MiRExpress: Analyzing high-throughput sequencing data for profiling microRNA expression

BMC Bioinformatics

Volumn 10, Issue , 2009, Pages 328-

  Wang, Wei Chi ^a   Lin, Feng Mao ^a   Chang, Wen Chi ^a,b   Lin, Kuan Yu ^b,c   Huang, Hsien Da ^a   Lin, Na Sheng ^b,c  

^a NATIONAL CHIAO TUNG UNIVERSITY   (Taiwan)

^b NATIONAL CHENG KUNG UNIVERSITY   (Taiwan)

^c INSTITUTE OF PLANT AND MICROBIAL BIOLOGY   (Taiwan)

Author keywords

[No Author keywords available]

Indexed keywords

EXPRESSION PROFILING; HIGH-THROUGHPUT SEQUENCING; MICRORNA EXPRESSION; MIRNA REGULATIONS; OLIGONUCLEOTIDE ARRAYS; OLIGONUCLEOTIDE MICROARRAY; SECOND GENERATION; STAND-ALONE SOFTWARE;

OLIGONUCLEOTIDES; TOOLS;

RNA;

MICRORNA;

ARABIDOPSIS; ARTICLE; COMPUTER PROGRAM; GENE EXPRESSION PROFILING; GENETIC DATABASE; GENETIC REGULATION; HIGH THROUGHPUT SCREENING; HUMAN; NONHUMAN; PLANT GENETICS; PROTEIN EXPRESSION; RNA ANALYSIS; SEQUENCE ANALYSIS; SPECIES DIFFERENCE;

COMPUTATIONAL BIOLOGY; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENOME, HUMAN; GENOME, PLANT; HUMANS; MICRORNAS; SEQUENCE ANALYSIS, RNA; SOFTWARE;

ANIMALIA;

EID: 70449639806     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-10-328     Document Type: Article

References (34)

1. He L, Hannon GJ. MicroRNAs: small RNAs with a big role in gene regulation. Nat Rev Genet 2004, 5(7):522-531. 10.1038/nrg1379, 15211354.
2. Esquela-Kerscher A, Slack FJ. Oncomirs - microRNAs with a role in cancer. Nat Rev Cancer 2006, 6(4):259-269. 10.1038/nrc1840, 16557279.
3. Davison TS, Johnson CD, Andruss BF. Analyzing micro-RNA expression using microarrays. Methods Enzymol 2006, 411:14-34. 10.1016/S0076-6879(06)11002-2, 16939783.
4. Liu CG, Spizzo R, Calin GA, Croce CM. Expression profiling of microRNA using oligo DNA arrays. Methods 2008, 44(1):22-30. 10.1016/j.ymeth.2007.10.010, 18158129.
5. Griffiths-Jones S, Saini HK, van Dongen S, Enright AJ. miRBase: tools for microRNA genomics. Nucleic Acids Res 2008, (36 Database):D154-158. 2238936, 17991681.
6. Porkka KP, Pfeiffer MJ, Waltering KK, Vessella RL, Tammela TL, Visakorpi T. MicroRNA expression profiling in prostate cancer. Cancer Res 2007, 67(13):6130-6135. 10.1158/0008-5472.CAN-07-0533, 17616669.
7. Zhao JJ, Hua YJ, Sun DG, Meng XX, Xiao HS, Ma X. Genome-wide microRNA profiling in human fetal nervous tissues by oligonucleotide microarray. Childs Nerv Syst 2006, 22(11):1419-1425. 10.1007/s00381-006-0173-9, 1705512, 16983573.
8. Fahlgren N, Howell MD, Kasschau KD, Chapman EJ, Sullivan CM, Cumbie JS, Givan SA, Law TF, Grant SR, Dangl JL. 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.
9. Glazov EA, Cottee PA, Barris WC, Moore RJ, Dalrymple BP, Tizard ML. A microRNA catalog of the developing chicken embryo identified by a deep sequencing approach. Genome Res 2008, 18(6):957-964. 10.1101/gr.074740.107, 2413163, 18469162.
10. Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, Berka J, Braverman MS, Chen YJ, Chen Z. Genome sequencing in microfabricated high-density picolitre reactors. Nature 2005, 437(7057):376-380. 1464427, 16056220.
11. Morin RD, O'Connor MD, Griffith M, Kuchenbauer F, Delaney A, Prabhu AL, Zhao Y, McDonald H, Zeng T, Hirst M. Application of massively parallel sequencing to microRNA profiling and discovery in human embryonic stem cells. Genome Res 2008, 18(4):610-621. 10.1101/gr.7179508, 2279248, 18285502.
12. Rajagopalan R, Vaucheret H, Trejo J, Bartel DP. A diverse and evolutionarily fluid set of microRNAs in Arabidopsis thaliana. Genes Dev 2006, 20(24):3407-3425. 10.1101/gad.1476406, 1698448, 17182867.
13. Stark A, Kheradpour P, Parts L, Brennecke J, Hodges E, Hannon GJ, Kellis M. Systematic discovery and characterization of fly microRNAs using 12 Drosophila genomes. Genome Res 2007, 17(12):1865-1879. 10.1101/gr.6593807, 2099594, 17989255.
14. Sunkar R, Zhou X, Zheng Y, Zhang W, Zhu JK. Identification of novel and candidate miRNAs in rice by high throughput sequencing. BMC Plant Biol 2008, 8:25. 10.1186/1471-2229-8-25, 2292181, 18312648.
15. Yao Y, Guo G, Ni Z, Sunkar R, Du J, Zhu JK, Sun Q. Cloning and characterization of microRNAs from wheat (Triticum aestivum L.). Genome Biol 2007, 8(6):R96. 10.1186/gb-2007-8-6-r96, 2394755, 17543110.
16. Kent WJ. BLAT--the BLAST-like alignment tool. Genome Res 2002, 12(4):656-664. 187518, 11932250.
17. 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.
18. Smith AD, Xuan Z, Zhang MQ. Using quality scores and longer reads improves accuracy of Solexa read mapping. BMC Bioinformatics 2008, 9:128. 10.1186/1471-2105-9-128, 2335322, 18307793.
19. Jiang H, Wong WH. SeqMap: mapping massive amount of oligonucleotides to the genome. Bioinformatics 2008, 24(20):2395-2396. 10.1093/bioinformatics/btn429, 18697769, 2562015.
20. Lin H, Zhang Z, Zhang MQ, Ma B, Li M. ZOOM! Zillions of oligos mapped. Bioinformatics 2008, 24(21):2431-2437. 10.1093/bioinformatics/btn416, 18684737.
21. Li H, Ruan J, Durbin R. Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res 2008, 18(11):1851-1858. 10.1101/gr.078212.108, 2577856, 18714091.
22. Li R, Li Y, Kristiansen K, Wang J. SOAP: short oligonucleotide alignment program. Bioinformatics 2008, 24(5):713-714. 10.1093/bioinformatics/btn025, 18227114.
23. Farrar M. Striped Smith-Waterman speeds database searches six times over other SIMD implementations. Bioinformatics 2007, 23(2):156-161. 10.1093/bioinformatics/btl582, 17110365.
24. Amariglio N, Rechavi G. A-to-I RNA editing: a new regulatory mechanism of global gene expression. Blood Cells Mol Dis 2007, 39(2):151-155. 10.1016/j.bcmd.2007.04.003, 17555993.
25. Das AK, Carmichael GG. ADAR editing wobbles the microRNA world. ACS Chem Biol 2007, 2(4):217-220. 10.1021/cb700064h, 17455896.
26. Habig JW, Dale T, Bass BL. miRNA editing--we should have inosine this coming. Mol Cell 2007, 25(6):792-793. 10.1016/j.molcel.2007.03.010, 2583401, 17386255.
27. Kawahara Y, Megraw M, Kreider E, Iizasa H, Valente L, Hatzigeorgiou AG, Nishikura K. Frequency and fate of microRNA editing in human brain. Nucleic Acids Res 2008, 36(16):5270-5280. 10.1093/nar/gkn479, 2532740, 18684997.
28. Lin NS, Lee YS, Lin BY, Lee CW, Hsu YH. The open reading frame of bamboo mosaic potexvirus satellite RNA is not essential for its replication and can be replaced with a bacterial gene. Proc Natl Acad Sci USA 1996, 93(7):3138-3142. 10.1073/pnas.93.7.3138, 39775, 8610182.
29. Zuker M. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res 2003, 31(13):3406-3415. 10.1093/nar/gkg595, 169194, 12824337.
30. Kuhn RM, Karolchik D, Zweig AS, Wang T, Smith KE, Rosenbloom KR, Rhead B, Raney BJ, Pohl A, Pheasant M. The UCSC Genome Browser Database: update 2009. Nucleic Acids Res 2009, (37 Database):D755-761. 10.1093/nar/gkn875, 2686463, 18996895.
31. Chang TH, Horng JT, Huang HD. RNALogo: a new approach to display structural RNA alignment. Nucleic Acids Res 2008, (36 Web Server):W91-96. 10.1093/nar/gkn258, 2447718, 18495753.
32. Creighton CJ, Nagaraja AK, Hanash SM, Matzuk MM, Gunaratne PH. A bioinformatics tool for linking gene expression profiling results with public databases of microRNA target predictions. RNA 2008, 14(11):2290-2296. 10.1261/rna.1188208, 2578856, 18812437.
33. Reid JG, Nagaraja AK, Lynn FC, Drabek RB, Muzny DM, Shaw CA, Weiss MK, Naghavi AO, Khan M, Zhu H. Mouse let-7 miRNA populations exhibit RNA editing that is constrained in the 5'-seed/cleavage/anchor regions and stabilize predicted mmu-let-7a:mRNA duplexes. Genome Res 2008, 18(10):1571-1581. 10.1101/gr.078246.108, 2556275, 18614752.
34. Creighton CJ, Reid JG, Gunaratne PH. Expression profiling of microRNAs by deep sequencing. Brief Bioinform 2009, 10(5):490-497. 10.1093/bib/bbp019, 19332473.