MiRspring: A compact standalone research tool for analyzing miRNA-seq data

Nucleic Acids Research

Volumn 41, Issue 15, 2013, Pages

  Humphreys, David T ^a,b   Suter, Catherine M ^a,b  

^a VICTOR CHANG CARDIAC RESEARCH INSTITUTE   (Australia)

^b UNIVERSITY OF NEW SOUTH WALES   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

MICRORNA;

ARTICLE; CONTROLLED STUDY; DATA ANALYSIS SOFTWARE; DATA PROCESSING; GENE CLUSTER; GENE EXPRESSION; GENETIC ALGORITHM; GENETIC DATABASE; GENETIC VARIABILITY; GENOMICS; HUMAN; HUMAN TISSUE; PRIORITY JOURNAL; QUALITY CONTROL; REPRODUCIBILITY; RESEARCH; RNA ANALYSIS; RNA PROCESSING; RNA SEQUENCE; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS;

ALGORITHMS; DATABASES, NUCLEIC ACID; GENE EXPRESSION PROFILING; GENOME, HUMAN; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; INTERNET; INVERTED REPEAT SEQUENCES; MICRORNAS; SEQUENCE ANALYSIS, RNA; SOFTWARE;

EID: 84883480053     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkt485     Document Type: Article

References (29)

1. Cheng,W.C., Chung,I.F., Huang,T.S., Chang,S.T., Sun,H.J., Tsai,C.F., Liang,M.L., Wong,T.T. and Wang,H.W. (2013) YM500: a small RNA sequencing (smRNA-seq) database for microRNA research. Nucleic Acids Res., 41, D285-D294
2. Cho,S., Jang,I., Jun,Y., Yoon,S., Ko,M., Kwon,Y., Choi,I., Chang,H., Ryu,D., Lee,B. et al. (2013) MiRGator v3.0: a microRNA portal for deep sequencing, expression profiling and mRNA targeting. Nucleic Acids Res., 41, D252-D257
3. Hackenberg,M., Sturm,M., Langenberger,D., Falcon-Perez,J.M. and Aransay,A.M. (2009) miRanalyzer: a microRNA detection and analysis tool for next-generation sequencing experiments. Nucleic Acids Res., 37, W68-W76
4. Kozomara,A. and Griffiths-Jones,S. (2011) miRBase: integrating microRNA annotation and deep-sequencing data. Nucleic Acids Res., 39, D152-D157
5. Lee,L.W., Zhang,S., Etheridge,A., Ma,L., Martin,D., Galas,D. and Wang,K. (2010) Complexity of the microRNA repertoire revealed by next-generation sequencing. RNA, 16, 2170-2180
6. Xie,F., Xiao,P., Chen,D., Xu,L. and Zhang,B. (2012) miRDeepFinder: a miRNA analysis tool for deep sequencing of plant small RNAs. Plant Mol. Biol., 80, 75-84
7. Yang,J.H., Shao,P., Zhou,H., Chen,Y.Q. and Qu,L.H. (2010) deepBase: a database for deeply annotating and mining deep sequencing data. Nucleic Acids Res., 38, D123-D130
8. Zhu,E., Zhao,F., Xu,G., Hou,H., Zhou,L., Li,X., Sun,Z. and Wu,J. (2010) mirTools: microRNA profiling and discovery based on high-throughput sequencing. Nucleic Acids Res., 38, W392-W397
9. Humphreys,D.T., Hynes,C.J., Patel,H.R., Wei,G.H., Cannon,L., Fatkin,D., Suter,C.M., Clancy,J.L. and Preiss,T. (2012) Complexity of murine cardiomyocyte miRNA biogenesis, sequence variant expression and function. PLoS One, 7, e30933
10. Sakib,M.N., Tang,J., Zheng,W.J. and Huang,C.T. (2011) Improving transmission efficiency of large sequence alignment/map (SAM) files. PLoS One, 6, e28251
11. Creighton,C.J., Reid,J.G. and Gunaratne,P.H. (2009) Expression profiling of microRNAs by deep sequencing. Brief. Bioinform., 10, 490-497
12. Cloonan,N., Wani,S., Xu,Q., Gu,J., Lea,K., Heater,S., Barbacioru,C., Steptoe,A.L., Martin,H.C., Nourbakhsh,E. et al. (2011) MicroRNAs and their isomiRs function cooperatively to target common biological pathways. Genome Biol., 12, R126
13. Burroughs,A.M., Ando,Y., de Hoon,M.J., Tomaru,Y., Suzuki,H., Hayashizaki,Y. and Daub,C.O. (2011) Deep-sequencing of human Argonaute-associated small RNAs provides insight into miRNA sorting and reveals Argonaute association with RNA fragments of diverse origin. RNA Biol., 8, 158-177
14. Consortium,E.P. (2011) A user's guide to the encyclopedia of DNA elements (ENCODE). PLoS Biol., 9, e1001046
15. Fejes-Toth,K., Sotirova,V., Sachidanandam,R., Assaf,G., Hannon,G.J., Kapranov,P., Foissac,S., Willingham,A.T., Duttagupta,R., Dumais,E. et al. (2009) Post-transcriptional processing generates a diversity of 50-modified long and short RNAs. Nature, 457, 1028-1032
16. Alon,S., Vigneault,F., Eminaga,S., Christodoulou,D.C., Seidman,J.G., Church,G.M. and Eisenberg,E. (2011) Barcoding bias in high-throughput multiplex sequencing of miRNA. Genome Res., 21, 1506-1511
17. Hafner,M., Renwick,N., Brown,M., Mihailovic,A., Holoch,D., Lin,C., Pena,J.T., Nusbaum,J.D., Morozov,P., Ludwig,J. et al. (2011) RNA-ligase-dependent biases in miRNA representation in deep-sequenced small RNA cDNA libraries. RNA, 17, 1697-1712
18. Toedling,J., Servant,N., Ciaudo,C., Farinelli,L., Voinnet,O., Heard,E. and Barillot,E. (2012) Deep-sequencing protocols influence the results obtained in small-RNA sequencing. PLoS One, 7, e32724
19. Hagan,J.P., Piskounova,E. and Gregory,R.I. (2009) Lin28 recruits the TUTase Zcchc11 to inhibit let-7 maturation in mouse embryonic stem cells. Nat. Struct. Mol. Biol., 16, 1021-1025
20. Heo,I., Ha,M., Lim,J., Yoon,M.J., Park,J.E., Kwon,S.C., Chang,H. and Kim,V.N. (2012) Mono-uridylation of premicroRNA as a key step in the biogenesis of group II let-7 microRNAs. Cell, 151, 521-532
21. Heo,I., Joo,C., Kim,Y.K., Ha,M., Yoon,M.J., Cho,J., Yeom,K.H., Han,J. and Kim,V.N. (2009) TUT4 in concert with Lin28 suppresses microRNA biogenesis through pre-microRNA uridylation. Cell, 138, 696-708
22. Rau,F., Freyermuth,F., Fugier,C., Villemin,J.P., Fischer,M.C., Jost,B., Dembele,D., Gourdon,G., Nicole,A., Duboc,D. et al. (2011) Misregulation of miR-1 processing is associated with heart defects in myotonic dystrophy. Nat. Struct. Mol. Biol., 18, 840-845
23. Baskerville,S. and Bartel,D.P. (2005) Microarray profiling of microRNAs reveals frequent coexpression with neighboring miRNAs and host genes. RNA, 11, 241-247
24. Leung,W.S., Lin,M.C., Cheung,D.W. and Yiu,S.M. (2008) Filtering of false positive microRNA candidates by a clusteringbased approach. BMC Bioinformatics, 9(Suppl
25. Morin,R.D., O'Connor,M.D., Griffith,M., Kuchenbauer,F., Delaney,A., Prabhu,A.L., Zhao,Y., McDonald,H., Zeng,T., Hirst,M. et al. (2008) Application of massively parallel sequencing to microRNA profiling and discovery in human embryonic stem cells. Genome Res., 18, 610-621
26. Thomas,M., Lieberman,J. and Lal,A. (2010) Desperately seeking microRNA targets. Nat. Struct. Mol. Biol., 17, 1169-1174
27. Mondol,V. and Pasquinelli,A.E. (2012) Let's make it happen: the role of let-7 microRNA in development. Curr. Top. Dev. Biol., 99, 1-30
28. Hornstein,E., Mansfield,J.H., Yekta,S., Hu,J.K., Harfe,B.D., McManus,M.T., Baskerville,S., Bartel,D.P. and Tabin,C.J. (2005) The microRNA miR-196 acts upstream of Hoxb8 and Shh in limb development. Nature, 438, 671-674
29. De Martino,I., Visone,R., Fedele,M., Petrocca,F., Palmieri,D., Martinez Hoyos,J., Forzati,F., Croce,C.M. and Fusco,A. (2009) Regulation of microRNA expression by HMGA1 proteins. Oncogene, 28, 1432-1442.