Please use this identifier to cite or link to this item: http://hdl.handle.net/11455/19493
標題: 前導微核糖核酸預測線上伺服系統
A Web Server for Precursor miRNA Prediction
作者: 蕭人豪
Shau, Ren-Hau
關鍵字: miRNA;前導微核糖核酸;small RNA;pre-miRNA;微核糖核酸
出版社: 資訊科學與工程學系所
引用: [1] Aurora Esquela-Kerscher & Frank J. Slack,Oncomirs — microRNAs with a role in cancer. Review. Nature Reviews Cancer 6, 2006,259-269 [2] Reinhart B J,Slack F J,Basson M, et al.The 21-nucleotide let7 RNA regulates developmental timing in Caenorhabditis elegans.Nature,2000,403:901~906 [3] Lee R C, Feinbaum R L, Ambros V.The C.elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14.Cell,1993,75:843~854 [4] Lee R C, Ambros V. An extensive class of small RNAs in Caenorhabditis elegans. Science,2001,294:862~864 [5] Reinhart B J,Weinstein E G,Rhoades M W,et al.MicroRNAs in plants.Genes Dev,2002,16(13):1616~1626 [6] Anthony K.L. Leung and Phillip A. Sharp.microRNAs: A Safeguard against Turmoil?Cell, 24 August 2007,Vol 130, 581-585 [7] Zhao B, Liang R, Ge L, Li W, Xiao H, Lin H, Ruan K, Jin Y. Identification of drought-induced microRNAs in rice. Biochem Biophys Res Commun, 2007, 354(2): 585−590 [8] Sunkar R, Zhu JK. Novel and stress-regulated microRNAs and other small RNAs from Arabidopsis. Plant Cell, 2004, 16(8): 2001−2019 [9] Leung AK, Sharp PA. microRNAs: a safeguard against turmoil? Cell, 2007, 130(4): 581−585 [10] Tomari Y, Zamore PD (2005) MicroRNA biogenesis: Drosha can''t cut it without a partner. Curr Biol 15:R61-64 [11] Xue C, Li F, He T, Liu GP, Li Y, Zhang X. Classification of real and pseudo microRNA precursors using local structure-sequence features and support vector machine. BMC Bioinformatics, 2005, 6(1): 310 [12] Ng KLS, Mishra SK. De novo SVM classification of pre-cursor microRNAs from genomic pseudo hairpins using global and intrinsic folding measures. Bioinformatics, 2007, 23(11): 1321−1330 [13] Sewer A, Paul N, Landgraf P, Aravin A, Pfeffer S, Brown-stein M, Tuschl T, van Nimwegen E, Zavolan M. Identifi-cation of clustered microRNAs using an ab initio predic-tion method. BMC Bioinformatics, 2005, 6(1): 267 [14] Pfeffer S, Sewer A, Lagos-Quintana M, Sheridan R, Sander C, Grasser 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. Identifica-tion of microRNAs of the herpesvirus family. Nat Me- thods, 2005, 2(4): 269−276 [15] Hertel J, Stadler PF. Hairpins in a Haystack: recognizing microRNA precursors in comparative genomics data. Bioinformatics, 2006, 22(14): e197−e202 [16] Helvik SA, Snove O Jr, Saetrom P. Reliable prediction of Drosha processing sites improves microRNA gene predic-tion. Bioinformatics, 2007, 23(2): 142−149 [17] Jiang P, Wu H, Wang W, Ma W, Sun X, Lu Z. MiPred: classification of real and pseudo microRNA precursors using random forest prediction model with combined fea-tures. Nucleic Acids Research, 2007, 35(Web Server issue): W339−W344 [18] Nam JW, Shin KR, Han J, Lee Y, Kim VN, Zhang BT. Human microRNA prediction through a probabilistic co-learning model of sequence and structure. Nucleic Aci- ds Res, 2005, 33(11): 3570−3581 [19] Bonnet E, Wuyts J, Rouze P, Van de Peer Y. Evidence that microRNA precursors, unlike other non-coding RNAs, have lower folding free energies than random sequences. Bioinformatics, 2004, 20(17): 2911−2917 [20] Berezikov E, Guryev V, van de BJ, Wienholds E, Plasterk RH, Cuppen E. Phylogenetic shadowing and computa-tional identification of human microRNA genes. Cell, 2005, 120(1): 21−24 [21] Yousef M, Nebozhyn M, Shatkay H, Kanterakis S, Showe LC, Showe MK. Combining multi-species genomic data for microRNA identification using a Naive Bayes classi-fier. Bioinformatics, 2006, 22(11): 1325−1334 [22] Lee, Y., C. Ahn, et al. (2003). "The nuclear RNase III Drosha initiates microRNA processing." Nature 425(6956): 415-9 [23] Tomari, Y. and P. D. Zamore (2005). "MicroRNA biogenesis: drosha can''t cut it without a partner." Curr Biol 15(2): R61-4. [24] Griffiths-Jones S, Grocock RJ, van Dongen S, Bateman A,Enright AJ. miRBase: microRNA sequences, targets and gene nomenclature. Nucleic Acids Res, 2006, 34(Suppl_1): D140−D144 [25] Zhao B, Liang R, Ge L, Li W, Xiao H, Lin H, Ruan K, Jin Y. Identification of drought-induced microRNAs in rice. Biochem Biophys Res Commun, 2007, 354(2): 585−590 [26] Sunkar R, Zhu JK. Novel and stress-regulated microRNAs and other small RNAs from Arabidopsis. Plant Cell, 2004, 16(8): 2001−2019 [27] Leung AK, Sharp PA. microRNAs: a safeguard against turmoil? Cell, 2007, 130(4): 581−585 [28] Lee Y, Kim M, Han J, Yeom KH, Lee S, Baek SH, Kim VN. MicroRNA genes are transcribed by RNA polymerase Ⅱ. EMBO Journal, 2004, 23: 4051-4060. [29] Bracht J, Hunter S, Eachus R, Weeks P, Pasquinelli AE. Trans-splicing and polyadenylation of let-7 microRNA primary transcripts. RNA. 2004 10:1586-1594. [30] Gasciolli V,Mallory AC,Barrel DP,Vancheret H (2005).Partially redundant functions of Arabidopsis DICER-like enzymes and a role for DCL4 in producing trans-acting siRNAs.Curr Biol,15 (16):1494~1500 [31] Mariana Lagos-Quintana,Reinhard Rauhut,Winfried Lendeckel,Thomas Tuschl. Identification of Novel Genes Coding for Small Expressed RNAs.Science 26 October 2001:Vol. 294. no. 5543, pp. 853 - 858. [32] Lau N C Weinstein E G Weinstein E G.An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans.Science,2001, 5543 P 858-862 [33] H.W. Huang , T.-Z. Liu, K.-H. Lee, C.-F. Tu, W.-C. Lee, T. Shimogiri, H. Mannen, S.S.-L. Li, cDNA cloning of pig testicular lactate dehydrogenase-C, thermal stability of the expressed enzyme, and polymorphism among strains., Gene, 242:151-154 (2000) [34] Lee P Lim, Nelson C Lau,Earl G Weinstein,Aliaa Abdelhakim,Soraya Yekta,Matthew W Rhoades,Christopher B Burge,David P Bartel Department of Biology, Massachusetts Institute of Technology, Cambridge 02139, USA.The microRNAs of Caenorhabditis elegans. Genes Dev. 2003 Apr 15;17 (8):991-1008 12672692 (P,S,E,B) Cited:54 [35] Mourelatos Z, Dostie J, Paushkin S, et al. miRNPs: A novel class of ribonucleoproteins containing numerous microRNAs. Genes Dev, 2002, 16: 720~728 [36] Houbaviy H B, Murray M F, Sharp P A. Embryonic stem cell-specific microRNAs. Dev Cell, 2003, 5: 351~358 [37] Dostie J, Mourelatos Z, Yang M, et al. Numerous microRNPs in neuronal cells containing novel microRNAs. RNA, 2003, 9: 180~186 [38] Kim J, Krichevsky A, Grad Y, et al. Identification of many mi-croRNAs that copurify with polyribosomes in mammalian neurons. Proc Natl Acad Sci USA, 2004, 101: 360~365 [39] Ambros V, Lee R C, Lavanway A, et al. MicroRNAs and other tiny endogenous RNAs in C. elegans. Curr Biol, 2003, 13: 807~818 [40] Aravin A A, Lagos-Quintana M, Yalcin A, et al. The small RNA profile during Drosophila melanogaster development. Dev Cell, 2003, 5: 337~350 [41] Wang J F, Zhou H, Chen Y Q, et al. Identification of 20 microRNAs from Oryza sativa. Nucl Acids Res, 2004, 32(5): 1688~1695 [42] Lee Y, Kim M, Han J, et al. MicroRNA genes are transcribed by RNA polymeraseⅡ. EMBO J, 2004, 23(20): 4051~4060 [43] Allawi H T, Dahlberg J E, Olson S, et al. Quantitation of microRNAs using a modified Invader assay. RNA, 2004, 10(7): 1153~1161 [44] Liu C G, Calin G A, Meloon B, et al. An oligonucleotide micro-chip for genome-wide microRNA profiling in human and mouse tissues. Proc Natl Acad Sci USA, 2004, 101(26): 9740~9744 [45] Johnson S M, Lin S Y, Slack F J. The time of appearance of the C. elegans let-7 microRNA is transcriptionally controlled utilizing a temporal regulatory element in its promoter. Dev Biol, 2003, 259(2): 364~379 [46] Mansfield J H, Harfe B D, Nissen R, et al. MicroRNA-responsive ‘sensor' transgenes uncover Hox-like and other developmentally regulated patterns of vertebrate microRNA expression. Nat Genet, 2004, 36(10): 1079~83 [47] Lim L P, Lau N C, Weinstein E G, et al. The microRNAs of Caenorhabditis elegans. Genes Dev, 2003, 17: 991~1008 [48] Lim L P, Glasner M E, Yekta S, et al. Vertebrate microRNA genes. Science, 2003, 299: 1540 [50] Ohler U, Yekta S, Lim LP, et al. Patterns of flanking sequence conservation and a characteristic upstream motif for microRNA gene identification. RNA, 2004, 10(9): 1309~1322 [51] Lai E C, Tomancak P, Williams R W, et al. Computational identi-fication of Drosophila microRNA genes. Genome Biol, 2003, 4: R42, 1~20 [52] Legendre M, Lambert A, Gautheret D. Profile-based detection of microRNA precursors in animal genomes. Bioinformatics, 2005, 21(7): 841~845 [53] Zuker, M., 2003. "Mfold web server for nucleic acid folding and hybridization prediction", Nucleic Acids Research, 31,3406-3415 [54] Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK.miRBase: the microRNA sequence database [55] miRNA SVM,https://demo1.interagon.com/miRNA/cgi-bin/MiRNASVM.cgi [56] mirz,http://www.mirz.unibas.ch/
摘要: 
微核糖核酸(micro RNA;miRNA)於近年來陸續備受重視,除了它本身是新發現的小分子核糖核酸(small RNA)成員之一外,miRNA在生物體內所扮演的角色,才是它之所以備受矚目的原因。miRNA最主要可以調控基因的表現,如細胞生長、組織分化、器官形成、胚胎發育等;透過miRNA進一步有效調控基因表現,將此一機制運用於病理方面,將更為有效地達到疾病治療之效果。目前miRNAs的發現除了實際透過生物實驗外,還可運用計算方式預測潛在miRNAs。透過計算方式預測miRNA除了能有效快速找到潛在 miRNAs外,更可以大量減少生物實驗成本。本論文提供一線上分析伺服系統,只需要給定微核糖核酸序列(RNA sequence),便能將序列中潛在含有成熟miRNA的前導微核糖核酸(precursor miRNA;pre-miRNA)尋找出來。本線上分析伺服系統除了能快速得知RNA 序列內是否含有當下已知miRNAs外,亦能預測出潛在的新miRNA,如此一來對於欲預測未知miRNA或快速取出miRNAs等需求,提供了一套方便及實用的服務平台。
URI: http://hdl.handle.net/11455/19493
其他識別: U0005-0108200817444400
Appears in Collections:資訊科學與工程學系所

Show full item record
 

Google ScholarTM

Check


Items in DSpace are protected by copyright, with all rights reserved, unless otherwise indicated.