MiRTar: An integrated system for identifying miRNA-target interactions in human

BMC Bioinformatics

Volumn 12, Issue , 2011, Pages

  Hsu, Justin B ^a   Chiu, Chih Min ^a   Hsu, Sheng Da ^a   Huang, Wei Yun ^a   Chien, Chia Hung ^a   Lee, Tzong Yi ^b   Huang, Hsien Da ^a  

^a NATIONAL CHIAO TUNG UNIVERSITY   (Taiwan)

^b YUAN ZE UNIVERSITY   (Taiwan)

Author keywords

[No Author keywords available]

Indexed keywords

ALTERNATIVE SPLICING; BIOLOGICAL FUNCTIONS; BIOLOGICAL PATHWAYS; INTEGRATED RESOURCES; INTEGRATED SYSTEMS; PREDICTION SYSTEMS; PROTEIN-CODING GENES; REGULATORY RELATIONSHIPS;

BIOLOGICAL SYSTEMS; GENES; INTEGRATED CONTROL; PROTEINS;

RNA;

MESSENGER RNA; MICRORNA;

3' UNTRANSLATED REGION; 5' UNTRANSLATED REGION; ARTICLE; GENE EXPRESSION REGULATION; GENETICS; HUMAN; METABOLISM; PROTEIN SYNTHESIS;

3' UNTRANSLATED REGIONS; 5' UNTRANSLATED REGIONS; GENE EXPRESSION REGULATION; HUMANS; MICRORNAS; PROTEIN BIOSYNTHESIS; RNA, MESSENGER;

EID: 79960681800     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-12-300     Document Type: Article

References (68)

1. Bartel DP. MicroRNAs: target recognition and regulatory functions. Cell 2009, 136(2):215-233. 10.1016/j.cell.2009.01.002, 19167326.
2. Lewis BP, Burge CB, Bartel DP. Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell 2005, 120(1):15-20. 10.1016/j.cell.2004.12.035, 15652477.
3. Friedman RC, Farh KK, Burge CB, Bartel DP. Most mammalian mRNAs are conserved targets of microRNAs. Genome Res 2009, 19(1):92-105. 2612969, 18955434.
4. Lall S, Grun D, Krek A, Chen K, Wang YL, Dewey CN, Sood P, Colombo T, Bray N, Macmenamin P, et al. A genome-wide map of conserved microRNA targets in C. elegans. Curr Biol 2006, 16(5):460-471. 10.1016/j.cub.2006.01.050, 16458514.
5. Stark A, Brennecke J, Russell RB, Cohen SM. Identification of Drosophila MicroRNA targets. PLoS Biol 2003, 1(3):E60. 10.1371/journal.pbio.0000060, 270017, 14691535.
6. Gaidatzis D, van Nimwegen E, Hausser J, Zavolan M. Inference of miRNA targets using evolutionary conservation and pathway analysis. BMC Bioinformatics 2007, 8:69. 10.1186/1471-2105-8-69, 1838429, 17331257.
7. Grun D, Wang YL, Langenberger D, Gunsalus KC, Rajewsky N. microRNA target predictions across seven Drosophila species and comparison to mammalian targets. PLoS Comput Biol 2005, 1(1):e13. 10.1371/journal.pcbi.0010013, 1183519, 16103902.
8. Hsu SD, LF M, Wu W, Liang C, Huang W, Chan W, Tsai W, Chen G, Lee C, Chiu C, Chien C, Wu M, Huang C, Tsou A, Huang H. miRTarBase: a database curates experimentally validated microRNA-target interactions. Nucleic Acids Research 2011,
9. Lewis BP, Shih IH, Jones-Rhoades MW, Bartel DP, Burge CB. Prediction of mammalian microRNA targets. Cell 2003, 115(7):787-798. 10.1016/S0092-8674(03)01018-3, 14697198.
10. Enright AJ, John B, Gaul U, Tuschl T, Sander C, Marks DS. MicroRNA targets in Drosophila. Genome Biol 2003, 5(1):R1. 10.1186/gb-2003-5-1-r1, 395733, 14709173.
11. Rehmsmeier M, Steffen P, Hochsmann M, Giegerich R. Fast and effective prediction of microRNA/target duplexes. Rna 2004, 10(10):1507-1517. 10.1261/rna.5248604, 1370637, 15383676.
12. Krek A, Grun D, Poy MN, Wolf R, Rosenberg L, Epstein EJ, MacMenamin P, da Piedade I, Gunsalus KC, Stoffel M, et al. Combinatorial microRNA target predictions. Nat Genet 2005, 37(5):495-500. 10.1038/ng1536, 15806104.
13. Kiriakidou M, Nelson PT, Kouranov A, Fitziev P, Bouyioukos C, Mourelatos Z, Hatzigeorgiou A. A combined computational-experimental approach predicts human microRNA targets. Genes Dev 2004, 18(10):1165-1178. 10.1101/gad.1184704, 415641, 15131085.
14. Hsu SD, Chu CH, Tsou AP, Chen SJ, Chen HC, Hsu PW, Wong YH, Chen YH, Chen GH, Huang HD. miRNAMap 2.0: genomic maps of microRNAs in metazoan genomes. Nucleic Acids Res 2008, (36 Database):D165-169.
15. Hsu PW, Huang HD, Hsu SD, Lin LZ, Tsou AP, Tseng CP, Stadler PF, Washietl S, Hofacker IL. miRNAMap: genomic maps of microRNA genes and their target genes in mammalian genomes. Nucleic Acids Res 2006, (34 Database):D135-139.
16. Xiao F, Zuo Z, Cai G, Kang S, Gao X, Li T. miRecords: an integrated resource for microRNA-target interactions. Nucleic Acids Res 2009, (37 Database):D105-110.
17. Alexiou P, Vergoulis T, Gleditzsch M, Prekas G, Dalamagas T, Megraw M, Grosse I, Sellis T, Hatzigeorgiou AG. miRGen 2.0: a database of microRNA genomic information and regulation. Nucleic Acids Res 2010, (38 Database):D137-141.
18. Megraw M, Sethupathy P, Corda B, Hatzigeorgiou AG. miRGen: a database for the study of animal microRNA genomic organization and function. Nucleic Acids Res 2007, (35 Database):D149-155.
19. Roubelakis MG, Zotos P, Papachristoudis G, Michalopoulos I, Pappa KI, Anagnou NP, Kossida S. Human microRNA target analysis and gene ontology clustering by GOmir, a novel stand-alone application. BMC Bioinformatics 2009, 10(Suppl 6):S20. 10.1186/1471-2105-10-S6-S20, 19811686.
20. Zhang Y. miRU: an automated plant miRNA target prediction server. Nucleic Acids Res 2005, (33 Web Server):W701-704.
21. Rusinov V, Baev V, Minkov IN, Tabler M. MicroInspector: a web tool for detection of miRNA binding sites in an RNA sequence. Nucleic Acids Res 2005, (33 Web Server):W696-700.
22. Miranda KC, Huynh T, Tay Y, Ang YS, Tam WL, Thomson AM, Lim B, Rigoutsos I. A pattern-based method for the identification of MicroRNA binding sites and their corresponding heteroduplexes. Cell 2006, 126(6):1203-1217. 10.1016/j.cell.2006.07.031, 16990141.
23. Long D, Lee R, Williams P, Chan CY, Ambros V, Ding Y. Potent effect of target structure on microRNA function. Nat Struct Mol Biol 2007, 14(4):287-294. 10.1038/nsmb1226, 17401373.
24. Nam S, Li M, Choi K, Balch C, Kim S, Nephew KP. MicroRNA and mRNA integrated analysis (MMIA): a web tool for examining biological functions of microRNA expression. Nucleic Acids Res 2009, (37 Web Server):W356-362.
25. Place RF, Li LC, Pookot D, Noonan EJ, Dahiya R. MicroRNA-373 induces expression of genes with complementary promoter sequences. Proc Natl Acad Sci USA 2008, 105(5):1608-1613. 10.1073/pnas.0707594105, 2234192, 18227514.
26. Easow G, Teleman AA, Cohen SM. Isolation of microRNA targets by miRNP immunopurification. RNA 2007, 13(8):1198-1204. 10.1261/rna.563707, 1924889, 17592038.
27. Grimson A, Farh KK, Johnston WK, Garrett-Engele P, Lim LP, Bartel DP. MicroRNA targeting specificity in mammals: determinants beyond seed pairing. Mol Cell 2007, 27(1):91-105. 10.1016/j.molcel.2007.06.017, 17612493.
28. Kloosterman WP, Wienholds E, Ketting RF, Plasterk RH. Substrate requirements for let-7 function in the developing zebrafish embryo. Nucleic Acids Res 2004, 32(21):6284-6291. 10.1093/nar/gkh968, 535676, 15585662.
29. Stark A, Lin MF, Kheradpour P, Pedersen JS, Parts L, Carlson JW, Crosby MA, Rasmussen MD, Roy S, Deoras AN, et al. Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures. Nature 2007, 450(7167):219-232. 10.1038/nature06340, 2474711, 17994088.
30. Nakamoto M, Jin P, O'Donnell WT, Warren ST. Physiological identification of human transcripts translationally regulated by a specific microRNA. Hum Mol Genet 2005, 14(24):3813-3821. 10.1093/hmg/ddi397, 16239240.
31. Duursma AM, Kedde M, Schrier M, le Sage C, Agami R. miR-148 targets human DNMT3b protein coding region. RNA 2008, 14(5):872-877. 10.1261/rna.972008, 2327368, 18367714.
32. Forman JJ, Legesse-Miller A, Coller HA. A search for conserved sequences in coding regions reveals that the let-7 microRNA targets Dicer within its coding sequence. Proc Natl Acad Sci USA 2008, 105(39):14879-14884. 10.1073/pnas.0803230105, 2567461, 18812516.
33. Orom UA, Nielsen FC, Lund AH. MicroRNA-10a binds the 5'UTR of ribosomal protein mRNAs and enhances their translation. Mol Cell 2008, 30(4):460-471. 10.1016/j.molcel.2008.05.001, 18498749.
34. Tay Y, Zhang J, Thomson AM, Lim B, Rigoutsos I. MicroRNAs to Nanog, Oct4 and Sox2 coding regions modulate embryonic stem cell differentiation. Nature 2008, 455(7216):1124-1128. 10.1038/nature07299, 18806776.
35. Zhou X, Duan X, Qian J, Li F. Abundant conserved microRNA target sites in the 5'-untranslated region and coding sequence. Genetica 2009,
36. Wang ET, Sandberg R, Luo S, Khrebtukova I, Zhang L, Mayr C, Kingsmore SF, Schroth GP, Burge CB. Alternative isoform regulation in human tissue transcriptomes. Nature 2008, 456(7221):470-476. 10.1038/nature07509, 2593745, 18978772.
37. Chen L, Zheng S. Studying alternative splicing regulatory networks through partial correlation analysis. Genome Biol 2009, 10(1):R3. 10.1186/gb-2009-10-1-r3, 2687791, 19133160.
38. Johnson JM, Castle J, Garrett-Engele P, Kan Z, Loerch PM, Armour CD, Santos R, Schadt EE, Stoughton R, Shoemaker DD. Genome-wide survey of human alternative pre-mRNA splicing with exon junction microarrays. Science 2003, 302(5653):2141-2144. 10.1126/science.1090100, 14684825.
39. Ghigna C, Valacca C, Biamonti G. Alternative splicing and tumor progression. Curr Genomics 2008, 9(8):556-570. 10.2174/138920208786847971, 2694562, 19516963.
40. Srebrow A, Kornblihtt AR. The connection between splicing and cancer. J Cell Sci 2006, 119(Pt 13):2635-2641.
41. Brinkman BM. Splice variants as cancer biomarkers. Clin Biochem 2004, 37(7):584-594. 10.1016/j.clinbiochem.2004.05.015, 15234240.
42. Wang GS, Cooper TA. Splicing in disease: disruption of the splicing code and the decoding machinery. Nat Rev Genet 2007, 8(10):749-761. 10.1038/nrg2164, 17726481.
43. Cartegni L, Chew SL, Krainer AR. Listening to silence and understanding nonsense: exonic mutations that affect splicing. Nat Rev Genet 2002, 3(4):285-298. 10.1038/nrg775, 11967553.
44. Cui Q, Yu Z, Purisima EO, Wang E. Principles of microRNA regulation of a human cellular signaling network. Mol Syst Biol 2006, 2:46. 1681519, 16969338.
45. Iliopoulos D, Malizos KN, Oikonomou P, Tsezou A. Integrative microRNA and proteomic approaches identify novel osteoarthritis genes and their collaborative metabolic and inflammatory networks. PLoS One 2008, 3(11):e3740. 10.1371/journal.pone.0003740, 2582945, 19011694.
46. Nam S, Kim B, Shin S, Lee S. miRGator: an integrated system for functional annotation of microRNAs. Nucleic Acids Res 2008, (36 Database):D159-164.
47. Papadopoulos GL, Alexiou P, Maragkakis M, Reczko M, Hatzigeorgiou AG. DIANA-mirPath: Integrating human and mouse microRNAs in pathways. Bioinformatics 2009, 25(15):1991-1993. 10.1093/bioinformatics/btp299, 19435746.
48. Wang X. miRDB: a microRNA target prediction and functional annotation database with a wiki interface. RNA 2008, 14(6):1012-1017. 10.1261/rna.965408, 2390791, 18426918.
49. Griffiths-Jones S, Saini HK, van Dongen S, Enright AJ. miRBase: tools for microRNA genomics. Nucleic Acids Res 2008, (36 Database):D154-158.
50. Koscielny G, Le Texier V, Gopalakrishnan C, Kumanduri V, Riethoven JJ, Nardone F, Stanley E, Fallsehr C, Hofmann O, Kull M, et al. ASTD: The Alternative Splicing and Transcript Diversity database. Genomics 2009, 93(3):213-220. 10.1016/j.ygeno.2008.11.003, 19059335.
51. Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW. GenBank. Nucleic Acids Res 2009, (37 Database):D26-31.
52. Sayers EW, Barrett T, Benson DA, Bryant SH, Canese K, Chetvernin V, Church DM, DiCuccio M, Edgar R, Federhen S, et al. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 2009, (37 Database):D5-15.
53. 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):D355-360.
54. Brennecke J, Stark A, Russell RB, Cohen SM. Principles of microRNA-target recognition. PLoS Biol 2005, 3(3):e85. 10.1371/journal.pbio.0030085, 1043860, 15723116.
55. John B, Enright AJ, Aravin A, Tuschl T, Sander C, Marks DS. Human MicroRNA targets. PLoS Biol 2004, 2(11):e363. 10.1371/journal.pbio.0020363, 521178, 15502875.
56. Wang Y, Sheng G, Juranek S, Tuschl T, Patel DJ. Structure of the guide-strand-containing argonaute silencing complex. Nature 2008, 456(7219):209-213. 10.1038/nature07315, 18754009.
57. Siepel A, Bejerano G, Pedersen JS, Hinrichs AS, Hou M, Rosenbloom K, Clawson H, Spieth J, Hillier LW, Richards S, et al. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res 2005, 15(8):1034-1050. 10.1101/gr.3715005, 1182216, 16024819.
58. Rhead B, Karolchik D, Kuhn RM, Hinrichs AS, Zweig AS, Fujita PA, Diekhans M, Smith KE, Rosenbloom KR, Raney BJ, et al. The UCSC Genome Browser database: update 2010. Nucleic Acids Res 2010, (38 Database):D613-619.
59. Robins H, Li Y, Padgett RW. Incorporating structure to predict microRNA targets. Proc Natl Acad Sci USA 2005, 102(11):4006-4009. 10.1073/pnas.0500775102, 554828, 15738385.
60. Bernhart SH, Hofacker IL, Stadler PF. Local RNA base pairing probabilities in large sequences. Bioinformatics 2006, 22(5):614-615. 10.1093/bioinformatics/btk014, 16368769.
61. Florea L, Hartzell G, Zhang Z, Rubin GM, Miller W. A computer program for aligning a cDNA sequence with a genomic DNA sequence. Genome Res 1998, 8(9):967-974. 310774, 9750195.
62. Kapustin Y, Souvorov A, Tatusova T, Lipman D. Splign: algorithms for computing spliced alignments with identification of paralogs. Biol Direct 2008, 3:20. 10.1186/1745-6150-3-20, 2440734, 18495041.
63. Wheelan SJ, Church DM, Ostell JM. Spidey: a tool for mRNA-to-genomic alignments. Genome Res 2001, 11(11):1952-1957. 311166, 11691860.
64. Huang HD, Horng JT, Lin FM, Chang YC, Huang CC. SpliceInfo: an information repository for mRNA alternative splicing in human genome. Nucleic Acids Res 2005, (33 Database):D80-85.
65. Wang Y, Lee CG. MicroRNA and cancer--focus on apoptosis. J Cell Mol Med 2009, 13(1):12-23.
66. Sengupta S, den Boon JA, Chen IH, Newton MA, Stanhope SA, Cheng YJ, Chen CJ, Hildesheim A, Sugden B, Ahlquist P. MicroRNA 29c is down-regulated in nasopharyngeal carcinomas, up-regulating mRNAs encoding extracellular matrix proteins. Proc Natl Acad Sci USA 2008, 105(15):5874-5878. 10.1073/pnas.0801130105, 2311339, 18390668.
67. Lin YC, Hsieh LC, Kuo MW, Yu J, Kuo HH, Lo WL, Lin RJ, Yu AL, Li WH. Human TRIM71 and its nematode homologue are targets of let-7 microRNA and its zebrafish orthologue is essential for development. Mol Biol Evol 2007, 24(11):2525-2534. 10.1093/molbev/msm195, 17890240.
68. Maragkakis M, Reczko M, Simossis VA, Alexiou P, Papadopoulos GL, Dalamagas T, Giannopoulos G, Goumas G, Koukis E, Kourtis K, et al. DIANA-microT web server: elucidating microRNA functions through target prediction. Nucleic Acids Res 2009, (37 Web Server):W273-276.