MiRDeep*: An integrated application tool for miRNA identification from RNA sequencing data

Nucleic Acids Research

Volumn 41, Issue 2, 2013, Pages 727-737

  An, Jiyuan ^a   Lai, John ^a   Lehman, Melanie L ^a,b   Nelson, Colleen C ^a,b  

^a QUEENSLAND UNIVERSITY OF TECHNOLOGY   (Australia)

^b UNIVERSITY OF BRITISH COLUMBIA   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

MICRORNA;

ALGORITHM; ARTICLE; CANCER CELL CULTURE; COMPUTER PROGRAM; CONTROLLED STUDY; GENE TARGETING; GENETIC DATABASE; HUMAN; HUMAN CELL; INFORMATION PROCESSING; MALE; MIRDEEP; PRIORITY JOURNAL; PROSTATE CANCER; PROTEIN SECONDARY STRUCTURE; RNA ANALYSIS; RNA SEQUENCE; RNA STRUCTURE; RNA TRANSCRIPTION; SEQUENCE ALIGNMENT; CHEMISTRY; GENE EXPRESSION PROFILING; GENETICS; HIGH THROUGHPUT SEQUENCING; METABOLISM; PROSTATE TUMOR; SEQUENCE ANALYSIS; TUMOR CELL LINE;

CELL LINE, TUMOR; GENE EXPRESSION PROFILING; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; MALE; MICRORNAS; PROSTATIC NEOPLASMS; SEQUENCE ANALYSIS, RNA; SOFTWARE;

MLCS; MLOWN;

EID: 84875476368     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gks1187     Document Type: Article

References (48)

1. Yang, J.S. and Lai, E.C. (2011) Alternative miRNA biogenesis pathways and the interpretation of core miRNA pathway mutants. Mol. Cell., 43, 892-903.
2. 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.
3. Djuranovic, S., Nahvi, A. and Green, R. (2011) A parsimonious model for gene regulation by miRNAs. Science, 331, 550-553.
4. Catto, J.W., Alcaraz, A., Bjartell, A.S., De Vere White, R., Evans, C.P., Fussel, S., Hamdy, F.C., Kallioniemi, O., Mengual, L., Schlomm, T. et al. (2011) MicroRNA in prostate, bladder, and kidney cancer: a systematic review. Eur. Urol., 59, 671-681.
5. Wang, D. and Tindall, D.J. (2011) Androgen action during prostate carcinogenesis. Methods Mol. Biol., 776, 25-44.
6. Perner, S., Mosquera, J.M., Demichelis, F., Hofer, M.D., Paris, P.L., Simko, J., Collins, C., Bismar, T.A., Chinnaiyan, A.M., De Marzo, A.M. et al. (2007) TMPRSS2-ERG fusion prostate cancer: an early molecular event associated with invasion. Am. J. Surg. Pathol., 31, 882-888. (Pubitemid 47165141)
7. Tomlins, S.A., Laxman, B., Varambally, S., Cao, X., Yu, J., Helgeson, B.E., Cao, Q., Prensner, J.R., Rubin, M.A., Shah, R.B. et al. (2008) Role of the TMPRSS2-ERG gene fusion in prostate cancer. Neoplasia, 10, 177-188. (Pubitemid 351240884)
8. Wang, W.L., Chatterjee, N., Chittur, S.V., Welsh, J. and Tenniswood, M.P. (2011) Effects of 1alpha, 25 dihydroxyvitamin D3 and testosterone on miRNA and mRNA expression in LNCaP cells. Mol. Cancer, 10, 58.
9. Ribas, J., Ni, X., Haffner, M., Wentzel, E.A., Salmasi, A.H., Chowdhury, W.H., Kudrolli, T.A., Yegnasubramanian, S., Luo, J., Rodriguez, R. et al. (2009) miR-21: an androgen receptor-regulated microRNA that promotes hormone-dependent and hormone-independent prostate cancer growth. Cancer Res., 69, 7165-7169.
10. Watahiki, A., Wang, Y., Morris, J., Dennis, K., O'Dwyer, H.M., Gleave, M. and Gout, P.W. (2011) MicroRNAs associated with metastatic prostate cancer. PLoS One, 6, e24950.
11. Martens-Uzunova, E.S., Jalava, S.E., Dits, N.F., van Leenders, G.J., Moller, S., Trapman, J., Bangma, C.H., Litman, T., Visakorpi, T. and Jenster, G. (2012) Diagnostic and prognostic signatures from the small non-coding RNA transcriptome in prostate cancer. Oncogene, 31, 978-991.
12. Ostling, P., Leivonen, S.K., Aakula, A., Kohonen, P., Makela, R., Hagman, Z., Edsjo, A., Kangaspeska, S., Edgren, H., Nicorici, D. et al. (2011) Systematic analysis of microRNAs targeting the androgen receptor in prostate cancer cells. Cancer Res., 71, 1956-1967.
13. Hackenberg, M., Rodriguez-Ezpeleta, N. and Aransay, A.M. (2011) miRanalyzer: an update on the detection and analysis of microRNAs in high-throughput sequencing experiments. Nucleic Acids Res., 39, W132-W138.
14. Hendrix, D., Levine, M. and Shi, W. (2010) miRTRAP, a computational method for the systematic identification of miRNAs from high throughput sequencing data. Genome Biol., 11, R39.
15. Mathelier, A. and Carbone, A. (2010) MIReNA: finding microRNAs with high accuracy and no learning at genome scale and from deep sequencing data. Bioinformatics, 26, 2226-2234.
16. Friedlander, M.R., Chen, W., Adamidi, C., Maaskola, J., Einspanier, R., Knespel, S. and Rajewsky, N. (2008) Discovering microRNAs from deep sequencing data using miRDeep. Nat. Biotechnol., 26, 407-415. (Pubitemid 351501815)
17. Friedlander, M.R., Mackowiak, S.D., Li, N., Chen, W. and Rajewsky, N. (2012) miRDeep2 accurately identifies known and hundreds of novel microRNA genes in seven animal clades. Nucleic Acids Res., 40, 37-52.
18. Langmead, B., Trapnell, C., Pop, M. and Salzberg, S.L. (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol., 10, R25.
19. Li, R., Yu, C., Li, Y., Lam, T.W., Yiu, S.M., Kristiansen, K. and Wang, J. (2009) SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics, 25, 1966-1967.
20. Hofacker, I.L. (2003) Vienna RNA secondary structure server. Nucleic Acids Res., 31, 3429-3431. (Pubitemid 37442172)
21. 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. (Pubitemid 40094598)
22. 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. (Pubitemid 46991392)
23. Friedman, R.C., Farh, K.K., Burge, C.B. and Bartel, D.P. (2009) Most mammalian mRNAs are conserved targets of microRNAs. Genome Res., 19, 92-105.
24. 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. (Pubitemid 351482785)
25. Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G. and Durbin, R. (2009) The sequence alignment/map format and SAMtools. Bioinformatics, 25, 2078-2079.
26. Moxon, S., Schwach, F., Dalmay, T., Maclean, D., Studholme, D.J. and Moulton, V. (2008) A toolkit for analysing large-scale plant small RNA datasets. Bioinformatics, 24, 2252-2253.
27. Friedlander, M.R., Chen, W., Adamidi, C., Maaskola, J., Einspanier, R., Knespel, S. and Rajewsky, N. (2008) Discovering microRNAs from deep sequencing data using miRDeep. Nat. Biotechnol., 26, 407-415. (Pubitemid 351501815)
28. Hofacker, I.L. (2003) Vienna RNA secondary structure server. Nucleic Acids Res., 31, 3429-3431. (Pubitemid 37442172)
29. Maragkakis, M., Vergoulis, T., Alexiou, P., Reczko, M., Plomaritou, K., Gousis, M., Kourtis, K., Koziris, N., Dalamagas, T. and Hatzigeorgiou, A.G. (2011) DIANA-microT Web server upgrade supports Fly and Worm miRNA target prediction and bibliographic miRNA to disease association. Nucleic Acids Res., 39, W145-W148.
30. Enright, A.J., John, B., Gaul, U., Tuschl, T., Sander, C. and Marks, D.S. (2003) MicroRNA targets in Drosophila. Genome Biol., 5, R1.
31. Bandyopadhyay, S. and Mitra, R. (2009) TargetMiner: microRNA target prediction with systematic identification of tissue-specific negative examples. Bioinformatics, 25, 2625-2631.
32. Wang, X. (2006) Systematic identification of microRNA functions by combining target prediction and expression profiling. Nucleic Acids Res., 34, 1646-1652.
33. Chen, C., Ridzon, D.A., Broomer, A.J., Zhou, Z., Lee, D.H., Nguyen, J.T., Barbisin, M., Xu, N.L., Mahuvakar, V.R., Andersen, M.R. et al. (2005) Real-time quantification of microRNAs by stem-loop RT-PCR. Nucleic Acids Res., 33, e179.
34. Cheng, A., Li, M., Liang, Y., Wang, Y., Wong, L., Chen, C., Vlassov, A.V. and Magdaleno, S. (2009) Stem-loop RT-PCR quantification of siRNAs in vitro and in vivo. Oligonucleotides, 19, 203-208.
35. Kaushal, A., Myers, S.A., Dong, Y., Lai, J., Tan, O.L., Bui, L.T., Hunt, M.L., Digby, M.R., Samaratunga, H., Gardiner, R.A. et al. (2008) A novel transcript from the KLKP1 gene is androgen regulated, down-regulated during prostate cancer progression and encodes the first non-serine protease identified from the human kallikrein gene locus. Prostate, 68, 381-399. (Pubitemid 351342644)
36. Griffiths-Jones, S., Saini, H.K., van Dongen, S. and Enright, A.J. (2008) miRBase: tools for microRNA genomics. Nucleic Acids Res., 36, D154-D158. (Pubitemid 351149713)
37. Tempel, S. and Tahi, F. (2012) A fast ab-initio method for predicting miRNA precursors in genomes. Nucleic Acids Res., 40, e80.
38. Farazi, T.A., Horlings, H.M., Ten Hoeve, J.J., Mihailovic, A., Halfwerk, H., Morozov, P., Brown, M., Hafner, M., Reyal, F., van Kouwenhove, M. et al. (2011) MicroRNA sequence and expression analysis in breast tumors by deep sequencing. Cancer Res., 71, 4443-4453.
39. Martens-Uzunova, E.S., Jalava, S.E., Dits, N.F., van Leenders, G.J., Moller, S., Trapman, J., Bangma, C.H., Litman, T., Visakorpi, T. and Jenster, G. (2011) Diagnostic and prognostic signatures from the small non-coding RNA transcriptome in prostate cancer. Oncogene, 31, 978-991.
40. Massard, C. and Fizazi, K. (2011) Targeting continued androgen receptor signaling in prostate cancer. Clin. Cancer Res., 17, 3876-3883.
41. Yang, J.H., Zhang, X.C., Huang, Z.P., Zhou, H., Huang, M.B., Zhang, S., Chen, Y.Q. and Qu, L.H. (2006) snoSeeker: an advanced computational package for screening of guide and orphan snoRNA genes in the human genome. Nucleic Acids Res., 34, 5112-5123. (Pubitemid 44742476)
42. 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.
43. Friedlander, M.R., Mackowiak, S.D., Li, N., Chen, W. and Rajewsky, N. (2012) miRDeep2 accurately identifies known and hundreds of novel microRNA genes in seven animal clades. Nucleic Acids Res., 40, 37-52.
44. 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.
45. Pantano, L., Estivill, X. and Marti, E. (2010) SeqBuster, a bioinformatic tool for the processing and analysis of small RNAs datasets, reveals ubiquitous miRNA modifications in human embryonic cells. Nucleic Acids Res., 38, e34.
46. 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.
47. Ronen, R., Gan, I., Modai, S., Sukacheov, A., Dror, G., Halperin, E. and Shomron, N. (2010) miRNAkey: a software for microRNA deep sequencing analysis. Bioinformatics, 26, 2615-2616.
48. Huang, P.J., Liu, Y.C., Lee, C.C., Lin, W.C., Gan, R.R., Lyu, P.C. and Tang, P. (2010) DSAP: deep-sequencing small RNA analysis pipeline. Nucleic Acids Res., 38, W385-W391.