miRTarBase - #MIRT130165


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pre-miRNA Information
pre-miRNA hsa-mir-548t   
Genomic Coordinates chr4: 173268160 - 173268233
Description Homo sapiens miR-548t stem-loop
Comment None
RNA Secondary Structure

Mature miRNA Information
Mature miRNA hsa-miR-548t-3p
Sequence 46| AAAAACCACAAUUACUUUUGCACCA |70
Evidence Not_experimental
Experiments
Editing Events in miRNAs
Modification Type Position on miR Chromosome DNA Strand Genomic Position (hg38) List of PMIDs Variant details
A-to-I 2 4 + 173268206 29233923 MiREDiBase
A-to-I 3 4 + 173268207 29233923 MiREDiBase
A-to-I 4 4 + 173268208 29233923 MiREDiBase
A-to-I 10 4 + 173268214 29233923 MiREDiBase
SNPs in miRNA
Mutant ID Mutant Position Mutant Source
rs73872515 5 dbSNP
rs1426966747 6 dbSNP
rs1158401109 21 dbSNP
rs943938928 24 dbSNP
Putative Targets

Gene Information
Gene Symbol TXNIP   
Synonyms ARRDC6, EST01027, HHCPA78, THIF, VDUP1
Description thioredoxin interacting protein
Transcript NM_006472   
Expression
Putative miRNA Targets on TXNIP
3'UTR of TXNIP
(miRNA target sites are highlighted)		 
>TXNIP|NM_006472|3'UTR
   1 GCATGTGGAAGAAAAGAAGCAGCTTTACCTACTTGTTTCTTTTTGTCTCTCTTCCTGGACACTCACTTTTTCAGAGACTC
  81 AACAGTCTCTGCAATGGAGTGTGGGTCCACCTTAGCCTCTGACTTCCTAATGTAGGAGGTGGTCAGCAGGCAATCTCCTG
 161 GGCCTTAAAGGATGCGGACTCATCCTCAGCCAGCGCCCATGTTGTGATACAGGGGTGTTTGTTGGATGGGTTTAAAAATA
 241 ACTAGAAAAACTCAGGCCCATCCATTTTCTCAGATCTCCTTGAAAATTGAGGCCTTTTCGATAGTTTCGGGTCAGGTAAA
 321 AATGGCCTCCTGGCGTAAGCTTTTCAAGGTTTTTTGGAGGCTTTTTGTAAATTGTGATAGGAACTTTGGACCTTGAACTT
 401 ACGTATCATGTGGAGAAGAGCCAATTTAACAAACTAGGAAGATGAAAAGGGAAATTGTGGCCAAAACTTTGGGAAAAGGA
 481 GGTTCTTAAAATCAGTGTTTCCCCTTTGTGCACTTGTAGAAAAAAAAGAAAAACCTTCTAGAGCTGATTTGATGGACAAT
 561 GGAGAGAGCTTTCCCTGTGATTATAAAAAAGGAAGCTAGCTGCTCTACGGTCATCTTTGCTTAGAGTATACTTTAACCTG
 641 GCTTTTAAAGCAGTAGTAACTGCCCCACCAAAGGTCTTAAAAGCCATTTTTGGAGCCTATTGCACTGTGTTCTCCTACTG
 721 CAAATATTTTCATATGGGAGGATGGTTTTCTCTTCATGTAAGTCCTTGGAATTGATTCTAAGGTGATGTTCTTAGCACTT
 801 TAATTCCTGTCAAATTTTTTGTTCTCCCCTTCTGCCATCTTAAATGTAAGCTGAAACTGGTCTACTGTGTCTCTAGGGTT
 881 AAGCCAAAAGACAAAAAAAATTTTACTACTTTTGAGATTGCCCCAATGTACAGAATTATATAATTCTAACGCTTAAATCA
 961 TGTGAAAGGGTTGCTGCTGTCAGCCTTGCCCACTGTGACTTCAAACCCAAGGAGGAACTCTTGATCAAGATGCCCAACCC
1041 TGTGATCAGAACCTCCAAATACTGCCATGAGAAACTAGAGGGCAGGTCTTCATAAAAGCCCTTTGAACCCCCTTCCTGCC
1121 CTGTGTTAGGAGATAGGGATATTGGCCCCTCACTGCAGCTGCCAGCACTTGGTCAGTCACTCTCAGCCATAGCACTTTGT
1201 TCACTGTCCTGTGTCAGAGCACTGAGCTCCACCCTTTTCTGAGAGTTATTACAGCCAGAAAGTGTGGGCTGAAGATGGTT
1281 GGTTTCATGTTTTTGTATTATGTATCTTTTTGTATGGTAAAGACTATATTTTGTACTTAACCAGATATATTTTTACCCCA
1361 GATGGGGATATTCTTTGTAAAAAATGAAAATAAAGTTTTTTTAATGGAAAAAAAAATGTCTGTGAAAAAAAAAAAAAAAA
1441 AA
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' accACGUUUUCAUUAACACCAAAAa 5'
             | || | | :|   ||||||| 
Target 5' attTTCATATGGGAGGATGGTTTTc 3'
 726 - 750 150.00 -6.40
2 
miRNA  3' acCACGUUUUCAUUAAC-ACCAAAaa 5'
            | || :|||  || | ||||||  
Target 5' gtGGGCTGAAG--ATGGTTGGTTTca 3'
 1264 - 1287 139.00 -11.10
3 
miRNA  3' acCAC---GUUUUCAUUAAC-----ACCAAAAa 5'
            |||   ||:::||: |||     ||| ||| 
Target 5' ttGTGATACAGGGGTGTTTGTTGGATGGGTTTa 3'
 202 - 234 131.00 -12.30
DRVs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
COSN31613608 26 COSMIC
COSN23013884 29 COSMIC
COSN30498918 54 COSMIC
COSN26345387 86 COSMIC
COSN31518012 87 COSMIC
COSN31544793 97 COSMIC
COSN13465511 153 COSMIC
COSN30168748 176 COSMIC
COSN22854620 212 COSMIC
COSN32082653 300 COSMIC
COSN20215506 357 COSMIC
COSN25793126 567 COSMIC
COSN31481257 609 COSMIC
COSN28929309 699 COSMIC
COSN31487417 731 COSMIC
COSN8319264 786 COSMIC
COSN7175900 895 COSMIC
COSN16130546 903 COSMIC
COSN31541469 950 COSMIC
COSN1404851 989 COSMIC
COSN31566757 1020 COSMIC
COSN30175504 1198 COSMIC
COSN28813251 1210 COSMIC
COSN31563457 1215 COSMIC
COSN17255712 1341 COSMIC
COSN8635856 1344 COSMIC
COSN16130598 1349 COSMIC
COSN8319265 1407 COSMIC
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs782324253 5 dbSNP
rs781922861 6 dbSNP
rs782164728 10 dbSNP
rs1042196726 11 dbSNP
rs1378865015 12 dbSNP
rs1238192616 14 dbSNP
rs1322340577 17 dbSNP
rs1223844421 20 dbSNP
rs782412186 20 dbSNP
rs782011331 23 dbSNP
rs1263824209 27 dbSNP
rs775233794 27 dbSNP
rs782126186 28 dbSNP
rs371598136 29 dbSNP
rs781829085 35 dbSNP
rs1179845309 39 dbSNP
rs762566229 45 dbSNP
rs187591491 47 dbSNP
rs782695925 49 dbSNP
rs1438233194 53 dbSNP
rs1176339594 56 dbSNP
rs1406774368 58 dbSNP
rs1405664156 61 dbSNP
rs371239177 62 dbSNP
rs763445640 66 dbSNP
rs191199120 68 dbSNP
rs1331993431 80 dbSNP
rs926556698 85 dbSNP
rs980068913 86 dbSNP
rs942069156 94 dbSNP
rs1380153984 102 dbSNP
rs1230279460 103 dbSNP
rs1310607527 110 dbSNP
rs1321232464 111 dbSNP
rs1199751130 115 dbSNP
rs1260570451 117 dbSNP
rs782040268 123 dbSNP
rs782156144 126 dbSNP
rs1198407308 128 dbSNP
rs1238455155 128 dbSNP
rs1472910620 134 dbSNP
rs1183259112 139 dbSNP
rs1410937390 144 dbSNP
rs1474596615 150 dbSNP
rs1171229323 157 dbSNP
rs1402347354 160 dbSNP
rs1464057644 161 dbSNP
rs1327900605 164 dbSNP
rs1359573889 167 dbSNP
rs983462122 171 dbSNP
rs1450421426 172 dbSNP
rs782151618 175 dbSNP
rs782730266 176 dbSNP
rs1219316893 182 dbSNP
rs751580661 189 dbSNP
rs1316562673 194 dbSNP
rs757127542 195 dbSNP
rs1279726855 196 dbSNP
rs782458723 199 dbSNP
rs1444522337 202 dbSNP
rs964973982 214 dbSNP
rs1018315568 215 dbSNP
rs1211711784 216 dbSNP
rs1235396722 239 dbSNP
rs1485173889 242 dbSNP
rs1193744753 246 dbSNP
rs1425196792 247 dbSNP
rs1000527363 251 dbSNP
rs782095422 264 dbSNP
rs782735059 269 dbSNP
rs1425527728 277 dbSNP
rs1415978448 281 dbSNP
rs1020648610 286 dbSNP
rs1375066981 292 dbSNP
rs182339054 293 dbSNP
rs896250928 294 dbSNP
rs1430590223 300 dbSNP
rs186992970 307 dbSNP
rs587669942 308 dbSNP
rs1280146264 309 dbSNP
rs1346661958 315 dbSNP
rs1216943737 318 dbSNP
rs1264644353 325 dbSNP
rs372245117 327 dbSNP
rs1247206460 328 dbSNP
rs1479008383 331 dbSNP
rs905099575 334 dbSNP
rs1394305473 335 dbSNP
rs1420489469 337 dbSNP
rs587633419 347 dbSNP
rs1358627658 351 dbSNP
rs1400205301 353 dbSNP
rs1324348440 357 dbSNP
rs587688547 366 dbSNP
rs880001759 372 dbSNP
rs1434993978 373 dbSNP
rs1303097894 380 dbSNP
rs1240339979 388 dbSNP
rs1378137080 388 dbSNP
rs1287737864 397 dbSNP
rs1348176239 402 dbSNP
rs7211 402 dbSNP
rs909194389 403 dbSNP
rs1252106635 405 dbSNP
rs139816793 405 dbSNP
rs983429530 408 dbSNP
rs1180677079 410 dbSNP
rs11537988 416 dbSNP
rs1378681121 420 dbSNP
rs1469875254 421 dbSNP
rs1163879673 425 dbSNP
rs1393031655 431 dbSNP
rs929395114 432 dbSNP
rs1325860264 434 dbSNP
rs1401411327 444 dbSNP
rs782760634 447 dbSNP
rs1449452453 451 dbSNP
rs1307615133 453 dbSNP
rs1333591721 454 dbSNP
rs923375748 455 dbSNP
rs587595014 458 dbSNP
rs144336702 461 dbSNP
rs587721930 462 dbSNP
rs979655270 466 dbSNP
rs1272484245 470 dbSNP
rs968300777 475 dbSNP
rs1458201715 478 dbSNP
rs782603988 483 dbSNP
rs1200297110 486 dbSNP
rs1248193527 499 dbSNP
rs1437439441 507 dbSNP
rs1188533701 516 dbSNP
rs1370225266 517 dbSNP
rs1020617601 518 dbSNP
rs1164375997 528 dbSNP
rs1471852789 528 dbSNP
rs1424966048 530 dbSNP
rs60016427 532 dbSNP
rs1329704935 535 dbSNP
rs1396260982 536 dbSNP
rs1390424829 537 dbSNP
rs1334409691 538 dbSNP
rs1341676501 540 dbSNP
rs1230906272 543 dbSNP
rs1009258927 547 dbSNP
rs960484146 549 dbSNP
rs1292204396 555 dbSNP
rs1318464304 556 dbSNP
rs1220448927 559 dbSNP
rs1249351897 560 dbSNP
rs1480204605 573 dbSNP
rs1201181041 578 dbSNP
rs17221751 580 dbSNP
rs1001967957 584 dbSNP
rs904984593 585 dbSNP
rs1491098482 591 dbSNP
rs1491237619 592 dbSNP
rs1479063432 600 dbSNP
rs1169206620 603 dbSNP
rs1372803185 604 dbSNP
rs1466890670 605 dbSNP
rs1038185991 606 dbSNP
rs1174735186 608 dbSNP
rs1005396171 609 dbSNP
rs887055645 610 dbSNP
rs1412581170 612 dbSNP
rs1311718841 614 dbSNP
rs1173796060 624 dbSNP
rs1293355589 625 dbSNP
rs1401723505 625 dbSNP
rs1306645745 627 dbSNP
rs1233700693 636 dbSNP
rs587625832 637 dbSNP
rs1210470225 640 dbSNP
rs1286782430 651 dbSNP
rs782317952 663 dbSNP
rs1489316693 676 dbSNP
rs929338953 678 dbSNP
rs923374357 680 dbSNP
rs1261621694 686 dbSNP
rs1434316789 688 dbSNP
rs1201416620 696 dbSNP
rs1393705612 697 dbSNP
rs1432427649 700 dbSNP
rs1172659571 707 dbSNP
rs1360531020 709 dbSNP
rs587680878 712 dbSNP
rs1361150127 715 dbSNP
rs1387331419 717 dbSNP
rs1303074471 720 dbSNP
rs755859477 720 dbSNP
rs1368560706 732 dbSNP
rs943471171 734 dbSNP
rs1287031216 735 dbSNP
rs1356195735 736 dbSNP
rs184403951 757 dbSNP
rs1260255804 760 dbSNP
rs1489078465 762 dbSNP
rs979622524 764 dbSNP
rs879951227 765 dbSNP
rs587616307 768 dbSNP
rs968269660 772 dbSNP
rs1380513567 778 dbSNP
rs914194992 783 dbSNP
rs1420548122 786 dbSNP
rs987815665 789 dbSNP
rs587697781 795 dbSNP
rs1327851862 797 dbSNP
rs1391945520 798 dbSNP
rs587738475 799 dbSNP
rs1439880342 802 dbSNP
rs188801165 813 dbSNP
rs1034694017 814 dbSNP
rs1222326818 816 dbSNP
rs1306316807 824 dbSNP
rs1002338477 826 dbSNP
rs1322437540 827 dbSNP
rs17215345 829 dbSNP
rs1247537919 846 dbSNP
rs1271839122 855 dbSNP
rs969178468 869 dbSNP
rs1199631976 871 dbSNP
rs1240471150 871 dbSNP
rs1481382993 872 dbSNP
rs1175151496 877 dbSNP
rs1406527116 881 dbSNP
rs1166547639 886 dbSNP
rs879991460 893 dbSNP
rs1491067549 894 dbSNP
rs17215338 897 dbSNP
rs1331759889 899 dbSNP
rs1016711766 900 dbSNP
rs1297825524 901 dbSNP
rs1356080896 901 dbSNP
rs1440237012 901 dbSNP
rs1379912358 908 dbSNP
rs1230086645 914 dbSNP
rs1005366474 922 dbSNP
rs887026030 924 dbSNP
rs1334743209 928 dbSNP
rs199827526 932 dbSNP
rs998124411 939 dbSNP
rs1201940875 940 dbSNP
rs1231944411 943 dbSNP
rs587637170 946 dbSNP
rs901803859 949 dbSNP
rs193055505 950 dbSNP
rs587754573 951 dbSNP
rs11537987 952 dbSNP
rs943433626 954 dbSNP
rs1408014581 959 dbSNP
rs1169551439 961 dbSNP
rs1359958985 962 dbSNP
rs1416911570 974 dbSNP
rs1311094732 979 dbSNP
rs1354936972 981 dbSNP
rs1401073154 982 dbSNP
rs910662203 984 dbSNP
rs1272447258 992 dbSNP
rs1360566475 1002 dbSNP
rs1214348658 1006 dbSNP
rs1279834666 1011 dbSNP
rs587707558 1017 dbSNP
rs1312385871 1018 dbSNP
rs1212604008 1026 dbSNP
rs1277515542 1027 dbSNP
rs778849135 1031 dbSNP
rs587631368 1033 dbSNP
rs946900640 1034 dbSNP
rs7212 1035 dbSNP
rs1474423371 1037 dbSNP
rs1185681179 1038 dbSNP
rs1425637740 1040 dbSNP
rs185869681 1044 dbSNP
rs4755 1045 dbSNP
rs11537984 1056 dbSNP
rs782111820 1062 dbSNP
rs747400980 1067 dbSNP
rs939637061 1072 dbSNP
rs1374865849 1074 dbSNP
rs782357128 1081 dbSNP
rs587663814 1082 dbSNP
rs1320449964 1086 dbSNP
rs1325170860 1087 dbSNP
rs587731065 1088 dbSNP
rs1275758715 1100 dbSNP
rs781954705 1102 dbSNP
rs1235949373 1103 dbSNP
rs148808239 1104 dbSNP
rs1300821227 1105 dbSNP
rs1346774785 1107 dbSNP
rs1216697503 1109 dbSNP
rs13340 1112 dbSNP
rs969092902 1115 dbSNP
rs75291601 1117 dbSNP
rs1445163633 1118 dbSNP
rs1215023304 1120 dbSNP
rs1247001755 1121 dbSNP
rs587742862 1123 dbSNP
rs1455432809 1128 dbSNP
rs1191582395 1133 dbSNP
rs587632424 1134 dbSNP
rs1440595578 1137 dbSNP
rs1025436781 1138 dbSNP
rs782067883 1143 dbSNP
rs1382907398 1146 dbSNP
rs1324782358 1149 dbSNP
rs1397061837 1152 dbSNP
rs1439140528 1153 dbSNP
rs901116218 1156 dbSNP
rs1369745291 1160 dbSNP
rs1239380532 1162 dbSNP
rs1280747961 1164 dbSNP
rs13203 1168 dbSNP
rs1223087601 1173 dbSNP
rs1469822683 1180 dbSNP
rs73004671 1181 dbSNP
rs1252203121 1182 dbSNP
rs1458344032 1184 dbSNP
rs1184283201 1185 dbSNP
rs1362065982 1186 dbSNP
rs1163966506 1192 dbSNP
rs1469702544 1192 dbSNP
rs889195041 1193 dbSNP
rs1043797905 1203 dbSNP
rs1460375002 1209 dbSNP
rs1325623390 1223 dbSNP
rs782809435 1224 dbSNP
rs1391541737 1226 dbSNP
rs946785983 1234 dbSNP
rs1060179 1239 dbSNP
rs1333683268 1246 dbSNP
rs1293420506 1248 dbSNP
rs1440836776 1248 dbSNP
rs782123605 1249 dbSNP
rs1231405845 1251 dbSNP
rs1272265404 1251 dbSNP
rs1339831652 1252 dbSNP
rs781886945 1256 dbSNP
rs1248667835 1268 dbSNP
rs939585610 1269 dbSNP
rs1188706047 1271 dbSNP
rs928262975 1274 dbSNP
rs1259759524 1279 dbSNP
rs1474484411 1285 dbSNP
rs980844449 1286 dbSNP
rs1164841981 1288 dbSNP
rs1424714665 1290 dbSNP
rs1463841426 1293 dbSNP
rs1166587935 1295 dbSNP
rs1393839142 1298 dbSNP
rs587744932 1301 dbSNP
rs17215352 1304 dbSNP
rs1356845442 1312 dbSNP
rs587697405 1314 dbSNP
rs1292610322 1315 dbSNP
rs951155166 1319 dbSNP
rs782761667 1326 dbSNP
rs1327009960 1328 dbSNP
rs1229331365 1330 dbSNP
rs1249443048 1334 dbSNP
rs587759329 1341 dbSNP
rs1211893044 1348 dbSNP
rs1484739763 1356 dbSNP
rs1282482732 1357 dbSNP
rs139537792 1359 dbSNP
rs1263042191 1360 dbSNP
rs587711312 1362 dbSNP
rs1430853212 1367 dbSNP
rs965670628 1373 dbSNP
rs1191461016 1379 dbSNP
rs1372896149 1381 dbSNP
rs1474856821 1384 dbSNP
rs1173878766 1385 dbSNP
rs1376677555 1390 dbSNP
rs1432309416 1391 dbSNP
rs1311815383 1395 dbSNP
rs1385539659 1402 dbSNP
rs1383900622 1403 dbSNP
rs1293116545 1404 dbSNP
rs1325670923 1411 dbSNP
rs1018223865 1413 dbSNP
rs1210215430 1417 dbSNP
rs1305882263 1417 dbSNP
rs143469330 1417 dbSNP
rs79787359 1417 dbSNP
Experimental Support 1 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
Conditions HEK293
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 GSM545216. RNA binding protein: AGO2. Condition:miR-124 transfection ...

- Hafner M; Landthaler M; Burger L; Khorshid et al., 2010, Cell.

Article - Hafner M; Landthaler M; Burger L; Khorshid et al.
- Cell, 2010
RNA transcripts are subject to posttranscriptional gene regulation involving hundreds of RNA-binding proteins (RBPs) and microRNA-containing ribonucleoprotein complexes (miRNPs) expressed in a cell-type dependent fashion. We developed a cell-based crosslinking approach to determine at high resolution and transcriptome-wide the binding sites of cellular RBPs and miRNPs. The crosslinked sites are revealed by thymidine to cytidine transitions in the cDNAs prepared from immunopurified RNPs of 4-thiouridine-treated cells. We determined the binding sites and regulatory consequences for several intensely studied RBPs and miRNPs, including PUM2, QKI, IGF2BP1-3, AGO/EIF2C1-4 and TNRC6A-C. Our study revealed that these factors bind thousands of sites containing defined sequence motifs and have distinct preferences for exonic versus intronic or coding versus untranslated transcript regions. The precise mapping of binding sites across the transcriptome will be critical to the interpretation of the rapidly emerging data on genetic variation between individuals and how these variations contribute to complex genetic diseases.
LinkOut: [PMID: 20371350]
Experimental Support 2 for Functional miRNA-Target Interaction
miRNA:Target ----
Validation Method
Conditions HEK293
Disease 10628.0
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 GSM1065670. RNA binding protein: AGO2. Condition:4-thiouridine ...

- Memczak S; Jens M; Elefsinioti A; Torti F; et al., 2013, Nature.

Article - Memczak S; Jens M; Elefsinioti A; Torti F; et al.
- Nature, 2013
Circular RNAs (circRNAs) in animals are an enigmatic class of RNA with unknown function. To explore circRNAs systematically, we sequenced and computationally analysed human, mouse and nematode RNA. We detected thousands of well-expressed, stable circRNAs, often showing tissue/developmental-stage-specific expression. Sequence analysis indicated important regulatory functions for circRNAs. We found that a human circRNA, antisense to the cerebellar degeneration-related protein 1 transcript (CDR1as), is densely bound by microRNA (miRNA) effector complexes and harbours 63 conserved binding sites for the ancient miRNA miR-7. Further analyses indicated that CDR1as functions to bind miR-7 in neuronal tissues. Human CDR1as expression in zebrafish impaired midbrain development, similar to knocking down miR-7, suggesting that CDR1as is a miRNA antagonist with a miRNA-binding capacity ten times higher than any other known transcript. Together, our data provide evidence that circRNAs form a large class of post-transcriptional regulators. Numerous circRNAs form by head-to-tail splicing of exons, suggesting previously unrecognized regulatory potential of coding sequences.
LinkOut: [PMID: 23446348]
Experimental Support 3 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 GSM545216
Method / RBP PAR-CLIP / AGO2
Cell line / Condition HEK293 / miR-124 transfection
Location of target site ENST00000369317.4 | 3UTR | CCAUUUUUGGAGCCUAUUGCACUGUGUUCUCCUACUGCAAAUAUUUUCAUAUGGGAGGAUGGUUUUCUCUUCAUG
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 20371350 / GSE21578
CLIP-seq Viewer Link
CLIP-seq Support 2 for dataset GSM1065670
Method / RBP PAR-CLIP / AGO2
Cell line / Condition HEK293 / 4-thiouridine, 3_ML_LG
Location of target site ENST00000369317.4 | 3UTR | CCAUUUUUGGAGCCUAUUGCACUGUGUUCUCCUACUGCAAAUAUUUUCAUAUGGGAGGAUG
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 23446348 / GSE43573
CLIP-seq Viewer Link
CLIP-seq Support 3 for dataset SRR1045082
Method / RBP PAR-CLIP / AGO2
Cell line / Condition MCF7 / Untreated
Location of target site ENST00000369317.4 | 3UTR | CCUAUUGCACUGUGUUCUCCUACUGCAAAUAUUUUCAUAUGGGAGGAUGGUUUUCUCUUCAUGUAAG
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
MiRNA-Target Expression Profile (TCGA)
Tumor Pearson Correlation P-value for Pearson Correlation Spearman Correlation P-value for Spearman Correlation Samples Chart
168 hsa-miR-548t-3p Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT059365 ANP32E acidic nuclear phosphoprotein 32 family member E 2 2
MIRT072839 ARIH1 ariadne RBR E3 ubiquitin protein ligase 1 2 6
MIRT076945 PCGF2 polycomb group ring finger 2 2 6
MIRT083941 TFAP2C transcription factor AP-2 gamma 2 2
MIRT085401 ETS2 ETS proto-oncogene 2, transcription factor 2 2
MIRT109790 KLHL15 kelch like family member 15 2 2
MIRT114046 AKAP11 A-kinase anchoring protein 11 2 10
MIRT130165 TXNIP thioredoxin interacting protein 2 6
MIRT150013 MIDN midnolin 2 2
MIRT181258 ASH1L ASH1 like histone lysine methyltransferase 2 2
MIRT205594 NCL nucleolin 2 2
MIRT222253 ACTB actin beta 2 4
MIRT245653 EIF5AL1 eukaryotic translation initiation factor 5A-like 1 2 4
MIRT250947 CDK5R1 cyclin dependent kinase 5 regulatory subunit 1 2 4
MIRT252497 NWD1 NACHT and WD repeat domain containing 1 2 2
MIRT271990 ARF1 ADP ribosylation factor 1 2 4
MIRT280804 RNF11 ring finger protein 11 2 2
MIRT293803 FEM1A fem-1 homolog A 2 2
MIRT318231 RREB1 ras responsive element binding protein 1 2 2
MIRT341455 ATP6V0B ATPase H+ transporting V0 subunit b 2 2
MIRT347413 CEBPG CCAAT/enhancer binding protein gamma 2 4
MIRT351860 PLEKHA3 pleckstrin homology domain containing A3 2 2
MIRT357983 GRPEL2 GrpE like 2, mitochondrial 2 2
MIRT377094 PPP1CB protein phosphatase 1 catalytic subunit beta 2 2
MIRT407303 IGFBP5 insulin like growth factor binding protein 5 2 2
MIRT441564 LMOD3 leiomodin 3 2 2
MIRT442364 ZC3H12C zinc finger CCCH-type containing 12C 2 2
MIRT443228 ARL5B ADP ribosylation factor like GTPase 5B 2 2
MIRT443404 HMX3 H6 family homeobox 3 2 2
MIRT446055 NR5A2 nuclear receptor subfamily 5 group A member 2 2 2
MIRT448277 ZNF652 zinc finger protein 652 2 2
MIRT450822 KCNB1 potassium voltage-gated channel subfamily B member 1 2 2
MIRT453016 CCDC115 coiled-coil domain containing 115 2 17
MIRT454463 PPP2R2B protein phosphatase 2 regulatory subunit Bbeta 2 2
MIRT456360 CITED2 Cbp/p300 interacting transactivator with Glu/Asp rich carboxy-terminal domain 2 2 2
MIRT460007 DNALI1 dynein axonemal light intermediate chain 1 2 2
MIRT463154 ZNF385A zinc finger protein 385A 2 6
MIRT463766 YPEL2 yippee like 2 2 2
MIRT468310 SFT2D2 SFT2 domain containing 2 2 2
MIRT470668 POLR2D RNA polymerase II subunit D 2 4
MIRT478517 CTTN cortactin 2 2
MIRT480507 C11orf57 chromosome 11 open reading frame 57 2 2
MIRT484718 INHBA inhibin beta A subunit 2 12
MIRT485494 HMGN2 high mobility group nucleosomal binding domain 2 2 2
MIRT487302 SLC38A9 solute carrier family 38 member 9 2 2
MIRT487771 ANKEF1 ankyrin repeat and EF-hand domain containing 1 2 16
MIRT491876 YWHAZ tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein zeta 2 2
MIRT494304 CEP120 centrosomal protein 120 2 2
MIRT495396 TRIM24 tripartite motif containing 24 2 2
MIRT495646 CDK1 cyclin dependent kinase 1 2 2
MIRT496665 TMEM237 transmembrane protein 237 2 2
MIRT496837 ZNF460 zinc finger protein 460 2 2
MIRT498638 CHD4 chromodomain helicase DNA binding protein 4 2 10
MIRT503928 FBXL13 F-box and leucine rich repeat protein 13 2 4
MIRT506063 PPP2R2A protein phosphatase 2 regulatory subunit Balpha 2 2
MIRT506582 MIER3 MIER family member 3 2 4
MIRT506606 MAT2A methionine adenosyltransferase 2A 2 4
MIRT506844 KIF23 kinesin family member 23 2 6
MIRT508536 RPP14 ribonuclease P/MRP subunit p14 2 4
MIRT509669 ZNF354B zinc finger protein 354B 2 10
MIRT511170 MBNL3 muscleblind like splicing regulator 3 2 6
MIRT512147 COX6B1 cytochrome c oxidase subunit 6B1 2 2
MIRT512831 ID4 inhibitor of DNA binding 4, HLH protein 2 6
MIRT514558 XRCC3 X-ray repair cross complementing 3 2 4
MIRT515856 AJAP1 adherens junctions associated protein 1 2 4
MIRT521848 PNISR PNN interacting serine and arginine rich protein 2 4
MIRT525364 SYNM synemin 2 2
MIRT527120 ARHGAP15 Rho GTPase activating protein 15 2 2
MIRT527271 FBLN2 fibulin 2 2 2
MIRT527439 COL4A3 collagen type IV alpha 3 chain 2 2
MIRT527658 CD300E CD300e molecule 2 2
MIRT528334 TBC1D22B TBC1 domain family member 22B 2 2
MIRT529033 EXOC8 exocyst complex component 8 2 2
MIRT529321 PDE5A phosphodiesterase 5A 2 2
MIRT529677 TRPV2 transient receptor potential cation channel subfamily V member 2 2 2
MIRT529846 SMTN smoothelin 2 2
MIRT530385 ZNF431 zinc finger protein 431 2 2
MIRT530913 GPR85 G protein-coupled receptor 85 2 2
MIRT531794 KDR kinase insert domain receptor 2 2
MIRT532246 KLF2 Kruppel like factor 2 2 4
MIRT532658 CBX7 chromobox 7 2 2
MIRT533630 TMX3 thioredoxin related transmembrane protein 3 2 2
MIRT534811 RAB33B RAB33B, member RAS oncogene family 2 2
MIRT534975 PSD3 pleckstrin and Sec7 domain containing 3 2 2
MIRT536588 ITPKB inositol-trisphosphate 3-kinase B 2 2
MIRT536779 HNRNPD heterogeneous nuclear ribonucleoprotein D 2 2
MIRT538764 CABLES1 Cdk5 and Abl enzyme substrate 1 2 2
MIRT539294 ANGEL2 angel homolog 2 2 2
MIRT539621 SHISA9 shisa family member 9 2 2
MIRT539651 BUB1 BUB1 mitotic checkpoint serine/threonine kinase 2 2
MIRT540347 OPHN1 oligophrenin 1 2 2
MIRT540413 PITPNC1 phosphatidylinositol transfer protein, cytoplasmic 1 2 2
MIRT541396 CDC27 cell division cycle 27 2 2
MIRT542916 HSBP1 heat shock factor binding protein 1 2 2
MIRT544710 EIF5A eukaryotic translation initiation factor 5A 2 4
MIRT544998 MFF mitochondrial fission factor 2 4
MIRT553289 TSPAN3 tetraspanin 3 2 2
MIRT553455 TNRC6C trinucleotide repeat containing 6C 2 2
MIRT553782 TAF13 TATA-box binding protein associated factor 13 2 2
MIRT554656 ROBO1 roundabout guidance receptor 1 2 2
MIRT555104 PURB purine rich element binding protein B 2 2
MIRT557235 HNRNPA1 heterogeneous nuclear ribonucleoprotein A1 2 2
MIRT560861 GAL3ST3 galactose-3-O-sulfotransferase 3 2 2
MIRT561545 SON SON DNA binding protein 2 2
MIRT561554 SLMO2 PRELI domain containing 3B 2 2
MIRT563764 ZNF678 zinc finger protein 678 2 2
MIRT565653 SIX4 SIX homeobox 4 2 2
MIRT568080 CELF2 CUGBP Elav-like family member 2 2 2
MIRT568759 MYBL1 MYB proto-oncogene like 1 2 2
MIRT569078 CADM2 cell adhesion molecule 2 2 2
MIRT569509 THYN1 thymocyte nuclear protein 1 2 2
MIRT571268 CDKN2AIP CDKN2A interacting protein 2 2
MIRT571809 PHF19 PHD finger protein 19 2 2
MIRT572554 DKK3 dickkopf WNT signaling pathway inhibitor 3 2 2
MIRT573782 SLC24A4 solute carrier family 24 member 4 2 4
MIRT576441 Ccdc115 coiled-coil domain containing 115 2 10
MIRT576712 Slc30a3 solute carrier family 30 (zinc transporter), member 3 2 3
MIRT608377 PIWIL2 piwi like RNA-mediated gene silencing 2 2 2
MIRT608484 NKTR natural killer cell triggering receptor 2 6
MIRT610186 FAM49A family with sequence similarity 49 member A 2 2
MIRT611631 EDIL3 EGF like repeats and discoidin domains 3 2 2
MIRT613534 TRA2B transformer 2 beta homolog 2 2
MIRT616221 PTPN11 protein tyrosine phosphatase, non-receptor type 11 2 2
MIRT622370 SALL1 spalt like transcription factor 1 2 2
MIRT624371 CDK12 cyclin dependent kinase 12 2 2
MIRT624995 ZNF665 zinc finger protein 665 2 4
MIRT626875 AP3B1 adaptor related protein complex 3 beta 1 subunit 2 2
MIRT627737 RAP2B RAP2B, member of RAS oncogene family 2 4
MIRT628490 ADAT2 adenosine deaminase, tRNA specific 2 2 2
MIRT633647 PLEKHG7 pleckstrin homology and RhoGEF domain containing G7 2 4
MIRT634028 SLC30A3 solute carrier family 30 member 3 2 3
MIRT635923 GLTSCR2 NOP53 ribosome biogenesis factor 2 2
MIRT638287 SERBP1 SERPINE1 mRNA binding protein 1 2 2
MIRT641959 RNF115 ring finger protein 115 2 2
MIRT643573 CTNNA3 catenin alpha 3 2 2
MIRT645180 NOL9 nucleolar protein 9 2 4
MIRT647497 ZNF639 zinc finger protein 639 2 2
MIRT647682 PCK1 phosphoenolpyruvate carboxykinase 1 2 2
MIRT648422 MYOZ3 myozenin 3 2 2
MIRT650113 ZCCHC9 zinc finger CCHC-type containing 9 2 2
MIRT651076 ZNF518B zinc finger protein 518B 2 4
MIRT651415 ZADH2 zinc binding alcohol dehydrogenase domain containing 2 2 2
MIRT651456 XKR4 XK related 4 2 2
MIRT653619 SLC30A4 solute carrier family 30 member 4 2 2
MIRT653637 SLC30A1 solute carrier family 30 member 1 2 2
MIRT654896 POU2F1 POU class 2 homeobox 1 2 2
MIRT656483 MAP3K9 mitogen-activated protein kinase kinase kinase 9 2 2
MIRT658016 GABRA4 gamma-aminobutyric acid type A receptor alpha4 subunit 2 2
MIRT658041 FZD10 frizzled class receptor 10 2 2
MIRT660093 BTBD3 BTB domain containing 3 2 2
MIRT663923 MAGEF1 MAGE family member F1 2 2
MIRT665882 TGIF2 TGFB induced factor homeobox 2 2 2
MIRT669051 CEP128 centrosomal protein 128 2 2
MIRT669711 AAGAB alpha and gamma adaptin binding protein 2 2
MIRT686812 SNX2 sorting nexin 2 2 4
MIRT689883 SOD2 superoxide dismutase 2 2 2
MIRT693274 GLRX2 glutaredoxin 2 2 4
MIRT697056 BCAR1 BCAR1, Cas family scaffolding protein 2 2
MIRT703297 GID4 GID complex subunit 4 homolog 2 2
MIRT704087 DYRK2 dual specificity tyrosine phosphorylation regulated kinase 2 2 2
MIRT707719 CDC6 cell division cycle 6 2 2
MIRT708136 GK5 glycerol kinase 5 (putative) 2 2
MIRT709212 KLHL30 kelch like family member 30 2 2
MIRT710062 RWDD2A RWD domain containing 2A 2 2
MIRT712770 POU6F2 POU class 6 homeobox 2 2 2
MIRT715073 TMTC1 transmembrane and tetratricopeptide repeat containing 1 2 2
MIRT715387 TADA3 transcriptional adaptor 3 2 2
MIRT717712 NCKAP1 NCK associated protein 1 2 2
miRNA-Drug Resistance Associations
miRNA Drug Name CID NSC FDA Effect/Pattern Detection Method Level Phenotype Condition
hsa-mir-548t Paclitaxel 36314 NSC125973 approved sensitive cell line (W1)
hsa-mir-548t Cisplatin 5460033 NSC119875 approved sensitive cell line (W1)
hsa-mir-548t Doxorubicin 31703 NSC123127 approved sensitive cell line (W1)
hsa-mir-548t Topotecan 60699 NSC609699 approved sensitive cell line (W1)
hsa-mir-548t Vincristine 5978 approved sensitive cell line (W1)
hsa-miR-548t-3p Oxaliplatin 6857599 NSC266046 approved sensitive High Colorectal Cancer cell line (SW480, HCT-116)
hsa-miR-548t-3p Gefitinib 123631 NSC715055 approved sensitive cell line (PC9)
hsa-miR-548t-3p Osimertinib 71496458 NSC779217 approved sensitive cell line (HCC827)

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