>RPS21|NM_001024|3'UTR
   1 CTGGAGAGAATCACAGATGTGGAATATTTGTCATAAATAAATAATGAAAACCTAAAAAAAAAAAAAAAAAAAAAAA

ID	Duplex structure	Position	Score	MFE
1	miRNA 3' aaguaACCUGAC-----GACUACcgga 5' |||| | | |||| Target 5' ----cTGGAGAGAATCACAGATGtgga 3'	1 - 23	85.00	-6.80

Mutant ID	Mutant Position	Mutant Source
COSN30116005	7	COSMIC
COSN30155131	13	COSMIC
COSN30157359	17	COSMIC
COSN31561026	17	COSMIC
COSN30480915	25	COSMIC
COSN30152687	33	COSMIC
COSN1083052	43	COSMIC
COSN25796932	52	COSMIC

Mutant ID	Mutant Position	Mutant Source
rs772136838	2	dbSNP
rs780134477	16	dbSNP
rs747194934	17	dbSNP
rs201393003	20	dbSNP
rs114402901	21	dbSNP
rs1395723122	24	dbSNP
rs770198489	27	dbSNP
rs1471255407	28	dbSNP
rs1385214031	29	dbSNP
rs773703409	30	dbSNP
rs765291578	33	dbSNP
rs998401785	33	dbSNP
rs763382420	34	dbSNP
rs200506514	36	dbSNP
rs199998702	38	dbSNP
rs1404114209	39	dbSNP
rs752525519	42	dbSNP
rs1483137577	43	dbSNP
rs1201326372	45	dbSNP
rs1004245899	46	dbSNP
rs1446028055	47	dbSNP
rs755999197	49	dbSNP
rs1388975495	51	dbSNP
rs1429117749	52	dbSNP
rs763798161	53	dbSNP
rs753763497	54	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.