miRTarBase - #MIRT502790


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pre-miRNA Information
pre-miRNA hsa-mir-8055   
Genomic Coordinates chr8: 6622124 - 6622220
Description Homo sapiens miR-8055 stem-loop
Comment None
RNA Secondary Structure

Mature miRNA Information
Mature miRNA hsa-miR-8055
Sequence 65| CUUUGAGCACAUGAGCAGACGGA |87
Evidence Experimental
Experiments Illumina
DRVs in miRNA
Mutant ID Mutant Position Mutant Source
COSN29106641 21 COSMIC
SNPs in miRNA
Mutant ID Mutant Position Mutant Source
rs1387051240 1 dbSNP
rs773940954 2 dbSNP
rs1007521391 11 dbSNP
rs1425192922 13 dbSNP
rs1168057456 15 dbSNP
rs79123647 20 dbSNP
rs1049046267 21 dbSNP
rs561312343 22 dbSNP
Putative Targets

Gene Information
Gene Symbol CELSR3   
Synonyms ADGRC3, CDHF11, EGFL1, FMI1, HFMI1, MEGF2, RESDA1
Description cadherin EGF LAG seven-pass G-type receptor 3
Transcript NM_001407   
Expression
Putative miRNA Targets on CELSR3
3'UTR of CELSR3
(miRNA target sites are highlighted)		 
>CELSR3|NM_001407|3'UTR
   1 GGGGATGACGGCGTGGACGAGGAACAGCTGAGGGCGACAGAGGATCTAGGCTAACAGGAGAGACTCCAGGAGTGGGGGCA
  81 GATCCCAAGGCAGCCTCCTGCTCCCCAGTGGTGGGTGCCCCAGCTCTACCTGGTGTGGCAGGGCTGAGGCTCCATGTGCA
 161 TCTGTGAGCATGCGTGTGACAGGTGCAGAGACGGGGGACTGGAGGGAGACTTTTATACGTTTTGTACCTTTGTAACCAGA
 241 GAGATGCTTATGTTATTTTTCAGCTTTTCTGTCTCCTGGGGGGTTTGAGGCTGGGCTGGGAGGGGGAGGGAGATAGAGGG
 321 AGAGATGCAGTTTGACCCCATTTGGGTCCTGAGCAAACCCTATGCTCATCTCTCTCTCCTTCCTGGGGTGGACTCAGATG
 401 GGTGGGACACATGCCTTCCTCCCCCTATTCCACCCCCAAGTTGATCTGAGTATCGTCAGGGGCCCAAAGTACAGAATTGT
 481 TCTTTGCTTTTTATTGAATGCTCCAAAGGCCAAACTTCTGGGGCTGGGGGTTGGTCTTGGAAACAGGGGTCCTCTGACTT
 561 CCTCATGGGGGCTTGCTCATACCGCCCCTCCTGGTGGATGTGTGTGTTTATTATGTGGAGTCCCTGCCACTTACTGCCTT
 641 ATGACCTAGGACTGATGCTGTGGGGTGCTGGTGGAGCAGCTGATGTCGTGTTTACAGAGCAAGGCTTCCCTGTCTCCCAC
 721 GGGGAGGGGCTCGGGCCTCTAGTCAGACATTCCTGCAGAGGGTCGGTGGAGGGGTCATTCACCTGCCCCTGCAGCAAGCA
 801 AAAGTTGTCTGTGGTGCCATTTGATTCCCTGACACTGCCCCCTGCTTGAATTGATTCCGAAGGGTAGGGTGGGAAGGTGA
 881 GCAAAGGGAGCAGAAACAAGGGAATTCAAGACCCAGAATGTAGGTGCCACTGCCTCCTATGTTTACAGGATCCTCCGTGG
 961 CCCTAGGCACCTGGGCTGCAGGAAGTGACTCCGTTCCACTCCTCCTTTATTCCCTTAAAAAGGGAAAAATGACTGTTACG
1041 ACCCTGTTCACAAAACTCTTACTTTTGCTATTTTGTCTGCTGTCCAGAACTGAAGACTTTAAAATTTTGTTACTGTTTAC
1121 AAGTCCAGATTCAAAAAATGTTTTTACTTTGTTTACAACTCAAAACTTTGAGTTTTACACTTTGTTTACAGTAGATAATT
1201 TTTTTTCCTTTGTTTCCAAGTGAAAGGTAGGGAAAGTGGGAGAGGGACTTGGAGGACCCACCTGTGAGGACCCTGACCTG
1281 GCCATCTTGAGGGGTTTTCTAACCCCCAGGTCTCCCAGGCCGAAGGTCAGCCTTGAGTCCCGTTTAACAGCAGATCCAGA
1361 AGACCTTGAGAGTAGGCGTCCTCTAACCACGGGGGAGAGTGGCTGTGCAGGGCTGGGGGGTGGTCTGTGCAGACACCTCC
1441 TCACCCACCACCCCATGCATACTCTTGGGAAGCAGCTTCCTGGGAGATTAGAAATTCTACTTCCCTGACTGGAGCTAAAT
1521 CCCACCAGCCAGGACCCAAACTCTCCTTACCGAGAAGGACCCCAGCTCTTGAAGGGCTGAGTGGCCTGCTGGGGGTGGGA
1601 GGGTGTCTTTACTATGTCCTAGGTTTCGTAGATGCCCCTCTCTGGGGTTCCCCTCCTCCAGCCCAGCGGCCCTCTTTCCT
1681 GTCTGTGTAAATTGTTCCGTGAAGCCGCGCTCTGTTTTGGGAATAAACTTCTATAGAAAACAAAAAAAAAAAAA
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' agGCAGAC-----GAGUAC------ACGAGUUUc 5'
            | ||||     ||||||      |||||| | 
Target 5' gtCCTCTGACTTCCTCATGGGGGCTTGCTCATAc 3'
 549 - 582 131.00 -18.52
2 
miRNA  3' aggCAGACGAGUACACGAGUUUc 5'
             || |  ||| | || |||| 
Target 5' tgaGTATCGTCAGGGGCCCAAAg 3'
 447 - 469 128.00 -10.50
3 
miRNA  3' aggcAGACG---AGU-AC--ACGAGUUUc 5'
              |:|||   |:| ||  ||||| || 
Target 5' gttcTTTGCTTTTTATTGAATGCTCCAAa 3'
 479 - 507 125.00 -10.80
DRVs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
COSN30473482 1 COSMIC
COSN30173262 18 COSMIC
COSN30134390 19 COSMIC
COSN31589947 35 COSMIC
COSN30662591 122 COSMIC
COSN30730344 152 COSMIC
COSN30710461 173 COSMIC
COSN30542863 228 COSMIC
COSN229052 247 COSMIC
COSN31558936 248 COSMIC
COSN30174667 316 COSMIC
COSN7762737 353 COSMIC
COSN24720566 354 COSMIC
COSN1951516 520 COSMIC
COSN31597392 687 COSMIC
COSN26565292 700 COSMIC
COSN29468596 756 COSMIC
COSN1277923 891 COSMIC
COSN23707738 1428 COSMIC
COSN9552837 1512 COSMIC
COSN7699728 1551 COSMIC
COSN17948504 1552 COSMIC
COSN7699727 1699 COSMIC
SNPs in gene 3'UTRs
Mutant ID Mutant Position Mutant Source
rs757863136 4 dbSNP
rs1357803109 5 dbSNP
rs1393554816 5 dbSNP
rs200275511 9 dbSNP
rs764653747 10 dbSNP
rs757246976 11 dbSNP
rs753753780 12 dbSNP
rs370155183 13 dbSNP
rs549551361 18 dbSNP
rs775599300 19 dbSNP
rs767710344 26 dbSNP
rs759671919 28 dbSNP
rs1446606657 31 dbSNP
rs1359427340 34 dbSNP
rs147108034 35 dbSNP
rs1376783698 36 dbSNP
rs763284584 36 dbSNP
rs1370340696 38 dbSNP
rs1169555147 39 dbSNP
rs1276489496 54 dbSNP
rs1287224506 55 dbSNP
rs377494941 60 dbSNP
rs761278646 62 dbSNP
rs1014286960 63 dbSNP
rs574163783 64 dbSNP
rs1473170116 70 dbSNP
rs1423770681 74 dbSNP
rs896400097 75 dbSNP
rs925896236 77 dbSNP
rs1385443091 88 dbSNP
rs980112021 90 dbSNP
rs1309247789 94 dbSNP
rs1322264947 101 dbSNP
rs1403871741 103 dbSNP
rs561035136 104 dbSNP
rs567891164 111 dbSNP
rs61045611 117 dbSNP
rs1387805578 118 dbSNP
rs1219536569 123 dbSNP
rs527896685 132 dbSNP
rs560285482 148 dbSNP
rs1158612237 150 dbSNP
rs1203293913 154 dbSNP
rs926448601 155 dbSNP
rs1483423072 156 dbSNP
rs1198844118 170 dbSNP
rs1245465922 171 dbSNP
rs1479303359 173 dbSNP
rs992881586 192 dbSNP
rs1173485836 193 dbSNP
rs1419259211 196 dbSNP
rs1427358950 201 dbSNP
rs551464595 203 dbSNP
rs1038098324 207 dbSNP
rs1370827154 216 dbSNP
rs113862826 218 dbSNP
rs1321035153 219 dbSNP
rs908325432 220 dbSNP
rs1269314374 221 dbSNP
rs1362747162 224 dbSNP
rs1230426867 245 dbSNP
rs759127484 247 dbSNP
rs1209267381 251 dbSNP
rs1432786893 252 dbSNP
rs1453765862 261 dbSNP
rs922824253 266 dbSNP
rs749313611 271 dbSNP
rs1190891564 279 dbSNP
rs1448010316 280 dbSNP
rs1463986038 281 dbSNP
rs1390350392 282 dbSNP
rs1443659543 283 dbSNP
rs1160877557 284 dbSNP
rs114631130 287 dbSNP
rs1201466929 291 dbSNP
rs544328901 302 dbSNP
rs997126294 303 dbSNP
rs1298095725 307 dbSNP
rs1232130529 312 dbSNP
rs542498811 318 dbSNP
rs1244339109 319 dbSNP
rs1282444901 324 dbSNP
rs1358547159 329 dbSNP
rs900138895 338 dbSNP
rs1268028111 339 dbSNP
rs1463952578 341 dbSNP
rs1000396998 342 dbSNP
rs1249037443 344 dbSNP
rs1422815270 357 dbSNP
rs1184940326 360 dbSNP
rs1369902059 361 dbSNP
rs1018620872 362 dbSNP
rs1432633788 363 dbSNP
rs1364112366 365 dbSNP
rs1008561431 374 dbSNP
rs891584616 381 dbSNP
rs1014255824 388 dbSNP
rs1052876336 410 dbSNP
rs1397667467 411 dbSNP
rs895826515 425 dbSNP
rs1056342755 426 dbSNP
rs575106997 427 dbSNP
rs573957894 434 dbSNP
rs1394134674 439 dbSNP
rs904994693 441 dbSNP
rs1044679298 443 dbSNP
rs1342537248 450 dbSNP
rs948676063 452 dbSNP
rs917203622 454 dbSNP
rs992869945 455 dbSNP
rs1287844197 456 dbSNP
rs940080195 457 dbSNP
rs1391010682 462 dbSNP
rs372287637 471 dbSNP
rs762512656 473 dbSNP
rs1448059354 475 dbSNP
rs6809205 479 dbSNP
rs952969093 503 dbSNP
rs1188890752 505 dbSNP
rs1257811358 512 dbSNP
rs542877275 523 dbSNP
rs1442668439 524 dbSNP
rs1180779147 531 dbSNP
rs921456106 534 dbSNP
rs1444605473 540 dbSNP
rs1253527719 545 dbSNP
rs1046808204 559 dbSNP
rs1377068867 562 dbSNP
rs1464335486 564 dbSNP
rs976037031 565 dbSNP
rs572270271 566 dbSNP
rs6773261 574 dbSNP
rs1018562146 575 dbSNP
rs1008551380 583 dbSNP
rs955776376 584 dbSNP
rs1341231252 586 dbSNP
rs1284535288 588 dbSNP
rs1411815115 608 dbSNP
rs1289486845 618 dbSNP
rs975663145 640 dbSNP
rs1231465665 646 dbSNP
rs1258173111 658 dbSNP
rs1345209219 665 dbSNP
rs1450182625 668 dbSNP
rs1204020158 682 dbSNP
rs1249240484 686 dbSNP
rs1182321956 687 dbSNP
rs1031406719 688 dbSNP
rs1431398833 691 dbSNP
rs1200648862 694 dbSNP
rs1332351142 700 dbSNP
rs999964846 711 dbSNP
rs1428931847 713 dbSNP
rs1414250568 717 dbSNP
rs904324811 720 dbSNP
rs376705843 721 dbSNP
rs1298844469 727 dbSNP
rs1367474046 728 dbSNP
rs926248709 733 dbSNP
rs1303789366 736 dbSNP
rs1428022132 742 dbSNP
rs749681452 752 dbSNP
rs1389991033 764 dbSNP
rs1013248563 765 dbSNP
rs967571935 769 dbSNP
rs1205201462 771 dbSNP
rs1264354653 782 dbSNP
rs1487431612 788 dbSNP
rs1211547647 793 dbSNP
rs371459239 799 dbSNP
rs1020344329 804 dbSNP
rs1448610630 806 dbSNP
rs1186493725 818 dbSNP
rs992912667 820 dbSNP
rs1367233685 823 dbSNP
rs1171149434 826 dbSNP
rs367633250 827 dbSNP
rs1187380284 831 dbSNP
rs1483106987 844 dbSNP
rs1253291960 846 dbSNP
rs960004324 859 dbSNP
rs1482509233 864 dbSNP
rs1290397032 867 dbSNP
rs895768847 868 dbSNP
rs1395906640 869 dbSNP
rs1434798499 879 dbSNP
rs1295900810 887 dbSNP
rs1366831081 888 dbSNP
rs1228700728 910 dbSNP
rs577859604 913 dbSNP
rs556200170 917 dbSNP
rs537477262 919 dbSNP
rs1001568676 925 dbSNP
rs905108666 939 dbSNP
rs1353910661 949 dbSNP
rs1464407007 954 dbSNP
rs1206549100 955 dbSNP
rs111747505 956 dbSNP
rs769525406 974 dbSNP
rs1466379479 991 dbSNP
rs1187318567 992 dbSNP
rs567219377 993 dbSNP
rs1351218862 1003 dbSNP
rs1422102311 1007 dbSNP
rs748111121 1018 dbSNP
rs1408288117 1024 dbSNP
rs1457180171 1027 dbSNP
rs1046776533 1039 dbSNP
rs549434727 1039 dbSNP
rs921393691 1040 dbSNP
rs1376575774 1043 dbSNP
rs1407444915 1058 dbSNP
rs1293410476 1063 dbSNP
rs1328313703 1065 dbSNP
rs1226515609 1070 dbSNP
rs1388956578 1086 dbSNP
rs1329599613 1090 dbSNP
rs1163217578 1095 dbSNP
rs1209212625 1101 dbSNP
rs1237097863 1102 dbSNP
rs1482413334 1115 dbSNP
rs1183604199 1118 dbSNP
rs1258329799 1122 dbSNP
rs1472338246 1123 dbSNP
rs1157581699 1125 dbSNP
rs975646450 1130 dbSNP
rs1039758088 1141 dbSNP
rs942419707 1147 dbSNP
rs966004938 1150 dbSNP
rs1179367840 1151 dbSNP
rs1449786949 1151 dbSNP
rs912844565 1153 dbSNP
rs1246928422 1161 dbSNP
rs1223235239 1170 dbSNP
rs1407533626 1170 dbSNP
rs554816276 1172 dbSNP
rs1218380003 1175 dbSNP
rs955680749 1192 dbSNP
rs1031308779 1197 dbSNP
rs1000318600 1198 dbSNP
rs1212495521 1198 dbSNP
rs781145242 1200 dbSNP
rs566733260 1206 dbSNP
rs960096836 1207 dbSNP
rs1023214207 1217 dbSNP
rs1290357905 1225 dbSNP
rs1190910626 1233 dbSNP
rs1423525800 1242 dbSNP
rs1226647153 1246 dbSNP
rs1034480073 1254 dbSNP
rs188918248 1255 dbSNP
rs1427237300 1270 dbSNP
rs1227583659 1272 dbSNP
rs9811378 1275 dbSNP
rs1057050465 1277 dbSNP
rs770255154 1282 dbSNP
rs143282190 1303 dbSNP
rs1017227081 1306 dbSNP
rs778851650 1313 dbSNP
rs886913406 1321 dbSNP
rs1048393934 1322 dbSNP
rs931387771 1325 dbSNP
rs1325619063 1334 dbSNP
rs997996943 1335 dbSNP
rs1203056673 1341 dbSNP
rs921392271 1342 dbSNP
rs1391461513 1348 dbSNP
rs1040261847 1360 dbSNP
rs1438843578 1361 dbSNP
rs1245552164 1362 dbSNP
rs944243602 1377 dbSNP
rs139362931 1378 dbSNP
rs1194713800 1381 dbSNP
rs1399628288 1383 dbSNP
rs1425197188 1391 dbSNP
rs988322207 1393 dbSNP
rs185962846 1394 dbSNP
rs1169873254 1396 dbSNP
rs562066696 1397 dbSNP
rs542949702 1402 dbSNP
rs76178705 1406 dbSNP
rs1388099853 1408 dbSNP
rs1294360158 1409 dbSNP
rs527623185 1410 dbSNP
rs1266172798 1414 dbSNP
rs146528087 1415 dbSNP
rs375958721 1415 dbSNP
rs376324611 1415 dbSNP
rs969277362 1415 dbSNP
rs1319679079 1420 dbSNP
rs878941662 1421 dbSNP
rs1279379340 1424 dbSNP
rs1364641535 1434 dbSNP
rs1272207735 1437 dbSNP
rs1340150446 1444 dbSNP
rs1227853728 1446 dbSNP
rs1022739927 1454 dbSNP
rs1288327551 1455 dbSNP
rs1470241051 1457 dbSNP
rs1214665405 1460 dbSNP
rs1221198928 1461 dbSNP
rs146278097 1475 dbSNP
rs1303215019 1476 dbSNP
rs1194868848 1479 dbSNP
rs545251355 1481 dbSNP
rs181823161 1489 dbSNP
rs538266992 1490 dbSNP
rs1415823767 1491 dbSNP
rs1461896580 1504 dbSNP
rs9848518 1506 dbSNP
rs1319579249 1509 dbSNP
rs1367721145 1514 dbSNP
rs1386167659 1516 dbSNP
rs374086375 1523 dbSNP
rs1437096128 1532 dbSNP
rs1004094944 1541 dbSNP
rs1320498229 1545 dbSNP
rs887064125 1546 dbSNP
rs1027391040 1550 dbSNP
rs1319154285 1558 dbSNP
rs1430515293 1565 dbSNP
rs1447329662 1571 dbSNP
rs995548356 1575 dbSNP
rs899896324 1581 dbSNP
rs1282533997 1592 dbSNP
rs1337502843 1593 dbSNP
rs1234423111 1598 dbSNP
rs1359339762 1599 dbSNP
rs754054694 1608 dbSNP
rs1268120065 1617 dbSNP
rs1327481597 1621 dbSNP
rs1207308211 1622 dbSNP
rs1177819761 1625 dbSNP
rs1039767532 1628 dbSNP
rs944136871 1629 dbSNP
rs891258774 1632 dbSNP
rs1393959859 1639 dbSNP
rs1475283389 1640 dbSNP
rs1168751430 1642 dbSNP
rs1158331644 1650 dbSNP
rs1409718457 1654 dbSNP
rs1458597832 1655 dbSNP
rs1052553353 1657 dbSNP
rs778304875 1658 dbSNP
rs909228221 1661 dbSNP
rs1314681769 1668 dbSNP
rs1357439955 1672 dbSNP
rs1415516042 1675 dbSNP
rs1288242242 1678 dbSNP
rs1185679670 1680 dbSNP
rs1349195056 1686 dbSNP
rs925568397 1698 dbSNP
rs1241572509 1699 dbSNP
rs1261681040 1706 dbSNP
rs1343774851 1706 dbSNP
rs983445912 1707 dbSNP
rs951282633 1708 dbSNP
rs190258717 1721 dbSNP
rs544267785 1728 dbSNP
rs947051812 1731 dbSNP
rs915577966 1732 dbSNP
rs1376872226 1734 dbSNP
rs1018400738 1736 dbSNP
rs1171972443 1739 dbSNP
rs1377548792 1741 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 PAR-CLIP data was present in GSM545217. RNA binding protein: AGO2. Condition:miR-7 transfection ...

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

miRNA-target interactions (Provided by authors)
ID Duplex structure Position
1 
miRNA  3' aggcAGACGAGUACACGAGUUUc 5'
              |:||:|:|    |||||| 
Target 5' uuacUUUGUUUA-CAACUCAAAa 3'
 		4 - 25
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 1951.0
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 GSM714645. RNA binding protein: AGO2. Condition:completeT1 ...

- Kishore S; Jaskiewicz L; Burger L; Hausser et al., 2011, Nature methods.

Article - Kishore S; Jaskiewicz L; Burger L; Hausser et al.
- Nature methods, 2011
Cross-linking and immunoprecipitation (CLIP) is increasingly used to map transcriptome-wide binding sites of RNA-binding proteins. We developed a method for CLIP data analysis, and applied it to compare CLIP with photoactivatable ribonucleoside-enhanced CLIP (PAR-CLIP) and to uncover how differences in cross-linking and ribonuclease digestion affect the identified sites. We found only small differences in accuracies of these methods in identifying binding sites of HuR, which binds low-complexity sequences, and Argonaute 2, which has a complex binding specificity. We found that cross-link-induced mutations led to single-nucleotide resolution for both PAR-CLIP and CLIP. Our results confirm the expectation from original CLIP publications that RNA-binding proteins do not protect their binding sites sufficiently under the denaturing conditions used during the CLIP procedure, and we show that extensive digestion with sequence-specific RNases strongly biases the recovered binding sites. This bias can be substantially reduced by milder nuclease digestion conditions.
LinkOut: [PMID: 21572407]
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 ENST00000164024.4 | 3UTR | UUUUUACUUUGUUUACAACUCAAAACU
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 GSM545217
Method / RBP PAR-CLIP / AGO2
Cell line / Condition HEK293 / miR-7 transfection
Location of target site ENST00000164024.4 | 3UTR | UUUUUACUUUGUUUACAACUCAAAACUU
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 20371350 / GSE21578
CLIP-seq Viewer Link
CLIP-seq Support 3 for dataset GSM714645
Method / RBP PAR-CLIP / AGO2
Cell line / Condition HEK293 / completeT1, repB
Location of target site ENST00000164024.4 | 3UTR | UUUUUACUUUGUUUACAACUCAAAACUUUG
Tools used in this analysis TargetScan, miRTarCLIP, and Piranha
Article / Accession Series PMID: 21572407 / GSE28865
CLIP-seq Viewer Link
CLIP-seq Support 4 for dataset SRR1045082
Method / RBP PAR-CLIP / AGO2
Cell line / Condition MCF7 / Untreated
Location of target site ENST00000164024.4 | 3UTR | UUUUUACUUUGUUUACAACUCAAAACUUUG
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
192 hsa-miR-8055 Target Genes:
Functional analysis:
ID Target Description Validation methods
Strong evidence Less strong evidence
MIRT104178 PHTF2 putative homeodomain transcription factor 2 2 6
MIRT109489 KLHL15 kelch like family member 15 2 2
MIRT138601 HIF1A hypoxia inducible factor 1 alpha subunit 2 2
MIRT207609 COX5B cytochrome c oxidase subunit 5B 2 2
MIRT246311 HIST2H2AA3 histone cluster 2 H2A family member a3 2 4
MIRT246323 HIST2H2AA4 histone cluster 2 H2A family member a4 2 4
MIRT267508 FEN1 flap structure-specific endonuclease 1 2 2
MIRT271002 FLVCR1 feline leukemia virus subgroup C cellular receptor 1 2 2
MIRT378038 SMAD5 SMAD family member 5 2 4
MIRT442382 CLVS2 clavesin 2 2 2
MIRT443996 METRN meteorin, glial cell differentiation regulator 2 4
MIRT444222 TMEM136 transmembrane protein 136 2 2
MIRT445870 ALG14 ALG14, UDP-N-acetylglucosaminyltransferase subunit 2 2
MIRT463214 ZNF131 zinc finger protein 131 2 2
MIRT464523 UBXN2B UBX domain protein 2B 2 2
MIRT471509 PCGF3 polycomb group ring finger 3 2 6
MIRT474035 LONRF1 LON peptidase N-terminal domain and ring finger 1 2 2
MIRT481566 ARIH2 ariadne RBR E3 ubiquitin protein ligase 2 2 2
MIRT485415 LZIC leucine zipper and CTNNBIP1 domain containing 2 8
MIRT485724 CALM2 calmodulin 2 2 2
MIRT500745 TNRC6A trinucleotide repeat containing 6A 2 2
MIRT502790 CELSR3 cadherin EGF LAG seven-pass G-type receptor 3 2 6
MIRT503164 AGO2 argonaute 2, RISC catalytic component 2 4
MIRT504842 HAUS3 HAUS augmin like complex subunit 3 2 6
MIRT506559 MNX1 motor neuron and pancreas homeobox 1 2 4
MIRT511372 IKZF3 IKAROS family zinc finger 3 2 6
MIRT522117 NUDT3 nudix hydrolase 3 2 4
MIRT523755 FBXO27 F-box protein 27 2 4
MIRT525160 PGPEP1 pyroglutamyl-peptidase I 2 4
MIRT537294 FZD5 frizzled class receptor 5 2 2
MIRT537493 FAM168B family with sequence similarity 168 member B 2 2
MIRT538375 CRIM1 cysteine rich transmembrane BMP regulator 1 2 2
MIRT539394 ADO 2-aminoethanethiol dioxygenase 2 2
MIRT544124 PPIL1 peptidylprolyl isomerase like 1 2 2
MIRT547269 NUFIP2 NUFIP2, FMR1 interacting protein 2 2 2
MIRT548034 GOLIM4 golgi integral membrane protein 4 2 2
MIRT551641 CCDC127 coiled-coil domain containing 127 2 2
MIRT552585 ZCCHC9 zinc finger CCHC-type containing 9 2 2
MIRT552605 ZBTB8A zinc finger and BTB domain containing 8A 2 2
MIRT554174 SLC35E2B solute carrier family 35 member E2B 2 2
MIRT556914 IRF2BP2 interferon regulatory factor 2 binding protein 2 2 2
MIRT564288 MED26 mediator complex subunit 26 2 2
MIRT571375 TTPAL alpha tocopherol transfer protein like 2 4
MIRT572009 HIC2 HIC ZBTB transcriptional repressor 2 2 2
MIRT572339 CKAP2L cytoskeleton associated protein 2 like 2 4
MIRT572612 CNTLN centlein 2 2
MIRT572779 ZNF277 zinc finger protein 277 2 2
MIRT573258 DCAF10 DDB1 and CUL4 associated factor 10 2 2
MIRT573353 PDE3A phosphodiesterase 3A 2 4
MIRT573362 MAP2K6 mitogen-activated protein kinase kinase 6 2 2
MIRT574194 LMNB1 lamin B1 2 2
MIRT574453 RPS16 ribosomal protein S16 2 2
MIRT574849 C12orf73 chromosome 12 open reading frame 73 2 2
MIRT575356 Zxda zinc finger, X-linked, duplicated A 2 3
MIRT612192 CCDC77 coiled-coil domain containing 77 2 2
MIRT612974 GGCX gamma-glutamyl carboxylase 2 2
MIRT613749 UNKL unkempt family like zinc finger 2 2
MIRT614085 PDE4C phosphodiesterase 4C 2 2
MIRT614405 ADAT1 adenosine deaminase, tRNA specific 1 2 2
MIRT614441 WDR92 WD repeat domain 92 2 2
MIRT614518 SUB1 SUB1 homolog, transcriptional regulator 2 2
MIRT614653 NIPAL3 NIPA like domain containing 3 2 2
MIRT614720 TEAD3 TEA domain transcription factor 3 2 2
MIRT615556 SAR1A secretion associated Ras related GTPase 1A 2 2
MIRT616636 LRAT lecithin retinol acyltransferase 2 4
MIRT617210 CERS4 ceramide synthase 4 2 2
MIRT618934 SF3A3 splicing factor 3a subunit 3 2 2
MIRT619995 C1orf64 steroid receptor associated and regulated protein 2 2
MIRT620819 MKI67IP nucleolar protein interacting with the FHA domain of MKI67 1 1
MIRT621254 PDZD2 PDZ domain containing 2 2 2
MIRT622307 SETD5 SET domain containing 5 2 2
MIRT623324 MAN1C1 mannosidase alpha class 1C member 1 2 2
MIRT625066 ACSM2A acyl-CoA synthetase medium chain family member 2A 2 2
MIRT625443 RANGAP1 Ran GTPase activating protein 1 2 2
MIRT626182 SRFBP1 serum response factor binding protein 1 2 2
MIRT626701 TRIM65 tripartite motif containing 65 2 2
MIRT628925 TBRG4 transforming growth factor beta regulator 4 2 2
MIRT630883 SLC25A33 solute carrier family 25 member 33 2 2
MIRT631653 BRI3BP BRI3 binding protein 2 2
MIRT631696 C1QTNF6 C1q and TNF related 6 2 2
MIRT632864 GSPT1 G1 to S phase transition 1 2 2
MIRT635185 NFKBID NFKB inhibitor delta 2 2
MIRT636917 ZNF845 zinc finger protein 845 2 2
MIRT637048 RAB27A RAB27A, member RAS oncogene family 2 2
MIRT637599 ZNF554 zinc finger protein 554 2 2
MIRT638204 SPTLC2 serine palmitoyltransferase long chain base subunit 2 2 2
MIRT638839 CPE carboxypeptidase E 2 2
MIRT639005 ACO1 aconitase 1 2 2
MIRT640894 AMD1 adenosylmethionine decarboxylase 1 2 2
MIRT641402 SCN2B sodium voltage-gated channel beta subunit 2 2 2
MIRT642083 FBXL2 F-box and leucine rich repeat protein 2 2 2
MIRT643179 HYPK huntingtin interacting protein K 2 2
MIRT644205 CBS cystathionine-beta-synthase 2 2
MIRT645453 ANKS6 ankyrin repeat and sterile alpha motif domain containing 6 2 2
MIRT645797 OMA1 OMA1 zinc metallopeptidase 2 2
MIRT645960 TTF2 transcription termination factor 2 2 2
MIRT646334 CLIC6 chloride intracellular channel 6 2 2
MIRT646484 APBB3 amyloid beta precursor protein binding family B member 3 2 2
MIRT646611 SMOC2 SPARC related modular calcium binding 2 2 2
MIRT649392 SH2D4A SH2 domain containing 4A 2 2
MIRT650540 MSANTD2 Myb/SANT DNA binding domain containing 2 2 2
MIRT650679 CD82 CD82 molecule 2 2
MIRT652118 TRPM7 transient receptor potential cation channel subfamily M member 7 2 2
MIRT652588 TIMM8A translocase of inner mitochondrial membrane 8A 2 2
MIRT654807 PPT1 palmitoyl-protein thioesterase 1 2 2
MIRT655318 PCYOX1 prenylcysteine oxidase 1 2 2
MIRT655411 PAN2 PAN2 poly(A) specific ribonuclease subunit 2 2
MIRT659671 CD86 CD86 molecule 2 2
MIRT660190 BMPR1A bone morphogenetic protein receptor type 1A 2 2
MIRT660883 ADCYAP1R1 ADCYAP receptor type I 2 2
MIRT661695 MTO1 mitochondrial tRNA translation optimization 1 2 2
MIRT661765 BIVM basic, immunoglobulin-like variable motif containing 2 2
MIRT662787 TBC1D25 TBC1 domain family member 25 2 2
MIRT663733 ZNF285 zinc finger protein 285 2 2
MIRT663787 DDX53 DEAD-box helicase 53 2 2
MIRT664663 IMPA2 inositol monophosphatase 2 2 2
MIRT665702 TMX4 thioredoxin related transmembrane protein 4 2 2
MIRT667444 MAPK14 mitogen-activated protein kinase 14 2 2
MIRT667946 HMGCS1 3-hydroxy-3-methylglutaryl-CoA synthase 1 2 2
MIRT668776 DAAM1 dishevelled associated activator of morphogenesis 1 2 4
MIRT669824 ISCA2 iron-sulfur cluster assembly 2 2 2
MIRT670398 ZXDA zinc finger, X-linked, duplicated A 2 3
MIRT670402 ELP2 elongator acetyltransferase complex subunit 2 2 2
MIRT671112 ZNF573 zinc finger protein 573 2 2
MIRT671129 CD226 CD226 molecule 2 2
MIRT671145 ANKRD9 ankyrin repeat domain 9 2 2
MIRT671315 ACTR1A ARP1 actin related protein 1 homolog A 2 2
MIRT671329 FAM71F2 family with sequence similarity 71 member F2 2 2
MIRT671857 ZNF429 zinc finger protein 429 2 2
MIRT672009 PXMP4 peroxisomal membrane protein 4 2 2
MIRT672054 KIAA0930 KIAA0930 2 2
MIRT672466 RTTN rotatin 2 2
MIRT672642 SLC25A16 solute carrier family 25 member 16 2 4
MIRT672660 GTF2H5 general transcription factor IIH subunit 5 2 2
MIRT672755 UBE2V2 ubiquitin conjugating enzyme E2 V2 2 2
MIRT672839 ICOSLG inducible T-cell costimulator ligand 2 2
MIRT672917 LRRC2 leucine rich repeat containing 2 2 2
MIRT672983 KBTBD6 kelch repeat and BTB domain containing 6 2 2
MIRT673051 AGO3 argonaute 3, RISC catalytic component 2 2
MIRT673078 AK1 adenylate kinase 1 2 2
MIRT673143 C1orf50 chromosome 1 open reading frame 50 2 2
MIRT673303 UBE2G2 ubiquitin conjugating enzyme E2 G2 2 2
MIRT673319 THAP1 THAP domain containing 1 2 2
MIRT673339 SLC35F6 solute carrier family 35 member F6 2 2
MIRT673554 PLA2G16 phospholipase A2 group XVI 2 2
MIRT673656 ZNF440 zinc finger protein 440 2 2
MIRT673693 SGK494 uncharacterized serine/threonine-protein kinase SgK494 2 2
MIRT673720 EMCN endomucin 2 2
MIRT673840 CALCOCO2 calcium binding and coiled-coil domain 2 2 2
MIRT673869 KLF2 Kruppel like factor 2 2 2
MIRT673888 DCTN6 dynactin subunit 6 2 2
MIRT674180 PLEKHM3 pleckstrin homology domain containing M3 2 2
MIRT674579 SLC35B4 solute carrier family 35 member B4 2 2
MIRT674604 RBBP4 RB binding protein 4, chromatin remodeling factor 2 2
MIRT674737 SLC16A1 solute carrier family 16 member 1 2 2
MIRT674824 ADAMTS4 ADAM metallopeptidase with thrombospondin type 1 motif 4 2 2
MIRT674993 STRN3 striatin 3 2 2
MIRT675058 FGD6 FYVE, RhoGEF and PH domain containing 6 2 2
MIRT675072 CCR6 C-C motif chemokine receptor 6 2 2
MIRT675116 FSD2 fibronectin type III and SPRY domain containing 2 2 2
MIRT675158 YARS2 tyrosyl-tRNA synthetase 2 2 2
MIRT675254 LPP LIM domain containing preferred translocation partner in lipoma 2 2
MIRT675434 LEAP2 liver enriched antimicrobial peptide 2 2 2
MIRT675687 PIWIL1 piwi like RNA-mediated gene silencing 1 2 2
MIRT675772 YIPF4 Yip1 domain family member 4 2 2
MIRT675883 SNAP29 synaptosome associated protein 29 2 2
MIRT677923 SLC35E1 solute carrier family 35 member E1 2 2
MIRT678991 MBD1 methyl-CpG binding domain protein 1 2 2
MIRT679010 MTMR10 myotubularin related protein 10 2 2
MIRT679024 ZNF419 zinc finger protein 419 2 2
MIRT679392 IL10RB interleukin 10 receptor subunit beta 2 2
MIRT679407 GMCL1 germ cell-less, spermatogenesis associated 1 2 2
MIRT683745 C3orf36 chromosome 3 open reading frame 36 2 2
MIRT689266 ZNF99 zinc finger protein 99 2 2
MIRT690502 MDM2 MDM2 proto-oncogene 2 2
MIRT700939 PDP2 pyruvate dehyrogenase phosphatase catalytic subunit 2 2 2
MIRT702073 PCDHB11 protocadherin beta 11 2 2
MIRT705020 CALU calumenin 2 2
MIRT706196 ACOT9 acyl-CoA thioesterase 9 2 2
MIRT706253 MKLN1 muskelin 1 2 2
MIRT706540 GJD2 gap junction protein delta 2 2 2
MIRT707358 ORAI2 ORAI calcium release-activated calcium modulator 2 2 2
MIRT707407 RRP7A ribosomal RNA processing 7 homolog A 2 2
MIRT710638 GLUL glutamate-ammonia ligase 2 2
MIRT714213 C10orf71 chromosome 10 open reading frame 71 2 2
MIRT715646 USP6NL USP6 N-terminal like 2 2
MIRT717751 KCNRG potassium channel regulator 2 2
MIRT720793 GCH1 GTP cyclohydrolase 1 2 2
MIRT722254 POLQ DNA polymerase theta 2 2
MIRT723765 MPLKIP M-phase specific PLK1 interacting protein 2 2
MIRT724965 TNS1 tensin 1 2 2
MIRT736568 TP53INP1 tumor protein p53 inducible nuclear protein 1 3 0
miRNA-Drug Resistance Associations
miRNA Drug Name CID NSC FDA Effect/Pattern Detection Method Level Phenotype Condition
hsa-miR-8055 Cisplatin 5460033 NSC119875 approved sensitive cell line (CP20)

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