description ovo like transcriptional repressor 1
Transcript NM_004561   
Expression
Putative miRNA Targets on OVOL1
3'UTR of OVOL1
(miRNA target sites are highlighted)		 
>OVOL1|NM_004561|3'UTR
   1 GTGGCTCGAGCCCTGGGGGTGCTCCTGGAAGCCCCAAGAGCATCCAGGATTGCCTCCCAGCTGCCTGGCCAGCCCACCCT
  81 CCTGCAACCTCTCACCCGAACACCAGTGATCAGGACTGGAGCCCCCGTGCCTTGGTCTCCCCCCTGGGCACACGTGCTCA
 161 CTCAGGCCCAGCAATGACCTCTGCTCATTTTTGCATTTTTGACTTATGGGCCGAGGCTGTTCTGAGCCTGGGAAGATGTA
 241 CCTATGTCAAGAGAAGGGATGAGGCCAAGGCTGCCTTCAATTAGAAGCAGCCGCCCACAGAGACAGGCACTGTGTGCCTG
 321 GCAGCAGGACTTCCTACCCAGAGGAGGTTCGAGCTAGGATCCCACTGCCCCCGCCTCTCAGCACAGGGCAGGGGCTGCAG
 401 GTCCCCAGTGGACATCAGAGTCAAAAGCACTGGCAAAGGGTACCCCTGCAAACAACTGTGGTGGGGGCTGGCAGCAGACC
 481 CCCCACCTGGCAGGGCTTCTAATGCTCAGGGTTCTGGAGGGCTCTGTCCTTCCGGCAAGGAGAGGCACACATGTGTGCCC
 561 AGCCGTGTGTGTGCGTGTGCTTGTGTGTGTGCACTGCTGTGTGTGTGTGCACGCACAGGAAGCCTTTCCACATATCACCT
 641 CATTTCTAAGAAATAAACTACAAGGTGCCAAGAAGGTTTTATTTCCTTTTATTTTTTAAAGATGACAAATGTACAGATGT
 721 TAATATATTTTTGGTGCCAATGGCGATGTTTTTAAGAGTGGGATGGAGCTGGCTTTTCTCCATTCCCGTGCGCTTCTATT
 801 TATCCTGGACATTTCAAACCTCCTCTGTGCCTTGGCTCTGGGCGGGGGCTGCCCCAACCCACCCCCGTTCTTTGTACGTG
 881 CTGAGACAGCCACTAGAAGATCTTCCTCCAGCGGCGCCCTGGACGGCTGCTCCTGCGAACAGCCCATGGCATCTTCTGCT
 961 CTTCCCTCCCGGCTCTGCCCTGCACATCCTGTTGAGCCAAGCCCCAGTGACCCGGAGAGCTGGCCTGATGCTGAGAGTGT
1041 GTCCTCCTGGGGCTTTAGGGGGCAGGAAGGTGGGACGAATGACGATGCCCATCCACTACCTGAAGCACTAGGACACTCTT
1121 GCAGGGCCAGGCTGGAAGACCGGCCCTTTTCTTGGTTGAGTCAAAAGCCTTAGCACAGTGGCAAAAAATGGGACAGAATG
1201 ATGACCAGCACCTCAGAAACTTCCAGAGGGAGGAGAGGATTTGATGGCTACCAAATTGTATCTGTTGCCTTTTTTCTGAC
1281 TTTTTCACCTGACCAGGCTGGGGTTTGGAGTGGCTGTGGGGAGACCCGTCCTGGCTGGCTGGCTGGCTCCCTTGCTCCCT
1361 TGCTGCAGCTGGGAAAGGGGTTCTGGGTGTAAAGAGGTGTGCGTCTTGTGGGCCAAAGGGAAAAACAGGCAGGGGTCAGA
1441 GCCAGCCTGCCAGAGGCAAATGCAAAAGAGGTCCCCAGAACACAGCCAGCTGGGCAGCCCCTTAAAGCCAAACCCCACCT
1521 GAAGCAGAACCACTTTGGCCTCCCCTGCCCAAAATGGGTAGTGTCTACACGTCCCCGGGCTCAGGCTCAGGCCCAGCCCT
1601 GGGCTGACCTGAGAGGAAGGCTCCTTCCTGGACTGCCCTCTGAAATGTGTATAGATTGATTCTAAAATCTCTTGTTTCAC
1681 TTGACTTTAGAGTGTCTGGGACGCTGCTGTATTCTGAAAGTCACATAGCACACAGTAATGTTATCTGGAAGCTCTGTTTT
1761 TGTTTACATTTCTGTATCCCTGGGTTGACTGCCAATCCGAGGCCGTCATGAAGCTCTGTGTTGTCTGTTTTATTTTATAA
1841 CCTTCCTCTCAACTATTAAAATTAGAGATCTAATGTTTAAAAAAAAAAAAAAAAA
Target sites Provided by authors   Predicted by miRanda    DRVs    SNPs    DRVs & SNPs
miRNA-target interactions
(Predicted by miRanda)
ID Duplex structure Position Score MFE
1 
miRNA  3' uggGAGACUUUCCUUCGu 5'
             | |  | ||||||| 
Target 5' gtgCACGCACAGGAAGCc 3'
 607 - 624 143.00 -8.50
2 
miRNA  3' ugggaGACUUUCCUUCgu 5'
               ||||:||||||  
Target 5' ctgacCTGAGAGGAAGgc 3'
 1604 - 1621 141.00 -16.10
3 
miRNA  3' uggGAGA----CUUUCCUUCgu 5'
             ||:|    |: ||||||  
Target 5' gggCTTTAGGGGGCAGGAAGgt 3'
 1050 - 1071 125.00 -11.20
DRVs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
COSM3986363 1 COSMIC
COSN28645733 41 COSMIC
COSN30189902 49 COSMIC
COSN31540088 53 COSMIC
COSN30304466 596 COSMIC
COSN16131940 606 COSMIC
COSN20092380 660 COSMIC
COSN15662847 692 COSMIC
COSN20108397 692 COSMIC
COSN16117295 699 COSMIC
COSN28686544 705 COSMIC
COSN31553334 746 COSMIC
COSN31482662 793 COSMIC
COSN31660714 816 COSMIC
COSN8282747 972 COSMIC
COSN20108398 1346 COSMIC
COSN26160446 1393 COSMIC
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs772613012 2 dbSNP
rs1172604472 5 dbSNP
rs116504217 8 dbSNP
rs544115504 9 dbSNP
rs759808003 11 dbSNP
rs769867042 13 dbSNP
rs924250848 14 dbSNP
rs955757749 15 dbSNP
rs934320767 19 dbSNP
rs1442803220 20 dbSNP
rs988507925 21 dbSNP
rs1323696252 26 dbSNP
rs1427754891 32 dbSNP
rs774251802 36 dbSNP
rs72922786 41 dbSNP
rs1189527110 42 dbSNP
rs1037424524 49 dbSNP
rs920352857 52 dbSNP
rs1241289063 63 dbSNP
rs761669146 65 dbSNP
rs1047966529 78 dbSNP
rs909729285 90 dbSNP
rs890704807 98 dbSNP
rs748031232 99 dbSNP
rs140298315 127 dbSNP
rs900477105 128 dbSNP
rs1297877591 131 dbSNP
rs1302600964 136 dbSNP
rs1380143189 137 dbSNP
rs1313675054 139 dbSNP
rs1396139846 139 dbSNP
rs1011337778 140 dbSNP
rs1022339422 142 dbSNP
rs183016490 144 dbSNP
rs1220772961 145 dbSNP
rs1451505583 147 dbSNP
rs1383647726 149 dbSNP
rs1303645115 152 dbSNP
rs772949735 154 dbSNP
rs529855862 155 dbSNP
rs144263047 167 dbSNP
rs1266384598 176 dbSNP
rs1421601983 181 dbSNP
rs1466311736 183 dbSNP
rs1209839811 184 dbSNP
rs759119722 187 dbSNP
rs1246657485 194 dbSNP
rs1477221270 204 dbSNP
rs1351053019 206 dbSNP
rs1309573340 208 dbSNP
rs764501350 211 dbSNP
rs915825128 213 dbSNP
rs969715131 214 dbSNP
rs549082577 227 dbSNP
rs188576840 229 dbSNP
rs1370203201 236 dbSNP
rs1000829596 241 dbSNP
rs1156514483 242 dbSNP
rs1253208342 254 dbSNP
rs920342370 257 dbSNP
rs929076629 264 dbSNP
rs1031917639 268 dbSNP
rs956300915 274 dbSNP
rs1047913756 281 dbSNP
rs1209994435 286 dbSNP
rs912089948 293 dbSNP
rs1457331984 294 dbSNP
rs1325095215 296 dbSNP
rs944888733 299 dbSNP
rs539942337 305 dbSNP
rs1039259585 331 dbSNP
rs1290188108 332 dbSNP
rs1402861022 334 dbSNP
rs150749553 344 dbSNP
rs1323978114 347 dbSNP
rs1275286258 349 dbSNP
rs752002498 351 dbSNP
rs941217353 352 dbSNP
rs1037301632 367 dbSNP
rs550991862 373 dbSNP
rs1043740601 374 dbSNP
rs571084017 382 dbSNP
rs1286694492 386 dbSNP
rs1331257730 390 dbSNP
rs933948164 395 dbSNP
rs1452931434 404 dbSNP
rs768186151 406 dbSNP
rs902592650 410 dbSNP
rs1051706084 411 dbSNP
rs1204011082 417 dbSNP
rs1329308807 419 dbSNP
rs1269941480 421 dbSNP
rs1052305 428 dbSNP
rs560305965 431 dbSNP
rs890462316 433 dbSNP
rs999587234 439 dbSNP
rs1322754436 449 dbSNP
rs1008015350 462 dbSNP
rs79060510 478 dbSNP
rs1289753150 479 dbSNP
rs1333019324 479 dbSNP
rs1450441936 480 dbSNP
rs1224218708 488 dbSNP
rs1389381252 492 dbSNP
rs904637245 499 dbSNP
rs1322659577 500 dbSNP
rs959834728 505 dbSNP
rs1468653342 506 dbSNP
rs1014509718 514 dbSNP
rs756285516 515 dbSNP
rs1479235465 516 dbSNP
rs140732263 519 dbSNP
rs956270074 520 dbSNP
rs1465072985 521 dbSNP
rs780003561 522 dbSNP
rs1413759768 530 dbSNP
rs553378153 534 dbSNP
rs1472617317 535 dbSNP
rs969769336 536 dbSNP
rs980231074 537 dbSNP
rs973086385 543 dbSNP
rs1269382142 545 dbSNP
rs1227871078 549 dbSNP
rs760433731 551 dbSNP
rs1299866096 554 dbSNP
rs962800617 556 dbSNP
rs749471428 557 dbSNP
rs1359068202 558 dbSNP
rs1335514123 562 dbSNP
rs755215884 566 dbSNP
rs918453161 570 dbSNP
rs950430924 573 dbSNP
rs983176661 575 dbSNP
rs911867835 576 dbSNP
rs566505281 578 dbSNP
rs1039472183 582 dbSNP
rs1237972708 582 dbSNP
rs1212238550 583 dbSNP
rs1436019506 584 dbSNP
rs904605859 589 dbSNP
rs1226664094 598 dbSNP
rs1343095026 598 dbSNP
rs142200666 598 dbSNP
rs1410490306 605 dbSNP
rs535589178 613 dbSNP
rs975355097 614 dbSNP
rs1307770073 616 dbSNP
rs936119409 633 dbSNP
rs778642445 634 dbSNP
rs767529647 638 dbSNP
rs1043688905 643 dbSNP
rs902497671 651 dbSNP
rs555407627 654 dbSNP
rs891972697 668 dbSNP
rs79345966 670 dbSNP
rs1056438038 671 dbSNP
rs896563266 674 dbSNP
rs1203503217 687 dbSNP
rs3832788 687 dbSNP
rs1491087794 690 dbSNP
rs777721657 691 dbSNP
rs78712280 691 dbSNP
rs496388 692 dbSNP
rs1254235661 702 dbSNP
rs557779130 711 dbSNP
rs1014088319 712 dbSNP
rs577911857 717 dbSNP
rs1219562064 738 dbSNP
rs754584402 741 dbSNP
rs374403430 745 dbSNP
rs1290625190 746 dbSNP
rs1230135241 752 dbSNP
rs1235177141 757 dbSNP
rs1327667683 763 dbSNP
rs1288324184 780 dbSNP
rs905768710 788 dbSNP
rs184921811 789 dbSNP
rs773194846 792 dbSNP
rs552452431 799 dbSNP
rs528857464 813 dbSNP
rs1389512273 818 dbSNP
rs1398495541 819 dbSNP
rs1427546328 820 dbSNP
rs1170304850 822 dbSNP
rs1027592904 823 dbSNP
rs950334915 824 dbSNP
rs1426875157 827 dbSNP
rs1190432905 832 dbSNP
rs368592403 838 dbSNP
rs1410738403 840 dbSNP
rs1333771280 841 dbSNP
rs1223835130 844 dbSNP
rs1017050784 845 dbSNP
rs1450337047 848 dbSNP
rs1331866873 849 dbSNP
rs962483677 853 dbSNP
rs983124346 855 dbSNP
rs1018666865 858 dbSNP
rs1365170691 860 dbSNP
rs972463718 862 dbSNP
rs542763854 863 dbSNP
rs562519330 864 dbSNP
rs955224373 865 dbSNP
rs974924913 867 dbSNP
rs922116816 868 dbSNP
rs1175058413 877 dbSNP
rs946922663 878 dbSNP
rs1277304292 879 dbSNP
rs1478508825 887 dbSNP
rs370317955 887 dbSNP
rs764477902 895 dbSNP
rs979623542 901 dbSNP
rs531134539 911 dbSNP
rs879222046 913 dbSNP
rs1276088716 914 dbSNP
rs551194939 917 dbSNP
rs570953934 926 dbSNP
rs1247316674 927 dbSNP
rs1209838577 936 dbSNP
rs896563971 937 dbSNP
rs936032870 938 dbSNP
rs1193165916 941 dbSNP
rs1364039141 948 dbSNP
rs1297647910 965 dbSNP
rs551741291 971 dbSNP
rs139344672 972 dbSNP
rs1390483899 980 dbSNP
rs370604270 983 dbSNP
rs1466357111 989 dbSNP
rs1172172798 995 dbSNP
rs1168079293 997 dbSNP
rs150030132 1000 dbSNP
rs994686939 1007 dbSNP
rs1389825449 1009 dbSNP
rs1027539001 1015 dbSNP
rs886359488 1034 dbSNP
rs1002227059 1037 dbSNP
rs1254674284 1037 dbSNP
rs1181716162 1038 dbSNP
rs1483870974 1048 dbSNP
rs1004542919 1059 dbSNP
rs1203492682 1071 dbSNP
rs546961513 1074 dbSNP
rs1274969476 1078 dbSNP
rs1229957502 1084 dbSNP
rs1016564984 1085 dbSNP
rs551223135 1091 dbSNP
rs993853121 1094 dbSNP
rs1300468544 1097 dbSNP
rs1025358673 1099 dbSNP
rs955151586 1109 dbSNP
rs1428923911 1113 dbSNP
rs1366312762 1114 dbSNP
rs965803774 1116 dbSNP
rs974873781 1118 dbSNP
rs1028753974 1119 dbSNP
rs1366733835 1122 dbSNP
rs1018561276 1123 dbSNP
rs1424866484 1129 dbSNP
rs189912069 1134 dbSNP
rs1180446095 1136 dbSNP
rs567774351 1142 dbSNP
rs879566761 1143 dbSNP
rs1463163345 1144 dbSNP
rs1353839528 1147 dbSNP
rs956988397 1150 dbSNP
rs957371779 1152 dbSNP
rs1244931957 1155 dbSNP
rs1248602259 1161 dbSNP
rs774832781 1163 dbSNP
rs1286439741 1165 dbSNP
rs1408983011 1171 dbSNP
rs1350808397 1173 dbSNP
rs988840892 1182 dbSNP
rs913301215 1183 dbSNP
rs1432356542 1187 dbSNP
rs762325307 1203 dbSNP
rs948098998 1204 dbSNP
rs1157675854 1208 dbSNP
rs1045892558 1209 dbSNP
rs1376119430 1220 dbSNP
rs1045528118 1222 dbSNP
rs927460411 1223 dbSNP
rs491666 1224 dbSNP
rs930423675 1234 dbSNP
rs1449478945 1238 dbSNP
rs1387930295 1242 dbSNP
rs1266289516 1258 dbSNP
rs191174755 1259 dbSNP
rs1489211756 1262 dbSNP
rs1039043329 1269 dbSNP
rs1227650768 1273 dbSNP
rs1048964361 1276 dbSNP
rs537946564 1279 dbSNP
rs1386360581 1281 dbSNP
rs1386537453 1293 dbSNP
rs1322051846 1304 dbSNP
rs142762321 1316 dbSNP
rs1434185559 1318 dbSNP
rs1230848225 1325 dbSNP
rs557981236 1328 dbSNP
rs886343071 1329 dbSNP
rs144509153 1331 dbSNP
rs3831420 1331 dbSNP
rs1004827390 1341 dbSNP
rs1233436942 1346 dbSNP
rs1040308875 1347 dbSNP
rs901476506 1349 dbSNP
rs1018069978 1384 dbSNP
rs746025790 1390 dbSNP
rs1326415377 1391 dbSNP
rs1477276111 1391 dbSNP
rs1000762070 1393 dbSNP
rs1199043357 1397 dbSNP
rs1032661206 1403 dbSNP
rs577742887 1404 dbSNP
rs756300687 1409 dbSNP
rs1207588723 1410 dbSNP
rs1488150994 1413 dbSNP
rs1207841956 1414 dbSNP
rs183632135 1433 dbSNP
rs1029119319 1436 dbSNP
rs373506691 1437 dbSNP
rs189171708 1440 dbSNP
rs1200351176 1447 dbSNP
rs913270018 1450 dbSNP
rs1234169552 1460 dbSNP
rs1373501601 1468 dbSNP
rs1295450802 1475 dbSNP
rs1411541492 1484 dbSNP
rs756592770 1491 dbSNP
rs145371788 1501 dbSNP
rs566964554 1508 dbSNP
rs1401865468 1509 dbSNP
rs1031160633 1512 dbSNP
rs1173550293 1514 dbSNP
rs1364864634 1526 dbSNP
rs1436152945 1531 dbSNP
rs927459091 1538 dbSNP
rs956936460 1543 dbSNP
rs1161981833 1557 dbSNP
rs766434776 1558 dbSNP
rs753897528 1562 dbSNP
rs1449605204 1564 dbSNP
rs755164553 1571 dbSNP
rs1185241936 1572 dbSNP
rs573680508 1574 dbSNP
rs1279015609 1576 dbSNP
rs780378337 1576 dbSNP
rs779160019 1577 dbSNP
rs542602135 1578 dbSNP
rs61740441 1579 dbSNP
rs931413469 1587 dbSNP
rs1365932208 1588 dbSNP
rs1348296296 1590 dbSNP
rs1272009564 1592 dbSNP
rs1411114272 1596 dbSNP
rs1340432570 1620 dbSNP
rs1048907910 1622 dbSNP
rs907685090 1628 dbSNP
rs1307174355 1631 dbSNP
rs373620865 1633 dbSNP
rs1167649582 1634 dbSNP
rs1430007288 1636 dbSNP
rs1046682060 1639 dbSNP
rs1160978169 1648 dbSNP
rs1472405635 1650 dbSNP
rs1040658598 1653 dbSNP
rs901760764 1657 dbSNP
rs1238024346 1669 dbSNP
rs1189776684 1670 dbSNP
rs768816524 1670 dbSNP
rs1242450183 1672 dbSNP
rs1481987329 1672 dbSNP
rs1204624571 1685 dbSNP
rs890795952 1686 dbSNP
rs1007955651 1688 dbSNP
rs540128027 1689 dbSNP
rs564734866 1699 dbSNP
rs758119521 1701 dbSNP
rs899611082 1703 dbSNP
rs1001089578 1704 dbSNP
rs1050131136 1708 dbSNP
rs903602726 1711 dbSNP
rs777438209 1716 dbSNP
rs1307825235 1718 dbSNP
rs1032215583 1722 dbSNP
rs1030728310 1730 dbSNP
rs1404300390 1739 dbSNP
rs746913021 1746 dbSNP
rs1166923444 1749 dbSNP
rs956842246 1753 dbSNP
rs1410885968 1765 dbSNP
rs1020255970 1774 dbSNP
rs971404656 1779 dbSNP
rs1423332150 1782 dbSNP
rs1335989335 1783 dbSNP
rs1219446171 1785 dbSNP
rs1451176998 1793 dbSNP
rs558700587 1796 dbSNP
rs1025609691 1797 dbSNP
rs1425665241 1799 dbSNP
rs141420818 1800 dbSNP
rs958839463 1802 dbSNP
rs1368314215 1804 dbSNP
rs1431186029 1805 dbSNP
rs981173134 1806 dbSNP
rs560367754 1809 dbSNP
rs1027010865 1810 dbSNP
rs1349894139 1814 dbSNP
rs1327353718 1819 dbSNP
rs529259997 1828 dbSNP
rs1387866301 1832 dbSNP
rs186877554 1833 dbSNP
rs908635505 1839 dbSNP
rs1410431863 1841 dbSNP
rs1227375208 1845 dbSNP
rs1477830508 1853 dbSNP
rs943690627 1856 dbSNP
rs940478336 1859 dbSNP
rs1344043825 1866 dbSNP
rs1207487837 1871 dbSNP
rs1216942837 1873 dbSNP
Experimental Support 1 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
Conditions MCF7
Location of target site 3'UTR
Tools used in this research TargetScan , miRTarCLIP , Piranha
Original Description (Extracted from the article) ... PAR-CLIP data was present in SRR1045082. RNA binding protein: AGO2. Condition:Untreated ...

- Farazi TA; Ten Hoeve JJ; Brown M; et al., 2014, Genome biology.

Article - Farazi TA; Ten Hoeve JJ; Brown M; et al.
- Genome biology, 2014
BACKGROUND: Various microRNAs (miRNAs) are up- or downregulated in tumors. However, the repression of cognate miRNA targets responsible for the phenotypic effects of this dysregulation in patients remains largely unexplored. To define miRNA targets and associated pathways, together with their relationship to outcome in breast cancer, we integrated patient-paired miRNA-mRNA expression data with a set of validated miRNA targets and pathway inference. RESULTS: To generate a biochemically-validated set of miRNA-binding sites, we performed argonaute-2 photoactivatable-ribonucleoside-enhanced crosslinking and immunoprecipitation (AGO2-PAR-CLIP) in MCF7 cells. We then defined putative miRNA-target interactions using a computational model, which ranked and selected additional TargetScan-predicted interactions based on features of our AGO2-PAR-CLIP binding-site data. We subselected modeled interactions according to the abundance of their constituent miRNA and mRNA transcripts in tumors, and we took advantage of the variability of miRNA expression within molecular subtypes to detect miRNA repression. Interestingly, our data suggest that miRNA families control subtype-specific pathways; for example, miR-17, miR-19a, miR-25, and miR-200b show high miRNA regulatory activity in the triple-negative, basal-like subtype, whereas miR-22 and miR-24 do so in the HER2 subtype. An independent dataset validated our findings for miR-17 and miR-25, and showed a correlation between the expression levels of miR-182 targets and overall patient survival. Pathway analysis associated miR-17, miR-19a, and miR-200b with leukocyte transendothelial migration. CONCLUSIONS: We combined PAR-CLIP data with patient expression data to predict regulatory miRNAs, revealing potential therapeutic targets and prognostic markers in breast cancer.
LinkOut: [PMID: 24398324]
CLIP-seq Support 1 for dataset SRR1045082
Method / RBP PAR-CLIP / AGO2
Cell line / Condition MCF7 / Untreated
Location of target site ENST00000335987.3 | 3UTR | CCUUUCCACAUAUCACCUCAUUUCUAAG
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 24398324 / SRX388831
CLIP-seq Viewer Link
MiRNA-Target Expression Profile
Dataset Pearson Correlation P-value for Pearson Correlation Spearman Correlation P-value for Spearman Correlation Samples Chart
GSE32688 Pancreatic cancer -0.173 1.7e-1 -0.172 1.7e-1 32 Click to see details
GSE27834 Pluripotent stem cells -0.182 2.5e-1 -0.015 4.8e-1 16 Click to see details
GSE17306 Multiple myeloma 0.078 3.0e-1 0.377 3.8e-3 49 Click to see details
GSE21849 B cell lymphoma -0.1 3.0e-1 0.372 2.3e-2 29 Click to see details
GSE38974 Chronic obstructive pulmonary disease -0.094 3.3e-1 -0.151 2.4e-1 25 Click to see details
MiRNA-Target Expression Profile (TCGA)
Tumor Pearson Correlation P-value for Pearson Correlation Spearman Correlation P-value for Spearman Correlation Samples Chart
85 hsa-miR-516b-3p Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT077049 SMARCE1 SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily e, member 1 2 2
MIRT155261 IFNAR2 interferon alpha and beta receptor subunit 2 2 4
MIRT446119 ASTN1 astrotactin 1 2 2
MIRT447355 STOM stomatin 2 2
MIRT469329 RGP1 RGP1 homolog, RAB6A GEF complex partner 1 2 2
MIRT470201 PSAT1 phosphoserine aminotransferase 1 2 6
MIRT475944 GXYLT1 glucoside xylosyltransferase 1 2 4
MIRT498268 KIAA1644 KIAA1644 2 2
MIRT501725 OVOL1 ovo like transcriptional repressor 1 2 2
MIRT522860 KIAA1551 KIAA1551 2 2
MIRT527900 B3GALT5 beta-1,3-galactosyltransferase 5 2 4
MIRT528557 DNAAF3 dynein axonemal assembly factor 3 2 2
MIRT531250 PDF peptide deformylase, mitochondrial 2 2
MIRT534410 SENP1 SUMO1/sentrin specific peptidase 1 2 2
MIRT544656 MED19 mediator complex subunit 19 2 2
MIRT550681 YARS tyrosyl-tRNA synthetase 2 2
MIRT557208 HNRNPF heterogeneous nuclear ribonucleoprotein F 2 4
MIRT611532 DDB1 damage specific DNA binding protein 1 2 2
MIRT612087 TIMM10 translocase of inner mitochondrial membrane 10 2 2
MIRT616535 PARD6B par-6 family cell polarity regulator beta 2 4
MIRT616738 DCTN5 dynactin subunit 5 2 2
MIRT616754 SVOP SV2 related protein 2 4
MIRT617380 FAM227A family with sequence similarity 227 member A 2 2
MIRT617624 RAB3IP RAB3A interacting protein 2 2
MIRT620778 MT1A metallothionein 1A 2 2
MIRT623172 NAA50 N(alpha)-acetyltransferase 50, NatE catalytic subunit 2 2
MIRT626034 AREL1 apoptosis resistant E3 ubiquitin protein ligase 1 2 2
MIRT627376 PRICKLE4 prickle planar cell polarity protein 4 2 2
MIRT630533 AGO3 argonaute 3, RISC catalytic component 2 2
MIRT631686 NQO2 N-ribosyldihydronicotinamide:quinone reductase 2 2 2
MIRT633896 FGF10 fibroblast growth factor 10 2 2
MIRT635933 PLA2G12A phospholipase A2 group XIIA 2 2
MIRT636275 RFFL ring finger and FYVE like domain containing E3 ubiquitin protein ligase 2 2
MIRT636285 RAD51L3-RFFL RAD51L3-RFFL readthrough 2 2
MIRT636502 GDAP1L1 ganglioside induced differentiation associated protein 1 like 1 2 2
MIRT638037 SHPK sedoheptulokinase 2 2
MIRT639162 LAMTOR3 late endosomal/lysosomal adaptor, MAPK and MTOR activator 3 2 2
MIRT639571 GORASP1 golgi reassembly stacking protein 1 2 2
MIRT641248 CENPN centromere protein N 2 2
MIRT643650 MYOCD myocardin 2 2
MIRT645490 TRIM63 tripartite motif containing 63 2 2
MIRT648016 SLCO4C1 solute carrier organic anion transporter family member 4C1 2 2
MIRT648102 LRRFIP1 LRR binding FLII interacting protein 1 2 2
MIRT648729 HIST1H2BD histone cluster 1 H2B family member d 2 2
MIRT650177 LILRA2 leukocyte immunoglobulin like receptor A2 2 2
MIRT652787 TCEANC2 transcription elongation factor A N-terminal and central domain containing 2 2 2
MIRT653248 SORD sorbitol dehydrogenase 2 2
MIRT654859 PPM1F protein phosphatase, Mg2+/Mn2+ dependent 1F 2 2
MIRT655533 PAG1 phosphoprotein membrane anchor with glycosphingolipid microdomains 1 2 2
MIRT656390 MCU mitochondrial calcium uniporter 2 2
MIRT656881 KIF1C kinesin family member 1C 2 2
MIRT657083 JMY junction mediating and regulatory protein, p53 cofactor 2 2
MIRT657629 GPX8 glutathione peroxidase 8 (putative) 2 2
MIRT658295 FAM83F family with sequence similarity 83 member F 2 2
MIRT659432 COL1A1 collagen type I alpha 1 chain 2 2
MIRT659791 CBLB Cbl proto-oncogene B 2 2
MIRT660153 BRCC3 BRCA1/BRCA2-containing complex subunit 3 2 2
MIRT660490 ARRDC3 arrestin domain containing 3 2 2
MIRT660503 ARPC2 actin related protein 2/3 complex subunit 2 2 2
MIRT666356 SIKE1 suppressor of IKBKE 1 2 2
MIRT677774 FKTN fukutin 2 2
MIRT688556 DCAF16 DDB1 and CUL4 associated factor 16 2 2
MIRT697415 ZFP91 ZFP91 zinc finger protein 2 2
MIRT709468 KRTAP19-1 keratin associated protein 19-1 2 2
MIRT711154 WDR82P1 WD repeat domain 82 pseudogene 1 2 2
MIRT711467 SRD5A1 steroid 5 alpha-reductase 1 2 2
MIRT712515 ENPP5 ectonucleotide pyrophosphatase/phosphodiesterase 5 (putative) 2 2
MIRT712661 PCTP phosphatidylcholine transfer protein 2 2
MIRT713304 TYRP1 tyrosinase related protein 1 2 2
MIRT714597 HSPA4L heat shock protein family A (Hsp70) member 4 like 2 2
MIRT716603 MPPED1 metallophosphoesterase domain containing 1 2 2
MIRT717537 PYGO2 pygopus family PHD finger 2 2 2
MIRT718058 CYP3A5 cytochrome P450 family 3 subfamily A member 5 2 2
MIRT718539 PIGQ phosphatidylinositol glycan anchor biosynthesis class Q 2 2
MIRT719768 ZNF236 zinc finger protein 236 2 2
MIRT720162 PNPO pyridoxamine 5'-phosphate oxidase 2 2
MIRT720360 ZBTB8B zinc finger and BTB domain containing 8B 2 2
MIRT721182 HOPX HOP homeobox 2 2
MIRT721278 RAD54L2 RAD54 like 2 2 2
MIRT721357 ENTHD1 ENTH domain containing 1 2 2
MIRT721504 CARHSP1 calcium regulated heat stable protein 1 2 2
MIRT721918 LINGO2 leucine rich repeat and Ig domain containing 2 2 2
MIRT722278 LURAP1 leucine rich adaptor protein 1 2 2
MIRT722789 FUT4 fucosyltransferase 4 2 2
MIRT724390 ABAT 4-aminobutyrate aminotransferase 2 2
miRNA-Drug Associations
miRNA Small Melocule FDA CID Detection Method Condition PMID Year Expression Pattern of miRNA
miR-516b Glucose NULL 5793 Quantitative real-time PCR endothelial cells 24394957 2014 down-regulated
miR-516b Bromocriptine approved 31101 Microarray Prolactinoma 22366961 2012 up-regulated
miR-516b Bromocriptine approved 31101 Quantitative real-time PCR Prolactinoma 22366961 2012 up-regulated
miRNA-Drug Resistance Associations
miRNA Drug Name CID NSC FDA Effect/Pattern Detection Method Level Phenotype Condition
hsa-miR-516b-3p Paclitaxel 36314 NSC125973 approved sensitive High Pan-Cancer cell line (NCI-H460, NCI-H522, NCI-H322M, HOP62, A549, EKVX, MALME-3M, NCI-H226, HT-29, HCT-116, SE-620, HCT-15, HCC2998, COLO205, HS-578T, NCI/ADR-RES, OVCAR8, OVCAR4, ACHN, SN-12C, 786-O, CAKI-1, UO-31, TK-10, A498, SK-MEL-28, UACC-257, M14, UACC-62, SK
hsa-miR-516b-3p Ribavirin+Pegylated IFNa-2b sensitive tissue (chronic hepatitis C)
hsa-miR-516b-3p Testosterone+Exemestane sensitive cell line (MCF-7)
hsa-miR-516b-3p Cisplatin 5460033 NSC119875 approved sensitive cell line (MGC-803)
hsa-miR-516b-3p Docetaxel+Cisplatin+5-Fluorouracil sensitive tissue (hypopharyngeal squamous cell carcinoma)

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