ID	Duplex structure	Position	Score	MFE
1	miRNA 3' aggACUGGGGAUCUGGGUUGAc 5' ||||| ||:||::||| Target 5' ccaTGACC---AGGCCTGACTc 3'	45 - 63	132.00	-17.70
2	miRNA 3' aggacUGGGG----AU---CU---GGGUUGAc 5' ||||| || || ||||:|| Target 5' tccccACCCCCTTGTACTTGATTCCCCAGCTg 3'	246 - 277	131.00	-21.60
3	miRNA 3' aggacuGGGGAUCUGGGUUGac 5' ||||| |||| || Target 5' ccccttCCCCTTCACCCCACgt 3'	188 - 209	112.00	-20.30

Mutant ID	Mutant Position	Mutant Source
318924	244	ClinVar
318925	342	ClinVar
318926	343	ClinVar
COSN30096746	118	COSMIC
COSN31492407	175	COSMIC
COSN8497637	299	COSMIC
COSN17037408	332	COSMIC
COSN28087724	350	COSMIC
COSN31533057	351	COSMIC
COSN30538549	360	COSMIC
COSN31489109	362	COSMIC
COSN15157296	742	COSMIC
COSN9645498	834	COSMIC
COSN15848948	972	COSMIC
COSN17819902	1356	COSMIC
COSN5406409	1443	COSMIC
COSN5406410	1466	COSMIC

Mutant ID	Mutant Position	Mutant Source
rs776557423	2	dbSNP
rs920827090	7	dbSNP
rs929481204	10	dbSNP
rs1181472367	11	dbSNP
rs1047899710	12	dbSNP
rs761359958	13	dbSNP
rs1421787558	15	dbSNP
rs764991569	16	dbSNP
rs376319548	23	dbSNP
rs1263045695	24	dbSNP
rs1451790192	30	dbSNP
rs763403768	32	dbSNP
rs142064048	33	dbSNP
rs990098300	36	dbSNP
rs1039127322	37	dbSNP
rs1220379641	38	dbSNP
rs368747756	39	dbSNP
rs1430339222	40	dbSNP
rs764402414	44	dbSNP
rs192066047	48	dbSNP
rs977267255	49	dbSNP
rs1403890918	50	dbSNP
rs1054394963	52	dbSNP
rs891678537	55	dbSNP
rs1010032406	57	dbSNP
rs1185651516	58	dbSNP
rs572979591	61	dbSNP
rs991137929	62	dbSNP
rs1185408688	64	dbSNP
rs1024051979	71	dbSNP
rs1478163895	73	dbSNP
rs971200508	80	dbSNP
rs1219113443	83	dbSNP
rs147764660	84	dbSNP
rs1034502093	89	dbSNP
rs1367429040	92	dbSNP
rs1315963175	93	dbSNP
rs1256266768	97	dbSNP
rs1461474763	103	dbSNP
rs1276775042	111	dbSNP
rs931563363	123	dbSNP
rs1166677030	125	dbSNP
rs1332420642	126	dbSNP
rs1467684677	126	dbSNP
rs1048650217	127	dbSNP
rs908702653	130	dbSNP
rs1414474911	139	dbSNP
rs1289883441	147	dbSNP
rs867682530	148	dbSNP
rs1041214888	151	dbSNP
rs901216188	154	dbSNP
rs997346786	162	dbSNP
rs1360492686	165	dbSNP
rs962429511	180	dbSNP
rs546713293	183	dbSNP
rs920872056	184	dbSNP
rs1180223095	194	dbSNP
rs1312595661	196	dbSNP
rs950913857	201	dbSNP
rs1257274216	204	dbSNP
rs1203933634	207	dbSNP
rs983623495	209	dbSNP
rs1280818929	210	dbSNP
rs1217728502	219	dbSNP
rs912104979	237	dbSNP
rs1235153595	238	dbSNP
rs1310475676	240	dbSNP
rs577624873	244	dbSNP
rs1011489319	245	dbSNP
rs1298046581	252	dbSNP
rs544993543	253	dbSNP
rs1360430515	259	dbSNP
rs1328825607	270	dbSNP
rs1380492403	275	dbSNP
rs1039141034	283	dbSNP
rs921985739	287	dbSNP
rs936026831	288	dbSNP
rs1054830183	290	dbSNP
rs1486708879	290	dbSNP
rs891713447	293	dbSNP
rs1003588420	297	dbSNP
rs562943440	299	dbSNP
rs998651359	300	dbSNP
rs1198695191	303	dbSNP
rs1286925826	307	dbSNP
rs1035941832	311	dbSNP
rs1010147301	327	dbSNP
rs1256663227	328	dbSNP
rs1306701526	329	dbSNP
rs1229446333	335	dbSNP
rs1475254932	335	dbSNP
rs1300601189	338	dbSNP
rs530755836	339	dbSNP
rs1360786556	341	dbSNP
rs1409118873	342	dbSNP
rs886051909	342	dbSNP
rs1035511782	343	dbSNP
rs1185902855	343	dbSNP
rs1221287930	343	dbSNP
rs1411482285	343	dbSNP
rs1417475585	343	dbSNP
rs1474887554	343	dbSNP
rs397854666	343	dbSNP
rs1472091329	344	dbSNP
rs991687911	347	dbSNP
rs1485004190	348	dbSNP
rs1159350934	351	dbSNP
rs1260528421	352	dbSNP
rs1365953253	353	dbSNP
rs915561349	356	dbSNP
rs1233199795	359	dbSNP
rs1279502351	359	dbSNP
rs1291918525	359	dbSNP
rs1340670699	359	dbSNP
rs1397800780	360	dbSNP
rs1383730204	379	dbSNP
rs1293923284	381	dbSNP
rs1464821035	387	dbSNP
rs907075225	400	dbSNP
rs1001305949	402	dbSNP
rs1164195403	409	dbSNP
rs1478103703	411	dbSNP
rs1424486075	415	dbSNP
rs983763438	416	dbSNP
rs1426995091	423	dbSNP
rs1261221121	428	dbSNP
rs1034121687	435	dbSNP
rs1302797507	435	dbSNP
rs962749711	439	dbSNP
rs1489707479	448	dbSNP
rs995192843	450	dbSNP
rs1213660495	452	dbSNP
rs756527660	453	dbSNP
rs1224556978	456	dbSNP
rs951026057	459	dbSNP
rs781512302	460	dbSNP
rs780533954	465	dbSNP
rs1301465381	467	dbSNP
rs1388137197	473	dbSNP
rs1365308834	475	dbSNP
rs1324948789	478	dbSNP
rs1466099528	479	dbSNP
rs1306323833	480	dbSNP
rs940278442	481	dbSNP
rs1349926436	487	dbSNP
rs548851878	492	dbSNP
rs1224585291	495	dbSNP
rs983731699	496	dbSNP
rs912127807	497	dbSNP
rs1177147912	507	dbSNP
rs1041182499	520	dbSNP
rs1251572879	534	dbSNP
rs1193338924	536	dbSNP
rs1458627308	536	dbSNP
rs1240494710	537	dbSNP
rs922793934	538	dbSNP
rs141458112	542	dbSNP
rs932747376	547	dbSNP
rs975284786	548	dbSNP
rs147006778	553	dbSNP
rs893911110	557	dbSNP
rs750439577	559	dbSNP
rs1279524141	560	dbSNP
rs1326843690	562	dbSNP
rs1485994219	563	dbSNP
rs1395916011	566	dbSNP
rs1010889927	570	dbSNP
rs1467792074	571	dbSNP
rs936043967	576	dbSNP
rs1347394128	583	dbSNP
rs770233425	585	dbSNP
rs1393455237	589	dbSNP
rs1042417836	590	dbSNP
rs1173407041	592	dbSNP
rs1249045313	607	dbSNP
rs903069658	612	dbSNP
rs1177456162	614	dbSNP
rs546440500	615	dbSNP
rs1431815446	616	dbSNP
rs1256271791	627	dbSNP
rs990247754	628	dbSNP
rs1201633355	631	dbSNP
rs913268128	634	dbSNP
rs183818756	639	dbSNP
rs756202931	640	dbSNP
rs138139662	641	dbSNP
rs1437178820	642	dbSNP
rs1277528136	643	dbSNP
rs1238307040	650	dbSNP
rs1340936328	651	dbSNP
rs960169506	652	dbSNP
rs1012656442	653	dbSNP
rs1312560397	659	dbSNP
rs1288458785	660	dbSNP
rs1362886538	673	dbSNP
rs1157169442	679	dbSNP
rs1370067531	680	dbSNP
rs937203554	681	dbSNP
rs1442964937	682	dbSNP
rs1488627297	691	dbSNP
rs1023107831	705	dbSNP
rs1189035263	710	dbSNP
rs952482124	711	dbSNP
rs1256193332	719	dbSNP
rs1489055832	722	dbSNP
rs1056002598	729	dbSNP
rs983712363	732	dbSNP
rs1015220200	735	dbSNP
rs898250234	738	dbSNP
rs1215166747	741	dbSNP
rs79825013	742	dbSNP
rs1204283250	743	dbSNP
rs1300132702	746	dbSNP
rs1356963864	749	dbSNP
rs995704201	765	dbSNP
rs1386417177	767	dbSNP
rs749291849	768	dbSNP
rs768222606	772	dbSNP
rs1353715156	773	dbSNP
rs922774033	775	dbSNP
rs754993208	776	dbSNP
rs985667060	776	dbSNP
rs915292376	785	dbSNP
rs946792538	786	dbSNP
rs1391891878	806	dbSNP
rs1167826689	807	dbSNP
rs551039985	809	dbSNP
rs1302479388	814	dbSNP
rs1348294146	815	dbSNP
rs886796177	817	dbSNP
rs1416593123	818	dbSNP
rs1007871939	820	dbSNP
rs1272335818	825	dbSNP
rs1239934374	833	dbSNP
rs1306437454	837	dbSNP
rs754772444	846	dbSNP
rs1291754281	849	dbSNP
rs778522390	858	dbSNP
rs1234112742	859	dbSNP
rs966248475	860	dbSNP
rs140828389	865	dbSNP
rs1364367604	866	dbSNP
rs1268701768	867	dbSNP
rs1029614645	870	dbSNP
rs1332083788	872	dbSNP
rs957552420	877	dbSNP
rs771555845	882	dbSNP
rs558365012	890	dbSNP
rs946069490	892	dbSNP
rs1187255559	902	dbSNP
rs981380239	908	dbSNP
rs928566114	911	dbSNP
rs1411093759	915	dbSNP
rs1419359535	931	dbSNP
rs1167030246	940	dbSNP
rs1410612335	942	dbSNP
rs576594709	943	dbSNP
rs937218726	943	dbSNP
rs536979252	944	dbSNP
rs1491434293	949	dbSNP
rs1491237356	950	dbSNP
rs1461164449	951	dbSNP
rs1055715240	952	dbSNP
rs1270937183	952	dbSNP
rs898358057	955	dbSNP
rs555279681	957	dbSNP
rs573424611	959	dbSNP
rs1439073985	968	dbSNP
rs977015981	969	dbSNP
rs886827234	971	dbSNP
rs1007904268	972	dbSNP
rs113827466	978	dbSNP
rs1332694583	981	dbSNP
rs1444980662	984	dbSNP
rs1352301398	991	dbSNP
rs1327575740	992	dbSNP
rs1030306873	993	dbSNP
rs1171541129	1000	dbSNP
rs1453636000	1004	dbSNP
rs1380681186	1006	dbSNP
rs954324315	1013	dbSNP
rs772273914	1014	dbSNP
rs1231277754	1019	dbSNP
rs772930291	1024	dbSNP
rs1282662052	1025	dbSNP
rs374661349	1030	dbSNP
rs1347695032	1033	dbSNP
rs915447741	1036	dbSNP
rs946782541	1037	dbSNP
rs561800501	1047	dbSNP
rs1278475014	1052	dbSNP
rs1448052126	1053	dbSNP
rs996864129	1054	dbSNP
rs1029233331	1056	dbSNP
rs923925976	1058	dbSNP
rs939319349	1060	dbSNP
rs773586107	1061	dbSNP
rs1160962581	1068	dbSNP
rs1417280601	1071	dbSNP
rs1176700910	1079	dbSNP
rs1056486996	1083	dbSNP
rs534415389	1085	dbSNP
rs1274564684	1091	dbSNP
rs895683452	1097	dbSNP
rs1209042595	1101	dbSNP
rs558839176	1103	dbSNP
rs115156410	1105	dbSNP
rs990311695	1106	dbSNP
rs1218336803	1109	dbSNP
rs1315661856	1118	dbSNP
rs1212720862	1120	dbSNP
rs1273375131	1124	dbSNP
rs1044198819	1127	dbSNP
rs544696401	1131	dbSNP
rs746501444	1132	dbSNP
rs562980604	1133	dbSNP
rs1340707067	1134	dbSNP
rs1470120745	1139	dbSNP
rs574874533	1140	dbSNP
rs1241883777	1143	dbSNP
rs386790272	1149	dbSNP
rs11150595	1150	dbSNP
rs967401698	1151	dbSNP
rs561249562	1152	dbSNP
rs1420172039	1153	dbSNP
rs928681178	1156	dbSNP
rs958727266	1157	dbSNP
rs991846125	1162	dbSNP
rs896923265	1171	dbSNP
rs113911928	1181	dbSNP
rs931151555	1186	dbSNP
rs1396889904	1196	dbSNP
rs542904793	1200	dbSNP
rs187212114	1205	dbSNP
rs1007182750	1206	dbSNP
rs191966958	1208	dbSNP
rs1316032967	1216	dbSNP
rs763601477	1220	dbSNP
rs1380161915	1222	dbSNP
rs150230181	1223	dbSNP
rs1040808191	1224	dbSNP
rs1443039706	1230	dbSNP
rs1392148444	1233	dbSNP
rs1162883653	1234	dbSNP
rs1460931918	1253	dbSNP
rs960824935	1256	dbSNP
rs916619657	1259	dbSNP
rs1261501431	1262	dbSNP
rs1194615879	1278	dbSNP
rs551078635	1279	dbSNP
rs559174853	1280	dbSNP
rs1376373000	1288	dbSNP
rs1044312538	1301	dbSNP
rs138815841	1302	dbSNP
rs941167037	1306	dbSNP
rs1293538334	1308	dbSNP
rs1306506748	1315	dbSNP
rs1303915865	1317	dbSNP
rs1336585117	1319	dbSNP
rs1206421029	1326	dbSNP
rs996506490	1338	dbSNP
rs896865898	1340	dbSNP
rs764687119	1348	dbSNP
rs893360192	1349	dbSNP
rs530138953	1350	dbSNP
rs548562535	1351	dbSNP
rs1171308449	1354	dbSNP
rs182162636	1354	dbSNP
rs1397364930	1362	dbSNP
rs1447908063	1366	dbSNP
rs1011709261	1379	dbSNP
rs1218592750	1383	dbSNP
rs1372657408	1384	dbSNP
rs1020373063	1387	dbSNP
rs1174675901	1393	dbSNP
rs1455901997	1396	dbSNP
rs1393648656	1399	dbSNP
rs1193600229	1409	dbSNP
rs1438873473	1410	dbSNP
rs997981704	1411	dbSNP
rs774542153	1416	dbSNP
rs1480108321	1424	dbSNP
rs1280527560	1431	dbSNP
rs762247854	1435	dbSNP
rs534223265	1437	dbSNP
rs889483604	1441	dbSNP
rs1002948620	1448	dbSNP
rs1022525752	1449	dbSNP
rs1035725857	1450	dbSNP
rs1471762291	1455	dbSNP
rs1370017395	1472	dbSNP
rs1313793311	1477	dbSNP
rs767581645	1478	dbSNP
rs999655179	1479	dbSNP
rs375428172	1480	dbSNP
rs1173347456	1482	dbSNP
rs1031176283	1484	dbSNP
rs961067227	1491	dbSNP
rs991475069	1492	dbSNP
rs1401029235	1499	dbSNP
rs186851430	1502	dbSNP
rs992294843	1511	dbSNP
rs916549618	1518	dbSNP
rs919843303	1523	dbSNP
rs1484458601	1528	dbSNP
rs1320225225	1531	dbSNP
rs149364337	1532	dbSNP
rs1205436909	1550	dbSNP
rs952617991	1556	dbSNP
rs984767607	1557	dbSNP
rs909766473	1559	dbSNP
rs1293956436	1566	dbSNP
rs941292927	1566	dbSNP
rs982692900	1572	dbSNP
rs1353750539	1577	dbSNP
rs1036819171	1582	dbSNP
rs750702610	1583	dbSNP
rs775542845	1584	dbSNP
rs933717392	1591	dbSNP
rs1050895076	1593	dbSNP
rs538377567	1596	dbSNP
rs1040838715	1598	dbSNP
rs565076239	1601	dbSNP
rs1259366679	1604	dbSNP
rs1204531202	1609	dbSNP
rs1335337837	1614	dbSNP
rs556662049	1617	dbSNP
rs1235139005	1619	dbSNP
rs1332977478	1623	dbSNP
rs1283882288	1625	dbSNP
rs529260222	1628	dbSNP
rs756182412	1629	dbSNP
rs1053423550	1630	dbSNP
rs896673738	1631	dbSNP
rs1351875190	1656	dbSNP
rs1435053483	1658	dbSNP
rs1395773877	1661	dbSNP
rs1014072339	1662	dbSNP
rs1225771861	1663	dbSNP
rs893382319	1665	dbSNP
rs969460302	1671	dbSNP

- 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.