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Welcome to mirTarPri
- mirTarPri is a web toolkit for prioritising candidate mirRNA targets in the context of functional genomic data. This method uses complementary information drawn from the semantic similarities of Gene Ontology [1] and distance proximity within protein protein interaction networks. In mirTarPri, prioritised candidate target genes for a specific miRNA are ranked according to their semantic similarity and distance proximity to known experimentally validated target genes (derived from tarBase [2], mirRecord [3] and mir2Disease [4]).
- mirTarPri provides users three branches (BP, MF, CC) of GeneOntology and six human protein-protein interaction networks (HPRD, MINT, BIND, IntAct, BioGrid, OPHID [5-10]) served as functional data context. Users can chose each two of them to prioritize candidate miRNA target list.
- mirTarPri also provides a full prioritized mirRNA target list of six commonly used methods (TargetScan, PicTar, PITA, DIANA-microT, miRanda and RNAhybrid [11-17]).
- mirTarPri will be regularly updated functional genomic data for user the most up-to-data results.
References
1. Massanet, R., Gallardo-Chacon, J.J., Caminal, P. and Perera, A. (2009) Search of phenotype related candidate genes using gene ontology-based semantic similarity and protein interaction information: application to Brugada syndrome. Conf Proc IEEE Eng Med Biol Soc, 2009, 7079-7082.
2. Papadopoulos, G.L., Reczko, M., Simossis, V.A., Sethupathy, P. and Hatzigeorgiou, A.G. (2009) The database of experimentally supported targets: a functional update of TarBase. Nucleic Acids Res, 37, D155-158.
3. Jiang, Q., Wang, Y., Hao, Y., Juan, L., Teng, M., Zhang, X., Li, M., Wang, G. and Liu, Y. (2009) miR2Disease: a manually curated database for microRNA deregulation in human disease. Nucleic Acids Res, 37, D98-104.
4. Xiao, F., Zuo, Z., Cai, G., Kang, S., Gao, X. and Li, T. (2009) miRecords: an integrated resource for microRNA-target interactions. Nucleic Acids Res, 37, D105-110.
5. Keshava Prasad, T.S., Goel, R., Kandasamy, K., Keerthikumar, S., Kumar, S., Mathivanan, S., Telikicherla, D., Raju, R., Shafreen, B., Venugopal, A. et al. (2009) Human Protein Reference Database--2009 update. Nucleic Acids Res, 37, D767-772.
6. Bader, G.D. and Hogue, C.W. (2000) BIND--a data specification for storing and describing biomolecular interactions, molecular complexes and pathways. Bioinformatics, 16, 465-477.
7. Chatr-aryamontri, A., Ceol, A., Palazzi, L.M., Nardelli, G., Schneider, M.V., Castagnoli, L. and Cesareni, G. (2007) MINT: the Molecular INTeraction database. Nucleic Acids Res, 35, D572-574.
8. Stark, C., Breitkreutz, B.J., Reguly, T., Boucher, L., Breitkreutz, A. and Tyers, M. (2006) BioGRID: a general repository for interaction datasets. Nucleic Acids Res, 34, D535-539.
9. Aranda, B., Achuthan, P., Alam-Faruque, Y., Armean, I., Bridge, A., Derow, C., Feuermann, M., Ghanbarian, A.T., Kerrien, S., Khadake, J. et al. The IntAct molecular interaction database in 2010. Nucleic Acids Res, 38, D525-531.
10. Brown, K.R. and Jurisica, I. (2005) Online predicted human interaction database. Bioinformatics, 21, 2076-2082.
11. Lewis, B.P., Shih, I.H., Jones-Rhoades, M.W., Bartel, D.P. and Burge, C.B. (2003) Prediction of mammalian microRNA targets. Cell, 115, 787-798.
12. Kertesz, M., Iovino, N., Unnerstall, U., Gaul, U. and Segal, E. (2007) The role of site accessibility in microRNA target recognition. Nat Genet, 39, 1278-1284.
13. Enright, A.J., John, B., Gaul, U., Tuschl, T., Sander, C. and Marks, D.S. (2003) MicroRNA targets in Drosophila. Genome Biol, 5, R1.
14. Kiriakidou, M., Nelson, P.T., Kouranov, A., Fitziev, P., Bouyioukos, C., Mourelatos, Z. and Hatzigeorgiou, A. (2004) A combined computational-experimental approach predicts human microRNA targets. Genes Dev, 18, 1165-1178.
15. Lewis, B.P., Burge, C.B. and Bartel, D.P. (2005) Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell, 120, 15-20.
16. Krek, A., Grun, D., Poy, M.N., Wolf, R., Rosenberg, L., Epstein, E.J., MacMenamin, P., da Piedade, I., Gunsalus, K.C., Stoffel, M. et al. (2005) Combinatorial microRNA target predictions. Nat Genet, 37, 495-500.
17. Rehmsmeier M, Steffen P, Hochsmann M, Giegerich R (2004) Fast and effective prediction of microRNA/target duplexes. Rna 10: 1507-1517
Contact Us
- Please email: lixia@hrbmu.edu.cn when you have any questions or problems about using mirTarPri.