IsomiRex: Web-based identification of microRNAs, isomiR variations and differential expression using next-generation sequencing datasets

FEBS Letters

Volumn 587, Issue 16, 2013, Pages 2629-2634

  Sablok, Gaurav ^a   Milev, Ivan ^b   Minkov, Georgi ^b   Minkov, Ivan ^b   Varotto, Claudio ^a   Yahubyan, Galina ^b   Baev, Vesselin ^b  

^a RESEARCH AND INNOVATION CENTRE   (Italy)

^b UNIVERSITY OF PLOVDIV   (Bulgaria)

Author keywords

isomiRs; MicroRNA; Next generation sequencing; Web platform

Indexed keywords

MICRORNA;

ARTICLE; GENE EXPRESSION; INTERNET; NEXT GENERATION SEQUENCE; ONLINE SYSTEM; PRIORITY JOURNAL; REFERENCE DATABASE; RNA SEQUENCE; SEQUENCE ANALYSIS;

ISOMIRS; MICRORNA; NEXT GENERATION SEQUENCING; WEB PLATFORM;

ALGORITHMS; ANIMALS; BASE SEQUENCE; DATABASES, GENETIC; GENE EXPRESSION PROFILING; HUMANS; INTERNET; MICRORNAS; MOLECULAR SEQUENCE DATA; REPRODUCIBILITY OF RESULTS; SEQUENCE ANALYSIS, RNA; SEQUENCE HOMOLOGY, NUCLEIC ACID; SOFTWARE;

ANIMALIA;

EID: 84881480813     PISSN: 00145793     EISSN: 18733468     Source Type: Journal    
DOI: 10.1016/j.febslet.2013.06.047     Document Type: Article

References (26)

1. D.P. Bartel MicroRNAs: genomics, biogenesis, mechanism, and function Cell 116 2004 281 297
2. D. Klevebring, N.R. Street, N. Fahlgren, K.D. Kasschau, J.C. Carrington, J. Lundeberg, and S. Jansson Genome-wide profiling of populus small RNAs BMC Genomics 10 2009 620
3. R. Sunkar, and G. Jagadeeswaran In silico identification of conserved microRNAs in large number of diverse plant species BMC Plant Biol. 8 2008 37
4. R. Sunkar, X. Zhou, Y. Zheng, W. Zhang, and J.K. Zhu Identification of novel and candidate miRNAs in rice by high throughput sequencing BMC Plant Biol. 8 2008 25
5. I. Alvarez-Garcia, and E.A. Miska MicroRNA functions in animal development and human disease Development 132 2005 4653 4662
6. J. Lu, G. Getz, E.A. Miska, E. Alvarez-Saavedra, J. Lamb, D. Peck, A. Sweet-Cordero, B.L. Ebert, R.H. Mak, A.A. Ferrando, J.R. Downing, T. Jacks, H.R. Horvitz, and T.R. Golub MicroRNA expression profiles classify human cancers Nature 435 2005 834 838
7. S. Volinia, G.A. Calin, C.G. Liu, S. Ambs, A. Cimmino, F. Petrocca, R. Visone, M. Iorio, C. Roldo, M. Ferracin, R.L. Prueitt, N. Yanaihara, G. Lanza, A. Scarpa, A. Vecchione, M. Negrini, C.C. Harris, and C.M. Croce A microRNA expression signature of human solid tumors defines cancer gene targets Proc. Natl. Acad. Sci. USA 103 2006 2257 2261
8. J. Stenvang, and S. Kauppinen MicroRNAs as targets for antisense-based therapeutics Expert Opin. Biol. Ther. 8 2008 59 81
9. J. Stenvang, M. Lindow, and S. Kauppinen Targeting of microRNAs for therapeutics Biochem. Soc. Trans. 36 2008 1197 1200
10. C.T. Neilsen, G.J. Goodall, and C.P. Bracken IsomiRs - the overlooked repertoire in the dynamic microRNAome Trends Genet. 28 2012 544 549
11. F. Llorens, M. Banez-Coronel, L. Pantano, J.A. Del Rio, I. Ferrer, X. Estivill, and E. Marti A highly expressed miR-101 isomiR is a functional silencing small RNA BMC Genomics 14 2013 104
12. N. Cloonan, S. Wani, Q. Xu, J. Gu, K. Lea, S. Heater, C. Barbacioru, A.L. Steptoe, H.C. Martin, E. Nourbakhsh, K. Krishnan, B. Gardiner, X. Wang, K. Nones, J.A. Steen, N.A. Matigian, D.L. Wood, K.S. Kassahn, N. Waddell, J. Shepherd, C. Lee, J. Ichikawa, K. McKernan, K. Bramlett, S. Kuersten, and S.M. Grimmond MicroRNAs and their isomiRs function cooperatively to target common biological pathways Genome Biol. 12 2011 R126
13. L. Guo, H. Li, T. Liang, J. Lu, Q. Yang, Q. Ge, and Z. Lu Consistent isomiR expression patterns and 3 addition events in miRNA gene clusters and families implicate functional and evolutionary relationships Mol. Biol. Rep. 39 2012 6699 6706
14. M. Colaiacovo, L. Bernardo, I. Centomani, C. Crosatti, L. Giusti, L. Orru, G. Tacconi, A. Lamontanara, L. Cattivelli, and P. Faccioli A survey of microRNA length variants contributing to miRnome complexity in peach (Prunus persica L.) Front. Plant Sci. 3 2012 165
15. F. Ahmed, and P.X. Zhao A comprehensive analysis of isomirs and their targets using high-throughput sequencing data for Arabidopsis thaliana J. Nat. Sci. Biol. Med. 2 2011 2
16. B. Georgieva, I. Milev, I. Minkov, I. Dimitrova, A.P. Bradford, and V. Baev Characterization of the uterine leiomyoma microRNAome by deep sequencing Genomics 99 2012 275 281
17. S. Griffiths-Jones, H.K. Saini, S. van Dongen, and A.J. Enright MiRBase: tools for microRNA genomics Nucleic Acids Res. 36 2008 D154 D158
18. B. Langmead, C. Trapnell, M. Pop, and S.L. Salzberg Ultrafast and memory-efficient alignment of short DNA sequences to the human genome Genome Biol. 10 2009 R25
19. S. Anders, and W. Huber Differential expression analysis for sequence count data Genome Biol. 11 2010 R106
20. S.L. Fernandez-Valverde, R.J. Taft, and J.S. Mattick Dynamic isomiR regulation in Drosophila development RNA 16 2010 1881 1888
21. R.D. Morin, M.D. O'Connor, M. Griffith, F. Kuchenbauer, A. Delaney, A.L. Prabhu, Y. Zhao, H. McDonald, T. Zeng, M. Hirst, C.J. Eaves, and M.A. Marra Application of massively parallel sequencing to microRNA profiling and discovery in human embryonic stem cells Genome Res. 18 2008 610 621
22. L.W. Lee, S. Zhang, A. Etheridge, and L. Ma Complexity of the microRNA repertoire revealed by next generation sequencing RNA 16 2010 2170 2180
23. W.C. Cheng, I.F. Chung, T.S. Huang, S.T. Chang, H.J. Sun, C.F. Tsai, M.L. Liang, T.T. Wong, and H.W. Wang YM500: a small RNA sequencing (smRNA-seq) database for microRNA research Nucleic Acids Res. 41 2013 D285 D294
24. H. Zhou, M.L. Arcila, Z. Li, E.J. Lee, C. Henzler, and J. Liu Deep annotation of mouse iso-miR and iso-moR variation Nucleic Acids Res. 40 2012 5864 5875
25. L. Pantano, X. Estivill, and E. Marti SeqBuster, a bioinformatics tool for the processing and analysis of small RNAs datasets, reveals ubiquitous miRNA modifications in human embryonic cells Nucleic Acids Res. 38 2010 e34
26. J. Ma, S. Yu, F. Wang, L. Bai, J. Xiao, Y. Jiang, L. Chen, J. Wang, A. Jiang, M. Li, and X. Li MicroRNA transcriptomes relate intermuscular adipose tissue to metabolic risk Int. J. Mol. Sci. 14 2013 8611 8624