MirTools 2.0 for non-coding RNA discovery, profiling and functional annotation based on high-throughput sequencing

RNA Biology

Volumn 10, Issue 7, 2013, Pages 1087-1092

  Wu, Jinyu ^a,b   Liu, Qi ^b   Wang, Xin ^b   Zheng, Jiayong ^c   Wang, Tao ^b   You, Mingcong ^b   Sun, Zhong Sheng ^b,d   Shi, Qinghua ^a  

^a UNIVERSITY OF SCIENCE AND TECHNOLOGY OF CHINA   (China)

^b WENZHOU MEDICAL UNIVERSITY   (China)

^c WENZHOU PEOPLE'S HOSPITAL   (China)

^d INSTITUTE OF GEOLOGY AND GEOPHYSICS   (China)

Author keywords

Mirna; Mirna targets; Mirtools; Ncrna; Next generation sequencing; Web server

Indexed keywords

MICRORNA; PIWI INTERACTING RNA; RIBOSOME RNA; SMALL NUCLEAR RNA; SMALL NUCLEOLAR RNA; TRANSCRIPTOME; TRANSFER RNA; UNTRANSLATED RNA;

ARTICLE; COMPUTER PROGRAM; CONTROLLED STUDY; GENE EXPRESSION; GENETIC ANALYSIS; HIGH THROUGHPUT SEQUENCING; MIRTOOL 2; PROTEIN PROTEIN INTERACTION; TAXONOMY;

MIRNA; MIRNA TARGETS; MIRTOOLS; NCRNA; NEXT-GENERATION SEQUENCING; WEB SERVER;

COMPUTATIONAL BIOLOGY; DATABASES, NUCLEIC ACID; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; INTERNET; MICRORNAS; MOLECULAR SEQUENCE ANNOTATION; RNA, UNTRANSLATED; TRANSCRIPTOME;

EID: 84880902774     PISSN: 15476286     EISSN: 15558584     Source Type: Journal    
DOI: 10.4161/rna.25193     Document Type: Article

References (36)

1. David R. Non-coding RNAS: A new member of the family. Nat Rev Mol Cell Biol 2012; 13:686; PMID:23011341; http://dx.doi.org/10.1038/nrm3449.
2. Ebert MS, Sharp PA. Roles for microRNAs in conferring robustness to biological processes. Cell 2012; 149:515-24; PMID:22541426; http://dx.doi.org/ 10.1016/j.cell.2012.04.005.
3. Karijolich J, Yu YT. Spliceosomal snRNA modifications and their function. RNA Biol 2010; 7:192-204; PMID:20215871; http://dx.doi.org/10.4161/rna.7.2. 11207.
4. Taft RJ, Glazov EA, Lassmann T, Hayashizaki Y, Carninci P, Mattick JS. Small RNAs derived from snoRNAs. RNA 2009; 15:1233-40; PMID:19474147; http://dx.doi.org/10.1261/rna.1528909.
5. Juliano C, Wang J, Lin H. Uniting germline and stem cells: The function of Piwi proteins and the piRNA pathway in diverse organisms. Annu Rev Genet 2011; 45:447-69; PMID:21942366; http://dx.doi.org/10.1146/annurev-genet-110410- 132541.
6. Rajasethupathy P, Antonov I, Sheridan R, Frey S, Sander C, Tuschl T, et al. A role for neuronal piRNAs in the epigenetic control of memory-related synaptic plasticity. Cell 2012; 149:693-707; PMID:22541438; http://dx.doi.org/ 10.1016/j.cell.2012.02.057.
7. Zhou L, Li X, Liu Q, Zhao F, Wu J. Small RNA transcriptome investigation based on next-generation sequencing technology. J Genet Genomics 2011; 38:505-13; PMID:22133681; http://dx.doi.org/10.1016/j.jgg.2011.08.006.
8. Friedländer MR, Chen W, Adamidi C, Maaskola J, Einspanier R, Knespel S, et al. Discovering microRNAs from deep sequencing data using miRDeep. Nat Biotechnol 2008; 26:407-15; PMID:18392026; http://dx.doi.org/10.1038/nbt1394.
9. Friedländer MR, Mackowiak SD, Li N, Chen W, Rajewsky N. miRDeep2 accurately identifies known and hundreds of novel microRNA genes in seven animal clades. Nucleic Acids Res 2012; 40:37-52; PMID:21911355; http://dx.doi.org/10. 1093/nar/gkr688.
10. Yang X, Li L. miRDeep-P: A computational tool for analyzing the microRNA transcriptome in plants. Bioinformatics 2011; 27:2614-5; PMID:21775303; http://dx.doi.org/10.1093/bioinformatics/btr430.
11. Ritchie W, Théodule FX, Gautheret D. Mireval: A web tool for simple microRNA prediction in genome sequences. Bioinformatics 2008; 24:1394-6; PMID:18453555; http://dx.doi.org/10.1093/bioinformatics/btn137.
12. Huang TH, Fan B, Rothschild MF, Hu ZL, Li K, Zhao SH. MiRFinder: An improved approach and software implementation for genome-wide fast microRNA precursor scans. BMC Bioinformatics 2007; 8:341; PMID:17868480; http://dx.doi.org/10.1186/1471-2105-8-341.
13. Ronen R, Gan I, Modai S, Sukacheov A, Dror G, Halperin E, et al. miRNAkey: A software for microRNA deep sequencing analysis. Bioinformatics 2010; 26:2615-6; PMID:20801911; http://dx.doi.org/10.1093/bioinformatics/btq493.
14. Hackenberg M, Sturm M, Langenberger D, Falcón-Pérez JM, Aransay AM. miRanalyzer: A microRNA detection and analysis tool for next-generation sequencing experiments. Nucleic Acids Res 2009; 37(Web Server issue):W68-76; PMID:19433510; http://dx.doi.org/10.1093/nar/gkp347.
15. Wang WC, Lin FM, Chang WC, Lin KY, Huang HD, Lin NS. miRExpress: Analyzing high-throughput sequencing data for profiling microRNA expression. BMC Bioinformatics 2009; 10:328; PMID:19821977; http://dx.doi.org/10.1186/1471- 2105-10-328.
16. Hendrix D, Levine M, Shi W. miRTRAP, a computational method for the systematic identification of miRNAs from high throughput sequencing data. Genome Biol 2010; 11:R39; PMID:20370911; http://dx.doi.org/10.1186/gb-2010-11-4-r39.
17. Huang PJ, Liu YC, Lee CC, Lin WC, Gan RR, Lyu PC, et al. DSAP: deep-sequencing small RNA analysis pipeline. Nucleic Acids Res 2010; 38(Web Server issue):W385-91; PMID:20478825; http://dx.doi.org/10.1093/nar/gkq392.
18. Mathelier A, Carbone A. MIReNA: finding microRNAs with high accuracy and no learning at genome scale and from deep sequencing data. Bioinformatics 2010; 26:2226-34; PMID:20591903; http://dx.doi.org/10.1093/bioinformatics/btq329.
19. Pantano L, Estivill X, Martí E. A non-biased framework for the annotation and classification of the non-miRNA small RNA transcriptome. Bioinformatics 2011; 27:3202-3; PMID:21976421; http://dx.doi.org/10.1093/ bioinformatics/btr527.
20. Fasold M, Langenberger D, Binder H, Stadler PF, Hoffmann S. DARIO: A ncRNA detection and analysis tool for next-generation sequencing experiments. Nucleic Acids Res 2011; 39(Web Server issue):W112-7; PMID:21622957; http://dx.doi.org/10.1093/nar/gkr357.
21. Chen CJ, Servant N, Toedling J, Sarazin A, Marchais A, Duvernois-Berthet E, et al. ncPRO-seq: A tool for annotation and profiling of ncRNAs in sRNA-seq data. Bioinformatics 2012; 28:3147-9; PMID:23044543; http://dx.doi.org/10.1093/ bioinformatics/bts587.
22. Zhang Y, Xu B, Yang Y, Ban R, Zhang H, Jiang X, et al. CPSS: A computational platform for the analysis of small RNA deep sequencing data. Bioinformatics 2012; 28:1925-7; PMID:22576177; http://dx.doi.org/10.1093/ bioinformatics/bts282.
23. Gupta V, Markmann K, Pedersen CN, Stougaard J, Andersen SU. shortran: A pipeline for small RNAseq data analysis. Bioinformatics 2012; 28:2698-700; PMID:22914220; http://dx.doi.org/10.1093/bioinformatics/bts496.
24. Ragan C, Mowry BJ, Bauer DC. Hybridizationbased reconstruction of small non-coding RNA transcripts from deep sequencing data. Nucleic Acids Res 2012; 40:7633-43; PMID:22705792; http://dx.doi.org/10.1093/nar/gks505.
25. Zywicki M, Bakowska-Zywicka K, Polacek N. Revealing stable processing products from ribosome-Associated small RNAs by deep-sequencing data analysis. Nucleic Acids Res 2012; 40:4013-24; PMID:22266655; http://dx.doi.org/10.1093/ nar/gks020.
26. Salari R, Aksay C, Karakoc E, Unrau PJ, Hajirasouliha I, Sahinalp SC. smyRNA: A novel Ab initio ncRNA gene finder. PLoS One 2009; 4:e5433; PMID:19415115; http://dx.doi.org/10.1371/journal.pone.0005433.
27. Zhu E, Zhao F, Xu G, Hou H, Zhou L, Li X, et al. mirTools: microRNA profiling and discovery based on high-throughput sequencing. Nucleic Acids Res 2010; 38(Web Server issue):W392-7; PMID:20478827; http://dx.doi.org/10.1093/nar/ gkq393.
28. Li Y, Zhang Z, Liu F, Vongsangnak W, Jing Q, Shen B. Performance comparison and evaluation of software tools for microRNA deep-sequencing data analysis. Nucleic Acids Res 2012; 40:4298-305; PMID:22287634; http://dx.doi.org/10.1093/nar/gks043.
29. Li R, Yu C, Li Y, Lam TW, Yiu SM, Kristiansen K, et al. SOAP2: An improved ultrafast tool for short read alignment. Bioinformatics 2009; 25:1966-7; PMID:19497933; http://dx.doi.org/10.1093/bioinformatics/btp336.
30. Cheng WC, Chung IF, Huang TS, Chang ST, Sun HJ, Tsai CF, et al. YM500: A small RNA sequencing (smRNA-seq) database for microRNA research. Nucleic Acids Res 2013; 41(Database issue):D285-94; PMID:23203880; http://dx.doi.org/10.1093/ nar/gks1238.
31. Zhang Y, Wang X, Kang L. A k-mer scheme to predict piRNAs and characterize locust piRNAs. Bioinformatics 2011; 27:771-6; PMID:21224287; http://dx.doi.org/10.1093/bioinformatics/btr016.
32. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, et al.; The Gene Ontology Consortium. Gene ontology: Tool for the unification of biology. Nat Genet 2000; 25:25-9; PMID:10802651; http://dx.doi.org/10.1038/ 75556.
33. Kanehisa M, Goto S, Furumichi M, Tanabe M, Hirakawa M. KEGG for representation and analysis of molecular networks involving diseases and drugs. Nucleic Acids Res 2010; 38(Database issue):D355-60; PMID:19880382; http://dx.doi.org/10.1093/nar/gkp896.
34. Jensen LJ, Kuhn M, Stark M, Chaffron S, Creevey C, Muller J, et al. STRING 8-A global view on proteins and their functional interactions in 630 organisms. Nucleic Acids Res 2009; 37(Database issue):D412-6; PMID:18940858; http://dx.doi.org/10.1093/nar/gkn760.
35. Lopes CT, Franz M, Kazi F, Donaldson SL, Morris Q, Bader GD. Cytoscape Web: An interactive web-based network browser. Bioinformatics 2010; 26:2347-8; PMID:20656902; http://dx.doi.org/10.1093/bioinformatics/btq430.
36. Audic S, Claverie JM. The significance of digital gene expression profiles. Genome Res 1997; 7:986-95; PMID:9331369.