메뉴 건너뛰기




Volumn 8, Issue 1, 2013, Pages

mirTarPri: Improved Prioritization of MicroRNA Targets through Incorporation of Functional Genomics Data

Author keywords

[No Author keywords available]

Indexed keywords

ALPHA SYNUCLEIN; EPIDERMAL GROWTH FACTOR RECEPTOR; INSULIN RECEPTOR SUBSTRATE 1; INSULIN RECEPTOR SUBSTRATE 2; MICRORNA; MICRORNA 7; P21 ACTIVATED KINASE 1; UNCLASSIFIED DRUG;

EID: 84872242932     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0053685     Document Type: Article
Times cited : (13)

References (63)
  • 1
    • 39749110083 scopus 로고    scopus 로고
    • Small non-coding RNAs in animal development
    • Stefani G, Slack FJ, (2008) Small non-coding RNAs in animal development. Nat Rev Mol Cell Biol 9: 219-230.
    • (2008) Nat Rev Mol Cell Biol , vol.9 , pp. 219-230
    • Stefani, G.1    Slack, F.J.2
  • 2
    • 43049134831 scopus 로고    scopus 로고
    • MicroRNomics: a newly emerging approach for disease biology
    • Zhang C, (2008) MicroRNomics: a newly emerging approach for disease biology. Physiol Genomics 33: 139-147.
    • (2008) Physiol Genomics , vol.33 , pp. 139-147
    • Zhang, C.1
  • 3
    • 58249088751 scopus 로고    scopus 로고
    • MicroRNAs: target recognition and regulatory functions
    • Bartel DP, (2009) MicroRNAs: target recognition and regulatory functions. Cell 136: 215-233.
    • (2009) Cell , vol.136 , pp. 215-233
    • Bartel, D.P.1
  • 4
    • 35148882865 scopus 로고    scopus 로고
    • Role of miRNA in carcinogenesis and biomarker selection: a methodological view
    • Ahmed FE, (2007) Role of miRNA in carcinogenesis and biomarker selection: a methodological view. Expert Rev Mol Diagn 7: 569-603.
    • (2007) Expert Rev Mol Diagn , vol.7 , pp. 569-603
    • Ahmed, F.E.1
  • 5
    • 62549098152 scopus 로고    scopus 로고
    • MicroRNAs: control and loss of control in human physiology and disease
    • Li M, Marin-Muller C, Bharadwaj U, Chow KH, Yao Q, et al. (2009) MicroRNAs: control and loss of control in human physiology and disease. World J Surg 33: 667-684.
    • (2009) World J Surg , vol.33 , pp. 667-684
    • Li, M.1    Marin-Muller, C.2    Bharadwaj, U.3    Chow, K.H.4    Yao, Q.5
  • 6
    • 65649138698 scopus 로고    scopus 로고
    • MicroRNA polymorphisms: the future of pharmacogenomics, molecular epidemiology and individualized medicine
    • Mishra PJ, Bertino JR, (2009) MicroRNA polymorphisms: the future of pharmacogenomics, molecular epidemiology and individualized medicine. Pharmacogenomics 10: 399-416.
    • (2009) Pharmacogenomics , vol.10 , pp. 399-416
    • Mishra, P.J.1    Bertino, J.R.2
  • 8
    • 34748821761 scopus 로고    scopus 로고
    • The role of site accessibility in microRNA target recognition
    • Kertesz M, Iovino N, Unnerstall U, Gaul U, Segal E, (2007) The role of site accessibility in microRNA target recognition. Nat Genet 39: 1278-1284.
    • (2007) Nat Genet , vol.39 , pp. 1278-1284
    • Kertesz, M.1    Iovino, N.2    Unnerstall, U.3    Gaul, U.4    Segal, E.5
  • 10
    • 2442672918 scopus 로고    scopus 로고
    • A combined computational-experimental approach predicts human microRNA targets
    • Kiriakidou M, Nelson PT, Kouranov A, Fitziev P, Bouyioukos C, et al. (2004) A combined computational-experimental approach predicts human microRNA targets. Genes Dev 18: 1165-1178.
    • (2004) Genes Dev , vol.18 , pp. 1165-1178
    • Kiriakidou, M.1    Nelson, P.T.2    Kouranov, A.3    Fitziev, P.4    Bouyioukos, C.5
  • 11
    • 11844278458 scopus 로고    scopus 로고
    • Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets
    • Lewis BP, Burge CB, Bartel DP, (2005) Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell 120: 15-20.
    • (2005) Cell , vol.120 , pp. 15-20
    • Lewis, B.P.1    Burge, C.B.2    Bartel, D.P.3
  • 13
    • 4644237189 scopus 로고    scopus 로고
    • Fast and effective prediction of microRNA/target duplexes
    • Rehmsmeier M, Steffen P, Hochsmann M, Giegerich R, (2004) Fast and effective prediction of microRNA/target duplexes. Rna 10: 1507-1517.
    • (2004) Rna , vol.10 , pp. 1507-1517
    • Rehmsmeier, M.1    Steffen, P.2    Hochsmann, M.3    Giegerich, R.4
  • 14
    • 33748346026 scopus 로고    scopus 로고
    • Perfect seed pairing is not a generally reliable predictor for miRNA-target interactions
    • Didiano D, Hobert O, (2006) Perfect seed pairing is not a generally reliable predictor for miRNA-target interactions. Nat Struct Mol Biol 13: 849-851.
    • (2006) Nat Struct Mol Biol , vol.13 , pp. 849-851
    • Didiano, D.1    Hobert, O.2
  • 16
    • 22244447130 scopus 로고    scopus 로고
    • Weighted sequence motifs as an improved seeding step in microRNA target prediction algorithms
    • Saetrom O, Snove O Jr, Saetrom P, (2005) Weighted sequence motifs as an improved seeding step in microRNA target prediction algorithms. Rna 11: 995-1003.
    • (2005) Rna , vol.11 , pp. 995-1003
    • Saetrom, O.1    Snove Jr., O.2    Saetrom, P.3
  • 17
    • 33749645474 scopus 로고    scopus 로고
    • miTarget: microRNA target gene prediction using a support vector machine
    • Kim SK, Nam JW, Rhee JK, Lee WJ, Zhang BT, (2006) miTarget: microRNA target gene prediction using a support vector machine. BMC Bioinformatics 7: 411.
    • (2006) BMC Bioinformatics , vol.7 , pp. 411
    • Kim, S.K.1    Nam, J.W.2    Rhee, J.K.3    Lee, W.J.4    Zhang, B.T.5
  • 18
    • 70450172473 scopus 로고    scopus 로고
    • Survey of Computational Algorithms for MicroRNA Target Prediction
    • Yue D, Liu H, Huang Y, (2009) Survey of Computational Algorithms for MicroRNA Target Prediction. Curr Genomics 10: 478-492.
    • (2009) Curr Genomics , vol.10 , pp. 478-492
    • Yue, D.1    Liu, H.2    Huang, Y.3
  • 19
    • 77954504259 scopus 로고    scopus 로고
    • Comparison and integration of target prediction algorithms for microRNA studies
    • Zhang Y, Verbeek FJ (2010) Comparison and integration of target prediction algorithms for microRNA studies. J Integr Bioinform 7.
    • (2010) J Integr Bioinform , vol.7
    • Zhang, Y.1    Verbeek, F.J.2
  • 20
    • 70350000602 scopus 로고    scopus 로고
    • TargetMiner: microRNA target prediction with systematic identification of tissue-specific negative examples
    • Bandyopadhyay S, Mitra R, (2009) TargetMiner: microRNA target prediction with systematic identification of tissue-specific negative examples. Bioinformatics 25: 2625-2631.
    • (2009) Bioinformatics , vol.25 , pp. 2625-2631
    • Bandyopadhyay, S.1    Mitra, R.2
  • 21
    • 40549138450 scopus 로고    scopus 로고
    • Comparing sequence and expression for predicting microRNA targets using GenMiR3
    • Huang JC, Frey BJ, Morris QD (2008) Comparing sequence and expression for predicting microRNA targets using GenMiR3. Pac Symp Biocomput: 52-63.
    • (2008) Pac Symp Biocomput , pp. 52-63
    • Huang, J.C.1    Frey, B.J.2    Morris, Q.D.3
  • 22
    • 36749005527 scopus 로고    scopus 로고
    • Using expression profiling data to identify human microRNA targets
    • Huang JC, Babak T, Corson TW, Chua G, Khan S, et al. (2007) Using expression profiling data to identify human microRNA targets. Nat Methods 4: 1045-1049.
    • (2007) Nat Methods , vol.4 , pp. 1045-1049
    • Huang, J.C.1    Babak, T.2    Corson, T.W.3    Chua, G.4    Khan, S.5
  • 23
    • 38849145861 scopus 로고    scopus 로고
    • Prediction of both conserved and nonconserved microRNA targets in animals
    • Wang X, El Naqa IM, (2008) Prediction of both conserved and nonconserved microRNA targets in animals. Bioinformatics 24: 325-332.
    • (2008) Bioinformatics , vol.24 , pp. 325-332
    • Wang, X.1    El Naqa, I.M.2
  • 24
    • 44349128983 scopus 로고    scopus 로고
    • Inferring microRNA activities by combining gene expression with microRNA target prediction
    • Cheng C, Li LM, (2008) Inferring microRNA activities by combining gene expression with microRNA target prediction. PLoS One 3: e1989.
    • (2008) PLoS One , vol.3
    • Cheng, C.1    Li, L.M.2
  • 25
    • 28944439309 scopus 로고    scopus 로고
    • Animal MicroRNAs confer robustness to gene expression and have a significant impact on 3′UTR evolution
    • Stark A, Brennecke J, Bushati N, Russell RB, Cohen SM, (2005) Animal MicroRNAs confer robustness to gene expression and have a significant impact on 3′UTR evolution. Cell 123: 1133-1146.
    • (2005) Cell , vol.123 , pp. 1133-1146
    • Stark, A.1    Brennecke, J.2    Bushati, N.3    Russell, R.B.4    Cohen, S.M.5
  • 26
    • 28344440823 scopus 로고    scopus 로고
    • MicroRNA function: multiple mechanisms for a tiny RNA?
    • Pillai RS, (2005) MicroRNA function: multiple mechanisms for a tiny RNA? Rna 11: 1753-1761.
    • (2005) Rna , vol.11 , pp. 1753-1761
    • Pillai, R.S.1
  • 27
    • 77956937207 scopus 로고    scopus 로고
    • The miR-15/107 group of microRNA genes: evolutionary biology, cellular functions, and roles in human diseases
    • Finnerty JR, Wang WX, Hebert SS, Wilfred BR, Mao G, et al. (2010) The miR-15/107 group of microRNA genes: evolutionary biology, cellular functions, and roles in human diseases. J Mol Biol 402: 491-509.
    • (2010) J Mol Biol , vol.402 , pp. 491-509
    • Finnerty, J.R.1    Wang, W.X.2    Hebert, S.S.3    Wilfred, B.R.4    Mao, G.5
  • 28
    • 84862562497 scopus 로고    scopus 로고
    • Detection of simultaneous group effects in microRNA expression and related target gene sets
    • Artmann S, Jung K, Bleckmann A, Beissbarth T, (2012) Detection of simultaneous group effects in microRNA expression and related target gene sets. PLoS One 7: e38365.
    • (2012) PLoS One , vol.7
    • Artmann, S.1    Jung, K.2    Bleckmann, A.3    Beissbarth, T.4
  • 29
    • 34249849395 scopus 로고    scopus 로고
    • Discovery of microRNA-mRNA modules via population-based probabilistic learning
    • Joung JG, Hwang KB, Nam JW, Kim SJ, Zhang BT, (2007) Discovery of microRNA-mRNA modules via population-based probabilistic learning. Bioinformatics 23: 1141-1147.
    • (2007) Bioinformatics , vol.23 , pp. 1141-1147
    • Joung, J.G.1    Hwang, K.B.2    Nam, J.W.3    Kim, S.J.4    Zhang, B.T.5
  • 30
    • 27544458484 scopus 로고    scopus 로고
    • Prediction of regulatory modules comprising microRNAs and target genes
    • Yoon S, De Micheli G, (2005) Prediction of regulatory modules comprising microRNAs and target genes. Bioinformatics 21Suppl 2: ii93-100.
    • (2005) Bioinformatics , vol.21
    • Yoon, S.1    De Micheli, G.2
  • 31
    • 1942435249 scopus 로고    scopus 로고
    • Micromanagers of gene expression: the potentially widespread influence of metazoan microRNAs
    • Bartel DP, Chen CZ, (2004) Micromanagers of gene expression: the potentially widespread influence of metazoan microRNAs. Nat Rev Genet 5: 396-400.
    • (2004) Nat Rev Genet , vol.5 , pp. 396-400
    • Bartel, D.P.1    Chen, C.Z.2
  • 32
    • 57649228450 scopus 로고    scopus 로고
    • Finding microRNA regulatory modules in human genome using rule induction
    • Tran DH, Satou K, Ho TB, (2008) Finding microRNA regulatory modules in human genome using rule induction. BMC Bioinformatics 9Suppl 12: S5.
    • (2008) BMC Bioinformatics , vol.9
    • Tran, D.H.1    Satou, K.2    Ho, T.B.3
  • 33
    • 34548339681 scopus 로고    scopus 로고
    • MicroRNA regulation of human protein protein interaction network
    • Liang H, Li WH, (2007) MicroRNA regulation of human protein protein interaction network. Rna 13: 1402-1408.
    • (2007) Rna , vol.13 , pp. 1402-1408
    • Liang, H.1    Li, W.H.2
  • 34
    • 0035733690 scopus 로고    scopus 로고
    • Correlation between transcriptome and interactome mapping data from Saccharomyces cerevisiae
    • Ge H, Liu Z, Church GM, Vidal M, (2001) Correlation between transcriptome and interactome mapping data from Saccharomyces cerevisiae. Nat Genet 29: 482-486.
    • (2001) Nat Genet , vol.29 , pp. 482-486
    • Ge, H.1    Liu, Z.2    Church, G.M.3    Vidal, M.4
  • 35
    • 9144264169 scopus 로고    scopus 로고
    • A map of the interactome network of the metazoan C. elegans
    • Li S, Armstrong CM, Bertin N, Ge H, Milstein S, et al. (2004) A map of the interactome network of the metazoan C. elegans. Science 303: 540-543.
    • (2004) Science , vol.303 , pp. 540-543
    • Li, S.1    Armstrong, C.M.2    Bertin, N.3    Ge, H.4    Milstein, S.5
  • 36
    • 27144530248 scopus 로고    scopus 로고
    • Towards a proteome-scale map of the human protein-protein interaction network
    • Rual JF, Venkatesan K, Hao T, Hirozane-Kishikawa T, Dricot A, et al. (2005) Towards a proteome-scale map of the human protein-protein interaction network. Nature 437: 1173-1178.
    • (2005) Nature , vol.437 , pp. 1173-1178
    • Rual, J.F.1    Venkatesan, K.2    Hao, T.3    Hirozane-Kishikawa, T.4    Dricot, A.5
  • 37
    • 83755205389 scopus 로고    scopus 로고
    • Prioritizing human cancer microRNAs based on genes' functional consistency between microRNA and cancer
    • Li X, Wang Q, Zheng Y, Lv S, Ning S, et al. (2011) Prioritizing human cancer microRNAs based on genes' functional consistency between microRNA and cancer. Nucleic Acids Res 39: e153.
    • (2011) Nucleic Acids Res , vol.39
    • Li, X.1    Wang, Q.2    Zheng, Y.3    Lv, S.4    Ning, S.5
  • 39
    • 58149179989 scopus 로고    scopus 로고
    • miR2Disease: a manually curated database for microRNA deregulation in human disease
    • Jiang Q, Wang Y, Hao Y, Juan L, Teng M, et al. (2009) miR2Disease: a manually curated database for microRNA deregulation in human disease. Nucleic Acids Res 37: D98-104.
    • (2009) Nucleic Acids Res , vol.37
    • Jiang, Q.1    Wang, Y.2    Hao, Y.3    Juan, L.4    Teng, M.5
  • 40
    • 58149186499 scopus 로고    scopus 로고
    • miRecords: an integrated resource for microRNA-target interactions
    • Xiao F, Zuo Z, Cai G, Kang S, Gao X, et al. (2009) miRecords: an integrated resource for microRNA-target interactions. Nucleic Acids Res 37: D105-110.
    • (2009) Nucleic Acids Res , vol.37
    • Xiao, F.1    Zuo, Z.2    Cai, G.3    Kang, S.4    Gao, X.5
  • 42
    • 0034069495 scopus 로고    scopus 로고
    • Gene ontology: tool for the unification of biology. The Gene Ontology Consortium
    • Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, et al. (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 25: 25-29.
    • (2000) Nat Genet , vol.25 , pp. 25-29
    • Ashburner, M.1    Ball, C.A.2    Blake, J.A.3    Botstein, D.4    Butler, H.5
  • 44
    • 0033930882 scopus 로고    scopus 로고
    • BIND-a data specification for storing and describing biomolecular interactions, molecular complexes and pathways
    • Bader GD, Hogue CW, (2000) BIND-a data specification for storing and describing biomolecular interactions, molecular complexes and pathways. Bioinformatics 16: 465-477.
    • (2000) Bioinformatics , vol.16 , pp. 465-477
    • Bader, G.D.1    Hogue, C.W.2
  • 48
    • 18744376914 scopus 로고    scopus 로고
    • Online predicted human interaction database
    • Brown KR, Jurisica I, (2005) Online predicted human interaction database. Bioinformatics 21: 2076-2082.
    • (2005) Bioinformatics , vol.21 , pp. 2076-2082
    • Brown, K.R.1    Jurisica, I.2
  • 50
    • 0003033112 scopus 로고
    • Using Information Content to Evaluate Semantic Similarity in a Taxonomy
    • Resnik P, (1995) Using Information Content to Evaluate Semantic Similarity in a Taxonomy. In Proceedings of IJCAI-95: 448-453.
    • (1995) In Proceedings of IJCAI-95 , pp. 448-453
    • Resnik, P.1
  • 51
    • 84860721982 scopus 로고    scopus 로고
    • A novel method to quantify gene set functional association based on gene ontology
    • Lv S, Li Y, Wang Q, Ning S, Huang T, et al. (2012) A novel method to quantify gene set functional association based on gene ontology. J R Soc Interface 9: 1063-1072.
    • (2012) J R Soc Interface , vol.9 , pp. 1063-1072
    • Lv, S.1    Li, Y.2    Wang, Q.3    Ning, S.4    Huang, T.5
  • 52
    • 34250764323 scopus 로고    scopus 로고
    • GOSim-an R-package for computation of information theoretic GO similarities between terms and gene products
    • Frohlich H, Speer N, Poustka A, Beissbarth T, (2007) GOSim-an R-package for computation of information theoretic GO similarities between terms and gene products. BMC Bioinformatics 8: 166.
    • (2007) BMC Bioinformatics , vol.8 , pp. 166
    • Frohlich, H.1    Speer, N.2    Poustka, A.3    Beissbarth, T.4
  • 55
    • 41549139527 scopus 로고    scopus 로고
    • Walking the interactome for prioritization of candidate disease genes
    • Kohler S, Bauer S, Horn D, Robinson PN, (2008) Walking the interactome for prioritization of candidate disease genes. Am J Hum Genet 82: 949-958.
    • (2008) Am J Hum Genet , vol.82 , pp. 949-958
    • Kohler, S.1    Bauer, S.2    Horn, D.3    Robinson, P.N.4
  • 56
    • 2342449399 scopus 로고    scopus 로고
    • Identification and characterization of a novel gene, C13orf25, as a target for 13q31-q32 amplification in malignant lymphoma
    • Ota A, Tagawa H, Karnan S, Tsuzuki S, Karpas A, et al. (2004) Identification and characterization of a novel gene, C13orf25, as a target for 13q31-q32 amplification in malignant lymphoma. Cancer Res 64: 3087-3095.
    • (2004) Cancer Res , vol.64 , pp. 3087-3095
    • Ota, A.1    Tagawa, H.2    Karnan, S.3    Tsuzuki, S.4    Karpas, A.5
  • 58
    • 82455172056 scopus 로고    scopus 로고
    • myMIR: a genome-wide microRNA targets identification and annotation tool
    • Corrada D, Viti F, Merelli I, Battaglia C, Milanesi L, (2011) myMIR: a genome-wide microRNA targets identification and annotation tool. Brief Bioinform 12: 588-600.
    • (2011) Brief Bioinform , vol.12 , pp. 588-600
    • Corrada, D.1    Viti, F.2    Merelli, I.3    Battaglia, C.4    Milanesi, L.5
  • 59
    • 78651266827 scopus 로고    scopus 로고
    • miRTarBase: a database curates experimentally validated microRNA-target interactions
    • Hsu SD, Lin FM, Wu WY, Liang C, Huang WC, et al. (2011) miRTarBase: a database curates experimentally validated microRNA-target interactions. Nucleic Acids Res 39: D163-169.
    • (2011) Nucleic Acids Res , vol.39
    • Hsu, S.D.1    Lin, F.M.2    Wu, W.Y.3    Liang, C.4    Huang, W.C.5
  • 61
    • 77950920903 scopus 로고    scopus 로고
    • Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP
    • Hafner M, Landthaler M, Burger L, Khorshid M, Hausser J, et al. (2010) Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP. Cell 141: 129-141.
    • (2010) Cell , vol.141 , pp. 129-141
    • Hafner, M.1    Landthaler, M.2    Burger, L.3    Khorshid, M.4    Hausser, J.5
  • 62
    • 67749132423 scopus 로고    scopus 로고
    • Argonaute HITS-CLIP decodes microRNA-mRNA interaction maps
    • Chi SW, Zang JB, Mele A, Darnell RB, (2009) Argonaute HITS-CLIP decodes microRNA-mRNA interaction maps. Nature 460: 479-486.
    • (2009) Nature , vol.460 , pp. 479-486
    • Chi, S.W.1    Zang, J.B.2    Mele, A.3    Darnell, R.B.4
  • 63
    • 78651307694 scopus 로고    scopus 로고
    • starBase: a database for exploring microRNA-mRNA interaction maps from Argonaute CLIP-Seq and Degradome-Seq data
    • Yang JH, Li JH, Shao P, Zhou H, Chen YQ, et al. (2010) starBase: a database for exploring microRNA-mRNA interaction maps from Argonaute CLIP-Seq and Degradome-Seq data. Nucleic Acids Res 39: D202-209.
    • (2010) Nucleic Acids Res , vol.39
    • Yang, J.H.1    Li, J.H.2    Shao, P.3    Zhou, H.4    Chen, Y.Q.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.