MMpred: Functional miRNA - mRNA interaction analyses by miRNA expression prediction

BMC Genomics

Volumn 13, Issue 1, 2012, Pages

  Stempor, Przemyslaw A ^a,b   Cauchi, Michael ^a   Wilson, Paul ^b  

^a CRANFIELD UNIVERSITY   (United Kingdom)

^b GLAXOSMITHKLINE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA; MICRORNA;

3' UNTRANSLATED REGION; ACCURACY; ARTICLE; CORRELATION ANALYSIS; GENE EXPRESSION; GENE INTERACTION; INTERACTIONS WITH RNA; MATHEMATICAL MODEL; PREDICTION; REGULATORY MECHANISM;

CHROMOSOME MAPPING; COMPUTATIONAL BIOLOGY; HUMANS; LINEAR MODELS; MICRORNAS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; REPRODUCIBILITY OF RESULTS; RNA, MESSENGER; TRANSCRIPTOME;

EID: 84868675774     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-13-620     Document Type: Article

References (43)

1. Taft RJ, Pang KC, Mercer TR, Dinger M, Mattick JS. Non-coding RNAs: regulators of disease. J Pathol 2010, 220:126-139. 10.1002/path.2638, 19882673.
2. Filipowicz W, Jaskiewicz L, Kolb FA, Pillai RS. Post-transcriptional gene silencing by siRNAs and miRNAs. Curr Opin Struct Biol 2005, 15:331-341. 10.1016/j.sbi.2005.05.006, 15925505.
3. Krispies R. Genetics. Small RNAs Reveal an Activating Side. Science (New York, N.Y.) 2006, 314:741-742.
4. Hu Z. Insight into microRNA regulation by analyzing the characteristics of their targets in humans. BMC Genomics 2009, 10:594. 10.1186/1471-2164-10-594, 2799441, 20003303.
5. Pauley KM, Cha S, Chan EKL. MicroRNA in autoimmunity and autoimmune diseases. J Autoimmun 2009, 32:189-194. 10.1016/j.jaut.2009.02.012, 2717629, 19303254.
6. Griffiths Jones S, Saini HK, Dongen S, van Enright AJ. miRBase: tools for microRNA genomics. Nucleic Acids Res 2008, 36:D154-D158. 10.1093/nar/gkn221, 2238936, 17991681.
7. Taft RJ, Pheasant M, Mattick JS. The relationship between non-protein-coding DNA and eukaryotic complexity. BioEssays 2007, 29:288-299. 10.1002/bies.20544, 17295292.
8. Baskerville S, Bartel DP. Array profiling of microRNAs reveals frequent coexpression with neighboring miRNAs and host genes. RNA (New York, N.Y.) 2005, 11:241-247.
9. Corcoran DL, Pandit KV, Gordon B, Bhattacharjee A, Kaminski N, Benos PV. Features of mammalian microRNA promoters emerge from polymerase II chromatin immunoprecipitation data. PLoS One 2009, 4:e5279. 10.1371/journal.pone.0005279, 2668758, 19390574.
10. Lutter D, Marr C, Krumsiek J, Lang EW, Theis FJ. Intronic microRNAs support their host genes by mediating synergistic and antagonistic regulatory effects. BMC Genomics 2010, 11:224. 10.1186/1471-2164-11-224, 2865499, 20370903.
11. Rodriguez A, Griffiths-Jones S, Ashurst JL, Bradley A. Identification of mammalian microRNA host genes and transcription units. Genome Res 2004, 14:1902-1910. 10.1101/gr.2722704, 524413, 15364901.
12. Kim Y-K, Kim VN. Processing of intronic microRNAs. EMBO J 2007, 26:775-783. 10.1038/sj.emboj.7601512, 1794378, 17255951.
13. Barik S. An intronic microRNA silences genes that are functionally antagonistic to its host gene. Nucleic Acids Res 2008, 36:5232-5241. 10.1093/nar/gkn513, 2532712, 18684991.
14. Zhu Y, Kalbfleisch T, Brennan MD, Li Y. A MicroRNA gene is hosted in an intron of a schizophrenia-susceptibility gene. Schizophr Res 2009, 109:86-89. 10.1016/j.schres.2009.01.022, 2664103, 19264453.
15. Callis TE, Pandya K, Seok HY, Tang R-H, Tatsuguchi M, Huang Z-P, Chen J-F, Deng Z, Gunn B, Shumate J, Willis MS, Selzman CH, Wang D-Z. MicroRNA-208a is a regulator of cardiac hypertrophy and conduction in mice. J Clin Invest 2009, 119:2772-2786. 10.1172/JCI36154, 2735902, 19726871.
16. Farh KK-H, Grimson A, Jan C, Lewis BP, Johnston WK, Lim LP, Burge CB, Bartel DP. The widespread impact of mammalian MicroRNAs on mRNA repression and evolution. Science (New York, N.Y.) 2005, 310:1817-1821.
17. Chen C-Z, Li L, Lodish HF, Bartel DP. MicroRNAs modulate hematopoietic lineage differentiation. Science (New York, N.Y.) 2004, 303:83-86.
18. Wulczyn FG, Smirnova L, Rybak A, Brandt C, Kwidzinski E, Ninnemann O, Strehle M, Seiler A, Schumacher S, Nitsch R. Post-transcriptional regulation of the let-7 microRNA during neural cell specification. FASEB J 2007, 21:415-426. 10.1096/fj.06-6130com, 17167072.
19. Tsang J, Zhu J, van Oudenaarden A. MicroRNA-mediated feedback and feedforward loops are recurrent network motifs in mammals. Mol Cell 2007, 26:753-767. 10.1016/j.molcel.2007.05.018, 2072999, 17560377.
20. Sah S, McCall MN, Eveleigh D, Wilson M, Irizarry RA. Performance evaluation of commercial miRNA expression array platforms. BMC research notes 2010, 3:80. 10.1186/1756-0500-3-80, 2853548, 20298588.
21. López-Romero P, González MA, Callejas S, Dopazo A, Irizarry RA. Processing of Agilent microRNA array data. BMC research notes 2010, 3:18. 10.1186/1756-0500-3-18, 2823597, 20205787.
22. Irizarry RA, Bolstad BM, Collin F, Cope LM, Hobbs B, Speed TP. Summaries of Affymetrix GeneChip probe level data. Nucleic Acids Res 2003, 31:e15. 10.1093/nar/gng015, 150247, 12582260.
23. Kozomara A, Griffiths-Jones S. miRBase: integrating microRNA annotation and deep-sequencing data. Nucleic Acids Res 2011, 39:D152-D157. 10.1093/nar/gkq1027, 3013655, 21037258.
24. Wang H-W, Wu Y-H, Hsieh J-Y, Liang M-L, Chao M-E, Liu D-J, Hsu M-T, Wong T-T. Pediatric primary central nervous system germ cell tumors of different prognosis groups show characteristic miRNome traits and chromosome copy number variations. BMC Genomics 2010, 11:132. 10.1186/1471-2164-11-132, 2837036, 20178649.
25. Shapiro SS, WILK MB. An analysis of variance test for normality (complete samples). Biometrika 1965, 52:591-611.
26. Taylor BS, Schultz N, Hieronymus H, Gopalan A, Xiao Y, Carver BS, Arora VK, Kaushik P, Cerami E, Reva B. Integrative Genomic Profiling of Human Prostate Cancer. Cancer Cell 2010, 18:11-22. 10.1016/j.ccr.2010.05.026, 3198787, 20579941.
27. Okoniewski M, Hey Y, Pepper S, Miller C. High correspondence between Affymetrix exon and standard expression arrays. Biotechniques 2007, 42:181-185. 10.2144/000112315, 17373482.
28. Pradervand S, Paillusson A, Thomas J, Weber J, Wirapati P, Hagenbüchle O, Harshman K. Affymetrix Whole-Transcript Human Gene 1.0 ST array is highly concordant with standard 3' expression arrays. Biotechniques 2008, 44:759-762. 10.2144/000112751, 18476829.
29. Robinson MD, Speed TP. A comparison of Affymetrix gene expression arrays. BMC Bioinformatics 2007, 8:449. 10.1186/1471-2105-8-449, 2216046, 18005448.
30. Ritchie W, Rajasekhar M, Flamant S, Rasko JEJ. Conserved expression patterns predict microRNA targets. PLoS Comput Biol 2009, 5:e1000513. 10.1371/journal.pcbi.1000513, 2736581, 19779543.
31. Kertesz M, Iovino N, Unnerstall U, Gaul U, Segal E. The role of site accessibility in microRNA target recognition. Nat Genet 2007, 39:1278-1284. 10.1038/ng2135, 17893677.
32. 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, 14:287-294. 10.1038/nsmb1226, 17401373.
33. Dohnal AM, Luger R, Paul P, Fuchs D, Felzmann T. CD40 ligation restores type 1 polarizing capacity in TLR4 activated dendritic cells that have ceased interleukin-12 expression. J Cell Mol Med 2009, 13:1741-1750. 10.1111/j.1582-4934.2008.00584.x, 20187300.
34. Warren HS, Elson CM, Hayden DL, Schoenfeld DA, Cobb JP, Maier RV, Moldawer LL, Moore EE, Harbrecht BG, Pelak K, Cuschieri J, Herndon DN, Jeschke MG, Finnerty CC, Brownstein BH, Hennessy L, Mason PH, Tompkins RG. A genomic score prognostic of outcome in trauma patients. Mol Med (Cambridge, Mass.) 2009, 15:220-227.
35. Zhou B, Xu W, Herndon D, Tompkins R, Davis R, Xiao W, Wong WH, Toner M, Warren HS, Schoenfeld DA, Rahme L, McDonald-Smith GP, Hayden D, Mason P, Fagan S, Yu Y-M, Cobb JP, Remick DG, Mannick JA, Lederer JA, Gamelli RL, Silver GM, West MA, Shapiro MB, Smith R, Camp DG, Qian W, Storey J, Mindrinos M, Tibshirani R, Lowry S, Calvano S, Chaudry I, Cohen M, Moore EE, Johnson J, Moldawer LL, Baker HV, Efron PA, Balis UGJ, Billiar TR, Ochoa JB, Sperry JL, Miller-Graziano CL, De AK, Bankey PE, Finnerty CC, Jeschke MG, Minei JP, Arnoldo BD, Hunt JL, Horton J, Brownstein B, Freeman B, Maier RV, Nathens AB, Cuschieri J, Gibran N, Klein M, O'Keefe G. Analysis of factorial time-course microarrays with application to a clinical study of burn injury. 2010, 107:9923-9928.
36. 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:D105-D110. 10.1093/nar/gkn851, 2686554, 18996891.
37. Gennarino VA, Sardiello M, Avellino R, Meola N, Maselli V, Anand S, Cutillo L, Ballabio A, Banfi S. MicroRNA target prediction by expression analysis of host genes. Genome Res 2009, 19:481-490. 2661810, 19088304.
38. Gennarino VA, Sardiello M, Mutarelli M, Dharmalingam G, Maselli V, Lago G, Banfi S. HOCTAR database: A unique resource for microRNA target prediction. Gene 2011, 480:51-58. 10.1016/j.gene.2011.03.005, 3113163, 21435384.
39. Huang JC, Babak T, Corson TW, Chua G, Khan S, Gallie BL, Hughes TR, Blencowe BJ, Frey BJ, Morris QD. Using expression profiling data to identify human microRNA targets. Nat Methods 2007, 4:1045-1049. 10.1038/nmeth1130, 18026111.
40. Biasiolo M, Sales G, Lionetti M, Agnelli L, Todoerti K, Bisognin A, Coppe A, Romualdi C, Neri A, Bortoluzzi S. Impact of host genes and strand selection on miRNA and miRNA* expression. PLoS One 2011, 6:e23854. 10.1371/journal.pone.0023854, 3166117, 21909367.
41. Kapur K, Xing Y, Ouyang Z, Wong WH. Exon arrays provide accurate assessments of gene expression. Genome Biol 2007, 8:R82. 10.1186/gb-2007-8-5-r82, 1929160, 17504534.
42. Pradervand S, Weber J, Thomas J, Bueno M, Wirapati P, Lefort K, Dotto GP, Harshman K. Impact of normalization on miRNA microarray expression profiling. RNA (New York, N.Y.) 2009, 15:493-501.
43. Enright AJ, John B, Gaul U, Tuschl T, Sander C, Marks DS. MicroRNA targets in Drosophila. Genome Biol 2003, 5:R1. 10.1186/gb-2003-5-1-r1, 395733, 14709173.