ToppMiR: Ranking microRNAs and their mRNA targets based on biological functions and context

Nucleic Acids Research

Volumn 42, Issue W1, 2014, Pages

  Wu, Chao ^a,b   Bardes, Eric E ^b   Jegga, Anil G ^a,b,c   Aronow, Bruce J ^a,b,c  

^a University of Cincinnati   (United States)

^b CINCINNATI CHILDREN'S HOSPITAL MEDICAL CENTER   (United States)

^c UNIVERSITY OF CINCINNATI   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA; MICRORNA;

ARTICLE; COMPUTER PROGRAM; DATA ANALYSIS; GENE EXPRESSION; GENE FUNCTION; GENE MUTATION; GENE TARGETING; GENETIC DATABASE; GENETIC VARIABILITY; MACHINE LEARNING; MEDLINE; MOLECULAR GENETICS; PRIORITY JOURNAL; PROTEIN INTERACTION;

GENE EXPRESSION PROFILING; GENE REGULATORY NETWORKS; INTERNET; MICRORNAS; RNA, MESSENGER; SOFTWARE;

EID: 84904820430     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gku409     Document Type: Article

References (44)

1. Nam,S., Li,M., Choi,K., Balch,C., Kim,S. and Nephew,K.P. (2009) MicroRNA and mRNA integrated analysis (MMIA): a web tool for examining biological functions of microRNA expression. Nucleic Acids Res., 37, W356-W362.
2. Mestdagh,P., Lefever,S., Pattyn,F., Ridzon,D., Fredlund,E., Fieuw,A., Ongenaert,M., Vermeulen,J., De Paepe,A., Wong,L. et al. (2011) The microRNA body map: dissecting microRNA function through integrative genomics. Nucleic Acids Res., 39, e136-e136.
3. Cho,S., Jun,Y., Lee,S., Choi,H.-S., Jung,S., Jang,Y., Park,C., Kim,S., Lee,S. and Kim,W. (2010) miRGator v2.0: an integrated system for functional investigation of microRNAs. Nucleic Acids Res., 39, D158-D162.
4. Bisognin,A., Sales,G., Coppe,A., Bortoluzzi,S. and Romualdi,C. (2012) MAGIA2: from miRNA and genes expression data integrative analysis to microRNA-transcription factor mixed regulatory circuits (2012 update). Nucleic Acids Res, 40, W13-W21.
5. Suzuki,H.I., Mihira,H., Watabe,T., Sugimoto,K. and Miyazono,K. (2012) Widespread inference of weighted microRNA-mediated gene regulation in cancer transcriptome analysis. Nucleic Acids Res., 41, e62-e62.
6. Bryan,K., Terrile,M., Bray,I.M., Domingo-Fernandéz,R., Watters,K.M., Koster,J., Versteeg,R. and Stallings,R.L. (2014) Discovery and visualization of miRNA-mRNA functional modules within integrated data using bicluster analysis. Nucleic Acids Res., 42, e17.
7. Li,J., Zhang,Y., Wang,Y., Zhang,C., Wang,Q., Shi,X., Li,C., Zhang,R. and Li,X. (2014) Functional combination strategy for prioritization of human miRNA target. Gene, 533, 132-141.
8. Chen,J., Bardes,E.E., Aronow,B.J. and Jegga,A.G. (2009) ToppGene Suite for gene list enrichment analysis and candidate gene prioritization. Nucleic Acids Res., 37, W305-W311.
9. Shannon,P., Markiel,A., Ozier,O., Baliga,N.S., Wang,J.T., Ramage,D., Amin,N., Schwikowski,B. and Ideker,T. (2003) Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res., 13, 2498-2504.
10. Bastian,M., Heymann,S. and Jacomy,M. (2009), Gephi: an open source software for exploring and manipulating networks. International AAAI Conference on Weblogs and Social Media. http://gephi.org/publications/gephi-bastian-feb09. pdf (13 May 2014, date last accessed).
11. 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.
12. Grün,D., Wang,Y.-L., Langenberger,D., Gunsalus,K.C. and Rajewsky,N. (2005) microRNA target predictions across seven Drosophila species and comparison to mammalian targets. PLoS Comput. Biol., 1, e13.
13. Lall,S., Grun,D., Krek,A., Chen,K., Wang,Y.-L., Dewey,C.N., Sood,P., Colombo,T., Bray,N., MacMenamin,P. et al. (2006) A genome-wide map of conserved microRNA targets in C. elegans. Curr. Biol., 16, 460-471.
14. Chen,K. and Rajewsky,N. (2006) Natural selection on human microRNA binding sites inferred from SNP data. Nat. Genet., 38, 1452-1456.
15. 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.
16. Betel,D., Wilson,M., Gabow,A., Marks,D.S. and Sander,C. (2008) The microRNA.org resource: targets and expression. Nucleic Acids Res., 36, D149-D153.
17. 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.
18. Friedman,RC, Farh,KK, Burge,CB and Bartel,DP. (2009) Most mammalian mRNAs are conserved targets of microRNAs. Genome Res., 19, 92-105.
19. Grimson,A., Farh,K.K.-H., 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.
20. Garcia,D.M., Baek,D., Shin,C., Bell,G.W., Grimson,A. and Bartel,D.P. (2011) Weak seed-pairing stability and high target-site abundance decrease the proficiency of lsy-6 and other microRNAs. Nat. Struct. Mol. Biol., 18, 1139-1146.
21. Subramanian,A., Tamayo,P., Mootha,V.K., Mukherjee,S., Ebert,B.L., Gillette,M.A., Paulovich,A., Pomeroy,S.L., Golub,T.R., Lander,E.S. et al. (2005) Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc. Natl. Acad. Sci. U.S.A., 102, 15545-15550.
22. Liberzon,A., Subramanian,A., Pinchback,R., Thorvaldsdóttir,H., Tamayo,P. and Mesirov,J.P. (2011) Molecular signatures database (MSigDB) 3.0. Bioinformatics, 27, 1739-1740.
23. 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.
24. 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-D110.
25. 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-D169.
26. Sethupathy,P., Megraw,M. and Hatzigeorgiou,A.G. (2006) A guide through present computational approaches for the identification of mammalian microRNA targets. Nat. Methods, 3, 881-886.
27. Maglott,D., Ostell,J., Pruitt,K.D. and Tatusova,T. (2011) Entrez Gene: gene-centered information at NCBI. Nucleic Acids Res., 39, D52-D57.
28. Kleinberg,J.M. (1999) Authoritative sources in a hyperlinked environment. J. ACM, 46, 604-632.
29. White,S. and Smyth,P. (2003), Proceedings of the ninth ACM SIGKDD International Conference on Knowledge Discovery and Data Mining. ACM, Washington, DC, pp. 266-275.
30. Madadhain,J., Fisher,D., Smyth,P. and Boey,Y. (2005) Analysis and visualization of network data using JUNG. J. Stat. Softw., 10, 1-35.
31. Zheng,B., Liang,L., Huang,S., Zha,R., Liu,L., Jia,D., Tian,Q., Wang,Q., Wang,C., Long,Z. et al. (2011) MicroRNA-409 suppresses tumour cell invasion and metastasis by directly targeting radixin in gastric cancers. Oncogene, 31, 4509-4516.
32. Futreal,P.A., Coin,L., Marshall,M., Down,T., Hubbard,T., Wooster,R., Rahman,N. and Stratton,M.R. (2004) A census of human cancer genes. Nat. Rev. Cancer, 4, 177-183.
33. Kim,J., Yoon,H., Ramírez,C.M., Lee,S.-M., Hoe,H.-S., Fernández-Hernando,C. and Kim,J. miR-106b impairs cholesterol efflux and increases A levels by repressing ABCA1 expression. Exp. Neurol.235(2) 476-483
34. Yang,B., Lin,H., Xiao,J., Lu,Y., Luo,X., Li,B., Zhang,Y., Xu,C., Bai,Y., Wang,H. et al. (2011) The muscle-specific microRNA miR-1 regulates cardiac arrhythmogenic potential by targeting GJA1 and KCNJ2. Nat. Med., 13, 486-491.
35. Rebustini,I.T., Hayashi,T., Reynolds,A.D., Dillard,M.L., Carpenter,E.M. and Hoffman,M.P. (2012) miR-200c regulates FGFR-dependent epithelial proliferation via Vldlr during submandibular gland branching morphogenesis. Development, 139, 191-202.
36. Schwanhäusser,B., Gossen,M., Dittmar,G. and Selbach,M. (2009) Global analysis of cellular protein translation by pulsed SILAC. Proteomics, 9, 205-209.
37. Selbach,M., Schwanhausser,B., Thierfelder,N., Fang,Z., Khanin,R. and Rajewsky,N. (2008) Widespread changes in protein synthesis induced by microRNAs. Nature, 455, 58-63.
38. Chen,J., Xu,H., Aronow,B. and Jegga,A. (2007) Improved human disease candidate gene prioritization using mouse phenotype. BMC Bioinformatics, 8, 392
39. Mallon,B.S., Chenoweth,J.G., Johnson,K.R., Hamilton,R.S., Tesar,P.J., Yavatkar,A.S., Tyson,L.J., Park,K., Chen,K.G. and Fann,Y.C. (2013) StemCellDB: the human pluripotent stem cell database at the National Institutes of Health. Stem Cell Res., 10, 57-66.
40. Kawamoto,S., Yoshii,J., Mizuno,K., Ito,K., Miyamoto,Y., Ohnishi,T., Matoba,R., Hori,N., Matsumoto,Y., Okumura,T. et al. (2000) BodyMap: a collection of 3 ESTs for analysis of human gene expression information. Genome Res., 10, 1817-1827.
41. Sese,J., Nikaidou,H., Kawamoto,S.,Minesaki,Y., Morishita,S. and Okubo,K. (2001) BodyMap incorporated PCR-based expression profiling data and a gene ranking system. Nucleic Acids Res., 29, 156-158.
42. Jiang,Q., Hao,Y., Wang,G., Juan,L., Zhang,T., Teng,M., Liu,Y. and Wang,Y. (2010) Prioritization of disease microRNAs through a human phenome-microRNAome network. BMC Syst. Biol., 4, S2
43. Palla,G., Derenyi,I., Farkas,I. and Vicsek,T. (2005) Uncovering the overlapping community structure of complex networks in nature and society. Nature, 435, 814-818.
44. Lempel,R. and Moran,S. (2000) SALSA: the stochastic approach for link-structure analysis. ACM Transact. Inf. Syst., 19, 387-401.