ID	Duplex structure	Position	Score	MFE
1	miRNA 3' uuACUGGGAUGGAUAAGUCAGUc 5' || | ||:|: ||||||| Target 5' gcTGCCAGCACTTGGTCAGTCAc 3'	1158 - 1180	157.00	-14.50
2	miRNA 3' uuaCUGGGAUGGAUAAGUCAGUc 5' |||:| || |||| || Target 5' gcgGACTCATCC---TCAGCCAg 3'	174 - 193	121.00	-14.70
3	miRNA 3' uuaCUGGGA-UGGAUAAGUC----AGUc 5' ||| || ||:| ||||| ||| Target 5' ctgGACACTCACTTTTTCAGAGACTCAa 3'	55 - 82	116.00	-11.92

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

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

- 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.

- 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.