MiREvo: An integrative microRNA evolutionary analysis platform for next-generation sequencing experiments

BMC Bioinformatics

Volumn 13, Issue 1, 2012, Pages

  Wen, Ming ^a   Shen, Yang ^a   Shi, Suhua ^a   Tang, Tian ^a  

^a SUN YAT SEN UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

ARABIDOPSIS; BIOLOGICAL PROCESS; COMPUTATIONAL TOOLS; DROSOPHILA MELANOGASTER; EVOLUTIONARY DISTANCE; EVOLUTIONARY DYNAMICS; GRAPHICAL USER INTERFACES (GUI); ILLUMINA; INTEGRATED SOFTWARE; MICRORNAS; MIRNA EXPRESSIONS; MULTIPLE SPECIES; NEXT-GENERATION SEQUENCING; NON-CODING RNAS; SMALL RNA; WHOLE GENOME ALIGNMENT;

ANIMALS; DYNAMICS; GRAPHICAL USER INTERFACES;

RNA;

ANIMALIA; ARABIDOPSIS; DROSOPHILA MELANOGASTER;

MICRORNA; TRANSCRIPTOME; UNTRANSLATED RNA;

ALGORITHM; ANIMAL; ARABIDOPSIS; ARTICLE; COMPUTER PROGRAM; DROSOPHILA MELANOGASTER; GENETICS; HIGH THROUGHPUT SEQUENCING; MOLECULAR EVOLUTION; SEQUENCE ANALYSIS;

ALGORITHMS; ANIMALS; ARABIDOPSIS; DROSOPHILA MELANOGASTER; EVOLUTION, MOLECULAR; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; MICRORNAS; RNA, UNTRANSLATED; SEQUENCE ANALYSIS, RNA; SOFTWARE; TRANSCRIPTOME;

EID: 84862488733     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-13-140     Document Type: Article

References (41)

1. Bartel DP. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 2004, 116(2):281-297. 10.1016/S0092-8674(04)00045-5, 14744438.
2. Voinnet O. Origin, biogenesis, and activity of plant microRNAs. Cell 2009, 136(4):669-687. 10.1016/j.cell.2009.01.046, 19239888.
3. Millar AA, Waterhouse PM. Plant and animal microRNAs: similarities and differences. Funct Integr Genomics 2005, 5(3):129-135. 10.1007/s10142-005-0145-2, 15875226.
4. Gerlach D, Kriventseva EV, Rahman N, Vejnar CE, Zdobnov EM. miROrtho: computational survey of microRNA genes. Nucleic Acids Res 2009, 37:D111-D117. 10.1093/nar/gkn707, 2686488, 18927110.
5. Thakur V, Wanchana S, Xu M, Bruskiewich R, Quick WP, Mosig A, Zhu XG. Characterization of statistical features for plant microRNA prediction. BMC Genomics 2011, 12:108. 10.1186/1471-2164-12-108, 3053258, 21324149.
6. Willmann MR, Poethig RS. Conservation and evolution of miRNA regulatory programs in plant development. Curr Opin Plant Biol 2007, 10(5):503-511. 10.1016/j.pbi.2007.07.004, 2080797, 17709279.
7. Adai A, Johnson C, Mlotshwa S, Archer-Evans S, Manocha V, Vance V, Sundaresan V. Computational prediction of miRNAs in Arabidopsis thaliana. Genome Res 2005, 15(1):78-91. 10.1101/gr.2908205, 540280, 15632092.
8. Berezikov E, Guryev V, van de Belt J, Wienholds E, Plasterk RH, Cuppen E. Phylogenetic shadowing and computational identification of human microRNA genes. Cell 2005, 120(1):21-24. 10.1016/j.cell.2004.12.031, 15652478.
9. Yang X, Li L. miRDeep-P: a computational tool for analyzing the microRNA transcriptome in plants. Bioinformatics 2011, 27:2614-2615.
10. Thomas M, Lieberman J, Lal A. Desperately seeking microRNA targets. Nat Struct Mol Biol 2010, 17(10):1169-1174. 10.1038/nsmb.1921, 20924405.
11. Meyers BC, Axtell MJ, Bartel B, Bartel DP, Baulcombe D, Bowman JL, Cao X, Carrington JC, Chen X, Green PJ, Griffiths-Jones S, Jacobsen SE, Mallory AC, Martienssen RA, Poethig RS, Qi Y, Vaucheret H, Voinnet O, Watanabe Y, Weigel D, Zhu JK. Criteria for annotation of plant MicroRNAs. Plant Cell 2008, 20(12):3186-3190. 10.1105/tpc.108.064311, 2630443, 19074682.
12. Berezikov E, Robine N, Samsonova A, Westholm JO, Naqvi A, Hung JH, Okamura K, Dai Q, Bortolamiol-Becet D, Martin R, Zhao Y, Zamore PD, Hannon GJ, Marra MA, Weng Z, Perrimon N, Lai EC. Deep annotation of Drosophila melanogaster microRNAs yields insights into their processing, modification, and emergence. Genome Res 2011, 21(2):203-215. 10.1101/gr.116657.110, 3032924, 21177969.
13. Song C, Wang C, Zhang C, Korir NK, Yu H, Ma Z, Fang J. Deep sequencing discovery of novel and conserved microRNAs in trifoliate orange (Citrus trifoliata). BMC Genomics 2010, 11:431. 10.1186/1471-2164-11-431, 2996959, 20626894.
14. Wang J, Czech B, Crunk A, Wallace A, Mitreva M, Hannon GJ, Davis RE. Deep small RNA sequencing from the nematode Ascaris reveals conservation, functional diversification, and novel developmental profiles. Genome Res 2011, 21:1462-1477. 10.1101/gr.121426.111, 3166831, 21685128.
15. Friedlander MR, Chen W, Adamidi C, Maaskola J, Einspanier R, Knespel S, Rajewsky N. Discovering microRNAs from deep sequencing data using miRDeep. Nat Biotechnol 2008, 26(4):407-415. 10.1038/nbt1394, 18392026.
16. Fahlgren N, Howell MD, Kasschau KD, Chapman EJ, Sullivan CM, Cumbie JS, Givan SA, Law TF, Grant SR, Dangl JL, Carrington JC. High-throughput sequencing of Arabidopsis microRNAs: evidence for frequent birth and death of MIRNA genes. PLoS One 2007, 2(2):e219. 10.1371/journal.pone.0000219, 1790633, 17299599.
17. Wang WC, Lin FM, Chang WC, Lin KY, Huang HD, Lin NS. miRExpress: Analyzing high-throughput sequencing data for profiling microRNA expression. BMC Bioinforma 2009, 10(1):328.
18. Hackenberg M, Sturm M, Langenberger D, Falcon-Perez JM, Aransay AM. miRanalyzer: a microRNA detection and analysis tool for next-generation sequencing experiments. Nucleic Acids Res 2009, 37(Web Server issue):W68-W76. 2703919, 19433510.
19. Moxon S, Schwach F, Dalmay T, Maclean D, Studholme DJ, Moulton V. A toolkit for analysing large-scale plant small RNA datasets. Bioinformatics 2008, 24(19):2252-2253. 10.1093/bioinformatics/btn428, 18713789.
20. Dezulian T, Remmert M, Palatnik JF, Weigel D, Huson DH. Identification of plant microRNA homologs. Bioinformatics 2006, 22(3):359-360. 10.1093/bioinformatics/bti802, 16317073.
21. Zhang R, Peng Y, Wang W, Su B. Rapid evolution of an X-linked microRNA cluster in primates. Genome Res 2007, 17(5):612-617. 10.1101/gr.6146507, 1855169, 17416744.
22. Friedlander 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 2011, 40:37-52. 3245920, 21911355.
23. Lu J, Fu Y, Kumar S, Shen Y, Zeng K, Xu A, Carthew R, Wu CI. Adaptive evolution of newly emerged micro-RNA genes in Drosophila. Mol Biol Evol 2008, 25(5):929-938. 10.1093/molbev/msn040, 18296702.
24. Tang TA, Kumar S, Shen Y, Lu JA, Wu ML, Shi SH, Li WH, Wu CI. Adverse interactions between micro-RNAs and target genes from different species. Proc Natl Acad Sci U S A 2010, 107(29):12935-12940. 10.1073/pnas.1007591107, 2919947, 20615957.
25. Lu J, Shen Y, Wu Q, Kumar S, He B, Shi S, Carthew RW, Wang SM, Wu CI. The birth and death of microRNA genes in Drosophila. Nat Genet 2008, 40(3):351-355. 10.1038/ng.73, 18278047.
26. Artzi S, Kiezun A, Shomron N. miRNAminer: a tool for homologous microRNA gene search. BMC Bioinforma 2008, 9:39.
27. Stark A, Lin MF, Kheradpour P, Pedersen JS, Parts L, Carlson JW, Crosby MA, Rasmussen MD, Roy S, Deoras AN, Ruby JG, Brennecke J, Hodges E, Hinrichs AS, Caspi A, Paten B, Park SW, Han MV, Maeder ML, Polansky BJ, Robson BE, Aerts S, van Helden J, Hassan B, Gilbert DG, Eastman DA, Rice M, Weir M, Hahn MW, Park Y, Dewey CN, Pachter L, Kent WJ, Haussler D, Lai EC, Bartel DP, Hannon GJ, Kaufman TC, Eisen MB, Clark AG, Smith D, Celniker SE, Gelbart WM, Kellis M. Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures. Nature 2007, 450(7167):219-232. 10.1038/nature06340, 2474711, 17994088.
28. Lindblad-Toh K, Garber M, Zuk O, Lin MF, Parker BJ, Washietl S, Kheradpour P, Ernst J, Jordan G, Mauceli E, Ward LD, Lowe CB, Holloway AK, Clamp M, Gnerre S, Alfoldi J, Beal K, Chang J, Clawson H, Cuff J, Di Palma F, Fitzgerald S, Flicek P, Guttman M, Hubisz MJ, Jaffe DB, Jungreis I, Kent WJ, Kostka D, Lara M, Martins AL, Massingham T, Moltke I, Raney BJ, Rasmussen MD, Robinson J, Stark A, Vilella AJ, Wen JY, Xie XH, Zody MC, Worley KC, Kovar CL, Muzny DM, Gibbs RA, Warren WC, Mardis ER, Weinstock GM, Wilson RK, Birney E, Margulies EH, Herrero J, Green ED, Haussler D, Siepel A, Goldman N, Pollard KS, Pedersen JS, Lander ES, Kellis M, Inst B, Med BC, Univ W. A high-resolution map of human evolutionary constraint using 29 mammals. Nature 2011, 478(7370):476-482. 10.1038/nature10530, 3207357, 21993624.
29. Thomas JW, Touchman JW, Blakesley RW, Bouffard GG, Beckstrom-Sternberg SM, Margulies EH, Blanchette M, Siepel AC, Thomas PJ, McDowell JC, Maskeri B, Hansen NF, Schwartz MS, Weber RJ, Kent WJ, Karolchik D, Bruen TC, Bevan R, Cutler DJ, Schwartz S, Elnitski L, Idol JR, Prasad AB, Lee-Lin SQ, Maduro VV, Summers TJ, Portnoy ME, Dietrich NL, Akhter N, Ayele K, Benjamin B, Cariaga K, Brinkley CP, Brooks SY, Granite S, Guan X, Gupta J, Haghighi P, Ho SL, Huang MC, Karlins E, Laric PL, Legaspi R, Lim MJ, Maduro QL, Masiello CA, Mastrian SD, McCloskey JC, Pearson R, Stantripop S, Tiongson EE, Tran JT, Tsurgeon C, Vogt JL, Walker MA, Wetherby KD, Wiggins LS, Young AC, Zhang LH, Osoegawa K, Zhu B, Zhao B, Shu CL, De Jong PJ, Lawrence CE, Smit AF, Chakravarti A, Haussler D, Green P, Miller W, Green ED. Comparative analyses of multi-species sequences from targeted genomic regions. Nature 2003, 424(6950):788-793. 10.1038/nature01858, 12917688.
30. Wang X, Gu J, Zhang MQ, Li Y. Identification of phylogenetically conserved microRNA cis-regulatory elements across 12 Drosophila species. Bioinformatics 2008, 24(2):165-171. 10.1093/bioinformatics/btm572, 18037683.
31. Langmead B. Aligning short sequencing reads with Bowtie. Curr Protoc Bioinformatics 2010, Chapter 11:Unit 11 17.
32. Wei Y, Chen S, Yang P, Ma Z, Kang L. Characterization and comparative profiling of the small RNA transcriptomes in two phases of locust. Genome Biol 2009, 10(1):R6. 10.1186/gb-2009-10-1-r6, 2687794, 19146710.
33. Friedlander MR, Adamidi C, Han T, Lebedeva S, Isenbarger TA, Hirst M, Marra M, Nusbaum C, Lee WL, Jenkin JC, Sanchez Alvarado A, Kim JK, Rajewsky N. High-resolution profiling and discovery of planarian small RNAs. Proc Natl Acad Sci U S A 2009, 106(28):11546-11551. 10.1073/pnas.0905222106, 2703670, 19564616.
34. Soares AR, Pereira PM, Santos B, Egas C, Gomes AC, Arrais J, Oliveira JL, Moura GR, Santos MA. Parallel DNA pyrosequencing unveils new zebrafish microRNAs. BMC Genomics 2009, 10:195. 10.1186/1471-2164-10-195, 2684549, 19397817.
35. Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res 2003, 13(1):103-107. 10.1101/gr.809403, 430961, 12529312.
36. Blanchette M, Kent WJ, Riemer C, Elnitski L, Smit AF, Roskin KM, Baertsch R, Rosenbloom K, Clawson H, Green ED, Haussler D, Miller W. Aligning multiple genomic sequences with the threaded blockset aligner. Genome Res 2004, 14(4):708-715. 10.1101/gr.1933104, 383317, 15060014.
37. Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A 2003, 100(20):11484-11489. 10.1073/pnas.1932072100, 208784, 14500911.
38. Benson G. Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res 1999, 27(2):573-580. 10.1093/nar/27.2.573, 148217, 9862982.
39. Zuyderduyn S. Statistical analysis and significance testing of serial analysis of gene expression data using a Poisson mixture model. BMC Bioinforma 2007, 8(1):282.
40. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997, 25(17):3389-3402. 10.1093/nar/25.17.3389, 146917, 9254694.
41. Shen Y, Lv Y, Huang L, Liu W, Wen M, Tang T, Zhang R, Hungate E, Shi S, Wu CI. Testing hypotheses on the rate of molecular evolution in relation to gene expression using microRNAs. Proc Natl Acad Sci U S A 2011, 108(38):15942-15947. 10.1073/pnas.1110098108, 3179107, 21911382.