Prediction of miRNA in HIV-1 genome and its targets through artificial neural network: A bioinformatics approach

Network Modeling and Analysis in Health Informatics and Bioinformatics

Volumn 1, Issue 4, 2012, Pages 141-151

  Gupta, Manish Kumar ^a   Agarwal, Kavita ^b   Prakash, Nutan ^c   Singh, Dev Bukhsh ^a   Misra, Krishna ^d  

^a CSJM UNIVERSITY   (India)

^b NATIONAL INSTITUTE OF IMMUNOLOGY   (India)

^c Shree M and N Virani Science College   (India)

^d SANJAY GANDHI POSTGRADUATE INSTITUTE OF MEDICAL SCIENCES   (India)

Author keywords

ANN; Gene target; HIV; MicroRNA; MiRBASE; Non coding RNA; Pre miRNA; RNAFold

Indexed keywords

MICRORNA; RNA PRECURSOR;

ARTICLE; ARTIFICIAL NEURAL NETWORK; BASE PAIRING; COMPUTER LANGUAGE; FOXK1 GENE; GENE; GENE SILENCING; HUMAN IMMUNODEFICIENCY VIRUS 1; NDUFS7 GENE; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEIN SECONDARY STRUCTURE; QUANTITATIVE ANALYSIS; RNA EXTRACTION; SIGNAL NOISE RATIO; SUFU GENE; VIRUS GENOME; WNT3A GENE;

EID: 84983041022     PISSN: None     EISSN: 21926670     Source Type: Journal    
DOI: 10.1007/s13721-012-0017-3     Document Type: Article

References (41)

1. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215(3): 403-410.
2. Ambros V, Bartel B, Bartel DP, Burge CB, Carrington JC, Chen X, Dreyfuss G, Eddy SR, Griffiths-Jones S, Marshall M, Matzke M, Ruvkun G, Tuschl T (2003) A uniform system for microRNA annotation. RNA 9(3): 277-279.
3. Anderson D, McNeill G (1995) Artificial neural networks technology. Kaman Sciences Corporation, US.
4. Arendt CW, Littman DR (2001) HIV: master of the host cell. Genome Biol 2: 1030. 1-1030. 4.
5. Bartel DP (2004) MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116: 281-297.
6. Chomova M, Racay P (2010) Mitochondrial complex I in the network of known and unknown facts. Gen Physiol Biophys 29(1): 3-11.
7. Delattre M, Briand S, Paces-Fessy M, Blanchet-Tournier MF (2001) The Suppressor of fused gene, involved in Hedgehog signal transduction in Drosophila, is conserved in mammals. Dev Genes Evol 209(5): 294-300.
8. Emerman M, Malim MH (1998) HIV-1 regulatory/accessory genes: keys to unraveling viral and host cell biology. Science 280: 1880-1884.
9. Griffiths-Jones S (2004) The microRNA Registry. NAR 32: D109-D111 (Database Issue).
10. Griffiths-Jones S, Grocock RJ, van Dongen S, Bateman A, Enright AJ (2006) miRBase: microRNA sequences, targets and gene nomenclature. Nucleic Acids Res 34: D140-D144.
11. Griffiths-Jones S, Saini HK, van Dongen S, Enright AJ (2008) miRBase: tools for microRNA genomics. NAR 36: D154-D158 (Database Issue).
12. Grishok A, Pasquinelli AE, Conte D, Li N, Parrish S, Ha I, Baillie DL, Fire A, Ruvkun G, Mello CC (2001) Genes and mechanisms related to RNA interference regulate expression of the small temporal RNAs that control C. elegans developmental timing. Cell 106: 23-34.
13. Gruber AR, Lorenz R, Bernhart SH, Neuböck R, Hofacker IL (2008) The Vienna RNA Websuite. Nucleic Acids Res 36(suppl 2): W70-W74.
14. Hammond SM, Bernstein E, Beach D, Hannon GJ (2000) An RNA-directed nuclease mediates post-transcriptional gene silencing in Drosophila cells. Nature 404: 293-296.
15. He L, Hannon GJ (2004) MicroRNAs: small RNAs with a big role in gene regulation. Nat Rev Genet 5(7): 522-531.
16. Huang JT, Lee V (2004) Identification and characterization of a novel human FOXK1 gene in silico. Int J Oncol 25(3): 751-757.
17. Hutvagner G, McLachlan J, Pasquinelli AE, Balint E, Tuschl T, Zamore PD (2001) A cellular function for the RNA-interference enzyme Dicer in the maturation of the let-7 small temporal RNA. Science 293: 834-838.
18. Ketting RF, Fischer SE, Bernstein E, Sijen T, Hannon GJ, Plasterk RH (2001) Dicer functions in RNA interference and in synthesis of small RNA involved in developmental timing in C. elegans. Genes Dev 15: 2654-2659.
19. Khan J, Wei JS, Ringnér M, Saal LH, Ladanyi M, Westermann F, Berthold F, Schwab M, Antonescu CR, Peterson C, Meltzer PS (2001) Classification and diagnostic prediction of cancers using gene expression profiling and artificial neural networks. Nat Med 7(6): 673-679.
20. Kiriakidou M, Nelson PT, Kouranov A, Fitziev P, Bouyioukos C, Mourelatos Z, Hatzigeorgiou A (2004) A combined computational-experimental approach predicts human microRNA targets. Genes Dev 18: 1165-1178.
21. Kozomara A, Griffiths-Jones S (2011) miRBase: integrating microRNA annotation and deep-sequencing data. NAR 39: D152-D157 (Database Issue).
22. Lai EC, Tomancak P, Williams RW, Rubin GM (2003) Computational identification of Drosophila microRNA genes. Genome Biol 4(7): R42.
23. Lee Y, Jeon K, Lee JT, Kim S, Kim VN (2002) MicroRNA maturation: stepwise processing and subcellular localization. EMBO J 21: 4663-4670.
24. Lee Y, Ahn C, Han J, Choi H, Kim J, Yim J, Lee J, Provost P, Rådmark O, Kim S, Kim VN (2003) The nuclear RNase III Drosha initiates microRNA processing. Nature 425: 415-419.
25. Lim LP, Glasner ME, Yekta S, Burge CB, Bartel DP (2003a) Vertebrate microRNA genes. Science 299: 1540.
26. Lim LP, Lau NC, Weinstein EG, Abdelhakim A, Yekta S, Rhoades MW, Burge CB, Bartel DP (2003b) The microRNAs of Caenorhabditis elegans. Genes Dev 17: 991.
27. Liou S-W, Huang Y-F (2012) An exon/intron disparity framework based on the nucleotide profile of single sequence. Netw Model Anal Health Inform Bioinforma 1: 19-25.
28. Maragkakis M, Alexiou P, Papadopoulos GL, Reczko M, Dalamagas T, Giannopoulos G, Goumas G, Koukis E, Kourtis K, Simossis VA, Sethupathy P, Vergoulis T, Koziris N, Sellis T, Tsanakas P, Hatzigeorgiou AG (2009a) Accurate microRNA target prediction correlates with protein repression levels. BMC Bioinform 10: 295.
29. Maragkakis M, Reczko M, Simossis VA, Alexiou P, Papadopoulos GL, Dalamagas T, Giannopoulos G, Goumas G, Koukis E, Kourtis K, Vergoulis T, Koziris N, Sellis T, Tsanakas P, Hatzigeorgiou AG (2009b) DIANA-microT web server: elucidating microRNA functions through target prediction. Nucleic Acids Res 37: W273-W276 (Web Server).
30. Mendes ND, Freitas AT, Sagot M-F (2009) Current tools for the identification of miRNA genes and their targets. Nucleic Acids Res 37(8): 2419-2433.
31. Merchant M, Vajdos FF, Ultsch M, Maun HR, Wendt U, Cannon J, Desmarais W, Lazarus RA, de Vos AM, de Sauvage FJ (2004) Suppressor of fused regulates Gli activity through a dual binding mechanism. Mol Cell Biol 24(19): 8627-8641.
32. Nathans R, Chu CY, Serquina AK, Lu CC, Cao H, Rana TM (2009) Cellular MicroRNA and P bodies modulate host-HIV-1 interactions. Mol Cell 34: 696-709.
33. Petrussa E, Bertolini A, Casolo V, Krajnáková J, Macrì F, Vianello A (2009) Mitochondrial bioenergetics linked to the manifestation of programmed cell death during somatic embryogenesis of Abies alba. Planta 231(1): 93-107.
34. Pfeffer S, Sewer A, Lagos-Quintana M, Sheridan R, Sander C, Grässer FA, van Dyk LF, Ho CK, Shuman S, Chien M, Russo JJ, Ju J, Randall G, Lindenbach BD, Rice CM, Simon V, Ho DD, Zavolan M, Tuschl T (2005) Identification of microRNAs of the herpesvirus family. Nat Methods 2(4): 269-276.
35. Saitoh T, Hirai M, Katoh M (2001) Molecular cloning and characterization of WNT3A and WNT14 clustered in human chromosome 1q42 region. Biochem Biophys Res Commun 284(5): 1168-1175.
36. Taylor MD, Liu L, Raffel C, Hui CC, Mainprize TG, Zhang X, Agatep R, Chiappa S, Gao L, Lowrance A et al (2002) Mutations in SUFU predispose to medulloblastoma. Nat Genet 31: 306-310.
37. Taylor MD, Zhang X, Liu L, Hui CC, Mainprize TG, Scherer SW et al (2004) Failure of a medulloblastoma-derived mutant of SUFU to suppress WNT signaling. Oncogene 23: 4577-4583.
38. Thomassen GO, Røsok O, Rognes T (2006) Computational prediction of MicroRNAs encoded in viral and other genomes. J Biomed Biotechnol 4: 95270.
39. van Hulse J, Khoshgoftaar TM, Al Napolitano, Wald R (2012) Threshold-based feature selection techniques for high-dimensional bioinformatics data. Netw Model Anal Health Inf Bioinform 1(1-2): 47-61.
40. Wang XW, Zhang J, Li F, Gu G, He T, Zhang XG, Li YD (2005) MicroRNA identification based on sequence and structure alignment. Bioinform 21(18): 3610-3614.
41. Zillner S, Sonntag D (2012) Image metadata reasoning for improved clinical decision support. Netw Model Anal Health Inform Bioinform 1: 37-46.