StarBase v2.0: Decoding miRNA-ceRNA, miRNA-ncRNA and protein-RNA interaction networks from large-scale CLIP-Seq data

Nucleic Acids Research

Volumn 42, Issue D1, 2014, Pages

  Li, Jun Hao ^a   Liu, Shun ^a   Zhou, Hui ^a   Qu, Liang Hu ^a   Yang, Jian Hua ^a  

^a SUN YAT SEN UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

ARGONAUTE PROTEIN; CIRCULAR RIBONUCLEIC ACID; COMPETING ENDOGENOUS RNA; MICRORNA; MICRORNA 21; RNA; RNA BINDING PROTEIN; UNCLASSIFIED DRUG; UNTRANSLATED RNA; LONG UNTRANSLATED RNA; MESSENGER RNA; RNA, CIRCULAR;

ARTICLE; BINDING SITE; COMPUTER GRAPHICS; COMPUTER INTERFACE; DATA ANALYSIS; FUNCTIONAL GENOMICS; GENE REGULATORY NETWORK; GENETIC DATABASE; INFORMATION RETRIEVAL; INFORMATION SERVICE; INTERACTIONS WITH RNA; ONCOGENE; PRIORITY JOURNAL; PROTEIN RNA BINDING; PSEUDOGENE; STARBASE V2.0 DATABASE; ANIMAL; GENOME; HIGH THROUGHPUT SEQUENCING; HUMAN; IMMUNOPRECIPITATION; INTERNET; METABOLISM; MOLECULAR GENETICS; MOUSE; NUCLEIC ACID DATABASE; PROCEDURES; SEQUENCE ANALYSIS; CALCULATION; COMPUTER PREDICTION; COMPUTER PROGRAM; GENE TARGETING; INFORMATION PROCESSING; MATHEMATICAL ANALYSIS; WEB BROWSER;

ANIMALS; ARGONAUTE PROTEINS; BINDING SITES; DATABASES, NUCLEIC ACID; GENE REGULATORY NETWORKS; GENOME; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; IMMUNOPRECIPITATION; INTERNET; MICE; MICRORNAS; MOLECULAR SEQUENCE ANNOTATION; ONCOGENES; PSEUDOGENES; RNA; RNA, LONG NONCODING; RNA, MESSENGER; RNA, UNTRANSLATED; RNA-BINDING PROTEINS; SEQUENCE ANALYSIS, RNA;

EID: 84891818924     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkt1248     Document Type: Article

References (43)

1. Batista, P.J. and Chang, H.Y. (2013) Long noncoding RNAs: cellular address codes in development and disease. Cell, 152, 1298-1307.
2. Yates, L.A., Norbury, C.J. and Gilbert, R.J. (2013) The long and short of microRNA. Cell, 153, 516-519.
3. Salmena, L., Poliseno, L., Tay, Y., Kats, L. and Pandolfi, P.P. (2011) A ceRNA hypothesis: the rosetta stone of a hidden RNA language? Cell, 146, 353-358.
4. Poliseno, L., Salmena, L., Zhang, J., Carver, B., Haveman, W.J. and Pandolfi, P.P. (2010) A coding-independent function of gene and pseudogene mRNAs regulates tumour biology. Nature, 465, 1033-1038.
5. Konig, J., Zarnack, K., Luscombe, N.M. and Ule, J. (2011) Protein-RNA interactions: new genomic technologies and perspectives. Nat. Rev. Genet., 13, 77-83.
6. Memczak, S., Jens, M., Elefsinioti, A., Torti, F., Krueger, J., Rybak, A., Maier, L., Mackowiak, S.D., Gregersen, L.H., Munschauer, M. et al. (2013) Circular RNAs are a large class of animal RNAs with regulatory potency. Nature, 495, 333-338.
7. Hansen, T.B., Jensen, T.I., Clausen, B.H., Bramsen, J.B., Finsen, B., Damgaard, C.K. and Kjems, J. (2013) Natural RNA circles function as efficient microRNA sponges. Nature, 495, 384-388.
8. Gupta, R.A., Shah, N., Wang, K.C., Kim, J., Horlings, H.M., Wong, D.J., Tsai, M.C., Hung, T., Argani, P., Rinn, J.L. et al. (2010) Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis. Nature, 464, 1071-1076.
9. Khalil, A.M., Guttman, M., Huarte, M., Garber, M., Raj, A., Rivea Morales, D., Thomas, K., Presser, A., Bernstein, B.E., van Oudenaarden, A. et al. (2009) Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression. Proc. Natl Acad. Sci. USA, 106, 11667-11672.
10. Cesana, M., Cacchiarelli, D., Legnini, I., Santini, T., Sthandier, O., Chinappi, M., Tramontano, A. and Bozzoni, I. (2011) A long noncoding RNA controls muscle differentiation by functioning as a competing endogenous RNA. Cell, 147, 358-369.
11. Franco-Zorrilla, J.M., Valli, A., Todesco, M., Mateos, I., Puga, M.I., Rubio-Somoza, I., Leyva, A., Weigel, D., Garcia, J.A. and Paz-Ares, J. (2007) Target mimicry provides a new mechanism for regulation of microRNA activity. Nat. Genet., 39, 1033-1037.
12. Tay, Y., Kats, L., Salmena, L., Weiss, D., Tan, S.M., Ala, U., Karreth, F., Poliseno, L., Provero, P., Di Cunto, F. et al. (2011) Coding-independent regulation of the tumor suppressor PTEN by competing endogenous mRNAs. Cell, 147, 344-357.
13. Karreth, F.A., Tay, Y., Perna, D., Ala, U., Tan, S.M., Rust, A.G., DeNicola, G., Webster, K.A., Weiss, D., Perez-Mancera, P.A. et al. (2011) In vivo identification of tumor-suppressive PTEN ceRNAs in an oncogenic BRAF-induced mouse model of melanoma. Cell, 147, 382-395.
14. Sumazin, P., Yang, X., Chiu, H.S., Chung, W.J., Iyer, A., Llobet-Navas, D., Rajbhandari, P., Bansal, M., Guarnieri, P., Silva, J. et al. (2011) An extensive microRNA-mediated network of RNA-RNA interactions regulates established oncogenic pathways in glioblastoma. Cell, 147, 370-381.
15. Darnell, R.B. (2010) HITS-CLIP: panoramic views of protein-RNA regulation in living cells. Wiley Interdiscip. Rev. RNA, 1, 266-286.
16. Ascano, M., Hafner, M., Cekan, P., Gerstberger, S. and Tuschl, T. (2012) Identification of RNA-protein interaction networks using PAR-CLIP. Wiley Interdiscip. Rev. RNA, 3, 159-177.
17. Yang, J.H., Li, J.H., Shao, P., Zhou, H., Chen, Y.Q. and Qu, L.H. (2011) starBase: a database for exploring microRNA-mRNA interaction maps from Argonaute CLIP-Seq and Degradome-Seq data. Nucleic Acids Res., 39, D202-D209.
18. Khorshid, M., Rodak, C. and Zavolan, M. (2011) CLIPZ: a database and analysis environment for experimentally determined binding sites of RNA-binding proteins. Nucleic Acids Res., 39, D245-D252.
19. Anders, G., Mackowiak, S.D., Jens, M., Maaskola, J., Kuntzagk, A., Rajewsky, N., Landthaler, M. and Dieterich, C. (2012) doRiNA: a database of RNA interactions in post-transcriptional regulation. Nucleic Acids Res., 40, D180-D186.
20. Jalali, S., Bhartiya, D., Lalwani, M.K., Sivasubbu, S. and Scaria, V. (2013) Systematic transcriptome wide analysis of lncRNA-miRNA interactions. PLoS One, 8, e53823.
21. Paraskevopoulou, M.D., Georgakilas, G., Kostoulas, N., Reczko, M., Maragkakis, M., Dalamagas, T.M. and Hatzigeorgiou, A.G. (2013) DIANA-LncBase: experimentally verified and computationally predicted microRNA targets on long non-coding RNAs. Nucleic Acids Res., 41, D239-D245.
22. Barrett, T., Wilhite, S.E., Ledoux, P., Evangelista, C., Kim, I.F., Tomashevsky, M., Marshall, K.A., Phillippy, K.H., Sherman, P.M., Holko, M. et al. (2013) NCBI GEO: archive for functional genomics data sets-update. Nucleic Acids Res., 41, D991-D995.
23. Corcoran, D.L., Georgiev, S., Mukherjee, N., Gottwein, E., Skalsky, R.L., Keene, J.D. and Ohler, U. (2011) PARalyzer: definition of RNA binding sites from PAR-CLIP short-read sequence data. Genome Biol., 12, R79.
24. Meyer, L.R., Zweig, A.S., Hinrichs, A.S., Karolchik, D., Kuhn, R.M., Wong, M., Sloan, C.A., Rosenbloom, K.R., Roe, G., Rhead, B. et al. (2013) The UCSC Genome Browser database: extensions and updates 2013. Nucleic Acids Res., 41, D64-D69.
25. Grimson, A., Farh, K.K., Johnston, W.K., Garrett-Engele, P., Lim, L.P. and Bartel, D.P. (2007) MicroRNA targeting specificity in mammals: determinants beyond seed pairing. Mol. Cell, 27, 91-105.
26. Kozomara, A. and Griffiths-Jones, S. (2011) miRBase: integrating microRNA annotation and deep-sequencing data. Nucleic Acids Res., 39, D152-D157.
27. Betel, D., Koppal, A., Agius, P., Sander, C. and Leslie, C. (2010) Comprehensive modeling of microRNA targets predicts functional non-conserved and non-canonical sites. Genome Biol., 11, R90.
28. 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.
29. Miranda, K.C., Huynh, T., Tay, Y., Ang, Y.S., Tam, W.L., Thomson, A.M., Lim, B. and Rigoutsos, I. (2006) A pattern-based method for the identification of MicroRNA binding sites and their corresponding heteroduplexes. Cell, 126, 1203-1217.
30. Quinlan, A.R. and Hall, I.M. (2010) BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics, 26, 841-842.
31. Harrow, J., Frankish, A., Gonzalez, J.M., Tapanari, E., Diekhans, M., Kokocinski, F., Aken, B.L., Barrell, D., Zadissa, A., Searle, S. et al. (2012) GENCODE: the reference human genome annotation for The ENCODE Project. Genome Res., 22, 1760-1774.
32. Benjamini, Y. and Hochberg, Y. (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. R. Stat. Soc. Ser. B, 57, 289-300.
33. Ashburner, M., Ball, C.A., Blake, J.A., Botstein, D., Butler, H., Cherry, J.M., Davis, A.P., Dolinski, K., Dwight, S.S., Eppig, J.T. et al. (2000) Gene Ontology: tool for the unification of biology. Nat. Genet., 25, 25-29.
34. Kanehisa, M., Goto, S., Sato, Y., Furumichi, M. and Tanabe, M. (2012) KEGG for integration and interpretation of large-scale molecular data sets. Nucleic Acids Res., 40, D109-DD114.
35. Mi, H., Lazareva-Ulitsky, B., Loo, R., Kejariwal, A., Vandergriff, J., Rabkin, S., Guo, N., Muruganujan, A., Doremieux, O., Campbell, M.J. et al. (2005) The PANTHER database of protein families, subfamilies, functions and pathways. Nucleic Acids Res., 33, D284-D288.
36. Matthews, L., Gopinath, G., Gillespie, M., Caudy, M., Croft, D., de Bono, B., Garapati, P., Hemish, J., Hermjakob, H., Jassal, B. et al. (2009) Reactome knowledgebase of human biological pathways and processes. Nucleic Acids Res., 37, D619-D622.
37. Liberzon, A., Subramanian, A., Pinchback, R., Thorvaldsdottir, H., Tamayo, P. and Mesirov, J.P. (2011) Molecular signatures database (MSigDB) 3.0. Bioinformatics, 27, 1739-1740.
38. Kuhn, R.M., Karolchik, D., Zweig, A.S., Wang, T., Smith, K.E., Rosenbloom, K.R., Rhead, B., Raney, B.J., Pohl, A., Pheasant, M. et al. (2009) The UCSC Genome Browser Database: update 2009. Nucleic Acids Res., 37, D755-D761.
39. Hubbard, T.J., Aken, B.L., Ayling, S., Ballester, B., Beal, K., Bragin, E., Brent, S., Chen, Y., Clapham, P., Clarke, L. et al. (2009) Ensembl 2009. Nucleic Acids Res., 37, D690-D697.
40. Hsu, S.D., Lin, F.M., Wu, W.Y., Liang, C., Huang, W.C., Chan, W.L., Tsai, W.T., Chen, G.Z., Lee, C.J., Chiu, C.M. et al. (2011) miRTarBase: a database curates experimentally validated microRNA-target interactions. Nucleic Acids Res., 39, D163-DD169.
41. Dooley, A.L., Winslow, M.M., Chiang, D.Y., Banerji, S., Stransky, N., Dayton, T.L., Snyder, E.L., Senna, S., Whittaker, C.A., Bronson, R.T. et al. (2011) Nuclear factor I/B is an oncogene in small cell lung cancer. Gene Dev., 25, 1470-1475.
42. Moon, H.G., Hwang, K.T., Kim, J.A., Kim, H.S., Lee, M.J., Jung, E.M., Ko, E., Han, W. and Noh, D.Y. (2011) NFIB is a potential target for estrogen receptor-negative breast cancers. Mol. Oncol., 5, 538-544.
43. Liu, K., Yan, Z., Li, Y. and Sun, Z. (2013) Linc2GO: a human LincRNA function annotation resource based on ceRNA hypothesis. Bioinformatics, 29, 2221-2222.