메뉴 건너뛰기




Volumn 14, Issue 1, 2013, Pages

BayMiR: Inferring evidence for endogenous miRNA-induced gene repression from mRNA expression profiles

Author keywords

[No Author keywords available]

Indexed keywords

3' UNTRANSLATED REGION; MESSENGER RNA; MICRORNA; TRANSCRIPTOME;

EID: 84883157920     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-14-592     Document Type: Article
Times cited : (3)

References (81)
  • 1
    • 58249088751 scopus 로고    scopus 로고
    • MicroRNAs: target recognition and regulatory functions
    • 10.1016/j.cell.2009.01.002, 3794896, 19167326
    • Bartel D. MicroRNAs: target recognition and regulatory functions. Cell 2009, 136(2):215-233. 10.1016/j.cell.2009.01.002, 3794896, 19167326.
    • (2009) Cell , vol.136 , Issue.2 , pp. 215-233
    • Bartel, D.1
  • 2
    • 14044251458 scopus 로고    scopus 로고
    • Human microRNA targets
    • 10.1371/journal.pbio.0020363, 521178, 15502875
    • John B, Enright A, Aravin A, Tuschl T, Sander C, Marks D, et al. Human microRNA targets. PLoS Biol 2004, 2(11):e363. 10.1371/journal.pbio.0020363, 521178, 15502875.
    • (2004) PLoS Biol , vol.2 , Issue.11
    • John, B.1    Enright, A.2    Aravin, A.3    Tuschl, T.4    Sander, C.5    Marks, D.6
  • 3
    • 79955859316 scopus 로고    scopus 로고
    • Biological functions of microRNAs: a review
    • 10.1007/s13105-010-0050-6, 20981514
    • Huang Y, Shen XJ, Zou Q, Wang SP, Tang SM, Zhang GZ. Biological functions of microRNAs: a review. J Physiol Biochem 2011, 67:129-139. 10.1007/s13105-010-0050-6, 20981514.
    • (2011) J Physiol Biochem , vol.67 , pp. 129-139
    • Huang, Y.1    Shen, X.J.2    Zou, Q.3    Wang, S.P.4    Tang, S.M.5    Zhang, G.Z.6
  • 4
    • 4644309196 scopus 로고    scopus 로고
    • The functions of animal microRNAs
    • 10.1038/nature02871, 15372042
    • Ambros V. The functions of animal microRNAs. Nature 2004, 431(7006):350-355. 10.1038/nature02871, 15372042.
    • (2004) Nature , vol.431 , Issue.7006 , pp. 350-355
    • Ambros, V.1
  • 5
    • 0141843656 scopus 로고    scopus 로고
    • The nuclear RNase III Drosha initiates microRNA processing
    • 10.1038/nature01957, 14508493
    • Lee Y, Ahn C, Han J, Choi H, Kim J, Yim J, Lee J, Provost P, Rådmark O, Kim S, et al. The nuclear RNase III Drosha initiates microRNA processing. Nature 2003, 425(6956):415-419. 10.1038/nature01957, 14508493.
    • (2003) Nature , vol.425 , Issue.6956 , pp. 415-419
    • Lee, Y.1    Ahn, C.2    Han, J.3    Choi, H.4    Kim, J.5    Yim, J.6    Lee, J.7    Provost, P.8    Rådmark, O.9    Kim, S.10
  • 6
    • 34447102459 scopus 로고    scopus 로고
    • Molecular basis for target RNA recognition and cleavage by human RISC
    • 10.1016/j.cell.2007.04.037, 17632058
    • Ameres S, Martinez J, Schroeder R. Molecular basis for target RNA recognition and cleavage by human RISC. Cell 2007, 130:101-112. 10.1016/j.cell.2007.04.037, 17632058.
    • (2007) Cell , vol.130 , pp. 101-112
    • Ameres, S.1    Martinez, J.2    Schroeder, R.3
  • 7
    • 0346094457 scopus 로고    scopus 로고
    • Prediction of mammalian microRNA targets
    • 10.1016/S0092-8674(03)01018-3, 14697198
    • Lewis B, Shih I, et al. Prediction of mammalian microRNA targets. Cell 2003, 115(7):787-798. 10.1016/S0092-8674(03)01018-3, 14697198.
    • (2003) Cell , vol.115 , Issue.7 , pp. 787-798
    • Lewis, B.1    Shih, I.2
  • 8
    • 34250805982 scopus 로고    scopus 로고
    • MicroRNA targeting specificity in mammals: determinants beyond seed pairing
    • 10.1016/j.molcel.2007.06.017, 3800283, 17612493
    • Grimson A, Farh K, Johnston W, Garrett-Engele P, Lim L, Bartel D. MicroRNA targeting specificity in mammals: determinants beyond seed pairing. Mol Cell 2007, 27:91-105. 10.1016/j.molcel.2007.06.017, 3800283, 17612493.
    • (2007) Mol Cell , vol.27 , pp. 91-105
    • Grimson, A.1    Farh, K.2    Johnston, W.3    Garrett-Engele, P.4    Lim, L.5    Bartel, D.6
  • 9
    • 77955963884 scopus 로고    scopus 로고
    • Comprehensive modeling of microRNA targets predicts functional non-conserved and non-canonical sites
    • 10.1186/gb-2010-11-8-r90, 2945792, 20799968
    • Betel D, Koppal A, Agius P, Sander C, Leslie C. Comprehensive modeling of microRNA targets predicts functional non-conserved and non-canonical sites. Genome Biol 2010, 11(8):R90. 10.1186/gb-2010-11-8-r90, 2945792, 20799968.
    • (2010) Genome Biol , vol.11 , Issue.8
    • Betel, D.1    Koppal, A.2    Agius, P.3    Sander, C.4    Leslie, C.5
  • 10
    • 84874646362 scopus 로고    scopus 로고
    • A biophysical miRNA-mRNA interaction model infers canonical and noncanonical targets
    • 10.1038/nmeth.2341, 23334102
    • Khorshid M, Hausser J, Zavolan M, van Nimwegen E. A biophysical miRNA-mRNA interaction model infers canonical and noncanonical targets. Nat Methods 2013, 10:253-255. 10.1038/nmeth.2341, 23334102.
    • (2013) Nat Methods , vol.10 , pp. 253-255
    • Khorshid, M.1    Hausser, J.2    Zavolan, M.3    van Nimwegen, E.4
  • 11
    • 4644237189 scopus 로고    scopus 로고
    • Fast and effective prediction of microRNA/target duplexes
    • 10.1261/rna.5248604, 1370637, 15383676
    • Rehmsmeier M, Steffen P, Hochsmann M, Giegerich R. Fast and effective prediction of microRNA/target duplexes. Rna 2004, 10(10):1507. 10.1261/rna.5248604, 1370637, 15383676.
    • (2004) Rna , vol.10 , Issue.10 , pp. 1507
    • Rehmsmeier, M.1    Steffen, P.2    Hochsmann, M.3    Giegerich, R.4
  • 12
    • 60149095444 scopus 로고    scopus 로고
    • Most mammalian mRNAs are conserved targets of microRNAs
    • 2612969, 18955434
    • Friedman RC, Farh KKH, Burge CB, Bartel DP. Most mammalian mRNAs are conserved targets of microRNAs. Genome Res 2009, 19:92-105. 2612969, 18955434.
    • (2009) Genome Res , vol.19 , pp. 92-105
    • Friedman, R.C.1    Farh, K.K.H.2    Burge, C.B.3    Bartel, D.P.4
  • 13
    • 35548996307 scopus 로고    scopus 로고
    • Determinants of targeting by endogenous and exogenous microRNAs and siRNAs
    • 10.1261/rna.768207, 2040081, 17872505
    • Nielsen C, Shomron N, Sandberg R, Hornstein E, Kitzman J, Burge C. Determinants of targeting by endogenous and exogenous microRNAs and siRNAs. Rna 2007, 13(11):1894. 10.1261/rna.768207, 2040081, 17872505.
    • (2007) Rna , vol.13 , Issue.11 , pp. 1894
    • Nielsen, C.1    Shomron, N.2    Sandberg, R.3    Hornstein, E.4    Kitzman, J.5    Burge, C.6
  • 14
    • 34347398567 scopus 로고    scopus 로고
    • Inference of miRNA targets using evolutionary conservation and pathway analysis
    • 10.1186/1471-2105-8-69, 1838429, 17331257
    • 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.
    • (2007) BMC Bioinformatics , vol.8 , pp. 69
    • Gaidatzis, D.1    Van Nimwegen, E.2    Hausser, J.3    Zavolan, M.4
  • 15
    • 34748821761 scopus 로고    scopus 로고
    • The role of site accessibility in microRNA target recognition
    • 10.1038/ng2135, 17893677
    • Kertesz M, Iovino N, Unnerstall U, Gaul U, Segal E. The role of site accessibility in microRNA target recognition. Nature Genet 2007, 39(10):1278-1284. 10.1038/ng2135, 17893677.
    • (2007) Nature Genet , vol.39 , Issue.10 , pp. 1278-1284
    • Kertesz, M.1    Iovino, N.2    Unnerstall, U.3    Gaul, U.4    Segal, E.5
  • 17
    • 34347393301 scopus 로고    scopus 로고
    • Spatial preferences of microRNA targets in 3' untranslated regions
    • 10.1186/1471-2164-8-152, 1904200, 17555584
    • Majoros W, Ohler U. Spatial preferences of microRNA targets in 3' untranslated regions. BMC Genomics 2007, 8:152. 10.1186/1471-2164-8-152, 1904200, 17555584.
    • (2007) BMC Genomics , vol.8 , pp. 152
    • Majoros, W.1    Ohler, U.2
  • 18
    • 80455154984 scopus 로고    scopus 로고
    • Weak seed-pairing stability and high target-site abundance decrease the proficiency of lsy-6 and other microRNAs
    • 10.1038/nsmb.2115, 3190056, 21909094
    • Garcia D, Baek D, Shin C, Bell G, Grimson A, Bartel D. Weak seed-pairing stability and high target-site abundance decrease the proficiency of lsy-6 and other microRNAs. Nat Struct Mol Biol 2011, 18(10):1139-1146. 10.1038/nsmb.2115, 3190056, 21909094.
    • (2011) Nat Struct Mol Biol , vol.18 , Issue.10 , pp. 1139-1146
    • Garcia, D.1    Baek, D.2    Shin, C.3    Bell, G.4    Grimson, A.5    Bartel, D.6
  • 20
    • 66249106716 scopus 로고    scopus 로고
    • Predicting microRNA targets and functions: traps for the unwary
    • 10.1038/nmeth0609-397, 19478799
    • Ritchie W, Flamant S, Rasko J. Predicting microRNA targets and functions: traps for the unwary. Nat Methods 2009, 6(6):397-398. 10.1038/nmeth0609-397, 19478799.
    • (2009) Nat Methods , vol.6 , Issue.6 , pp. 397-398
    • Ritchie, W.1    Flamant, S.2    Rasko, J.3
  • 22
    • 77952840905 scopus 로고    scopus 로고
    • MicroRNAs-targeting and target prediction
    • Saito T, Sætrom P. MicroRNAs-targeting and target prediction. New Biotechnol 2010, 27(3):243-249.
    • (2010) New Biotechnol , vol.27 , Issue.3 , pp. 243-249
    • Saito, T.1    Sætrom, P.2
  • 24
    • 74049088856 scopus 로고    scopus 로고
    • Lost in translation: an assessment and perspective for computational microRNA target identification
    • 10.1093/bioinformatics/btp565, 19789267
    • Alexiou P, Maragkakis M, Papadopoulos G, Reczko M, Hatzigeorgiou A. Lost in translation: an assessment and perspective for computational microRNA target identification. Bioinformatics 2009, 25(23):3049-3055. 10.1093/bioinformatics/btp565, 19789267.
    • (2009) Bioinformatics , vol.25 , Issue.23 , pp. 3049-3055
    • Alexiou, P.1    Maragkakis, M.2    Papadopoulos, G.3    Reczko, M.4    Hatzigeorgiou, A.5
  • 25
    • 77951953262 scopus 로고    scopus 로고
    • Got target?: computational methods for microRNA target prediction and their extension
    • 10.3858/emm.2010.42.4.032, 2859323, 20177143
    • Min H, Yoon S. Got target?: computational methods for microRNA target prediction and their extension. Exp Mol Med 2010, 42(4):233. 10.3858/emm.2010.42.4.032, 2859323, 20177143.
    • (2010) Exp Mol Med , vol.42 , Issue.4 , pp. 233
    • Min, H.1    Yoon, S.2
  • 26
    • 77955644289 scopus 로고    scopus 로고
    • Mammalian microRNAs predominantly act to decrease target mRNA levels
    • 10.1038/nature09267, 2990499, 20703300
    • Guo H, Ingolia N, Weissman J, Bartel D. Mammalian microRNAs predominantly act to decrease target mRNA levels. Nature 2010, 466(7308):835-840. 10.1038/nature09267, 2990499, 20703300.
    • (2010) Nature , vol.466 , Issue.7308 , pp. 835-840
    • Guo, H.1    Ingolia, N.2    Weissman, J.3    Bartel, D.4
  • 27
    • 80052266532 scopus 로고    scopus 로고
    • MicroRNAs can generate thresholds in target gene expression
    • 10.1038/ng.905, 3163764, 21857679
    • Mukherji S, Ebert M, Zheng G, Tsang J, Sharp P, van O. MicroRNAs can generate thresholds in target gene expression. Nat Genet 2011, 43(9):854-859. 10.1038/ng.905, 3163764, 21857679.
    • (2011) Nat Genet , vol.43 , Issue.9 , pp. 854-859
    • Mukherji, S.1    Ebert, M.2    Zheng, G.3    Tsang, J.4    Sharp, P.5    van, O.6
  • 28
    • 13944282215 scopus 로고    scopus 로고
    • Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs
    • 10.1038/nature03315, 15685193
    • Lim L, Lau N, Garrett-Engele P, Grimson A, Schelter J, Castle J, Bartel D, Linsley P, Johnson J. Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs. Nature 2005, 433(7027):769-773. 10.1038/nature03315, 15685193.
    • (2005) Nature , vol.433 , Issue.7027 , pp. 769-773
    • Lim, L.1    Lau, N.2    Garrett-Engele, P.3    Grimson, A.4    Schelter, J.5    Castle, J.6    Bartel, D.7    Linsley, P.8    Johnson, J.9
  • 29
    • 33644499134 scopus 로고    scopus 로고
    • Cell-type-specific signatures of microRNAs on target mRNA expression
    • 10.1073/pnas.0511045103, 1413820, 16477010
    • Sood P, Krek A, Zavolan M, Macino G, Rajewsky N. Cell-type-specific signatures of microRNAs on target mRNA expression. Proc Natl Acad Sci USA 2006, 103(8):2746. 10.1073/pnas.0511045103, 1413820, 16477010.
    • (2006) Proc Natl Acad Sci USA , vol.103 , Issue.8 , pp. 2746
    • Sood, P.1    Krek, A.2    Zavolan, M.3    Macino, G.4    Rajewsky, N.5
  • 30
    • 38349169664 scopus 로고    scopus 로고
    • Mechanisms of post-transcriptional regulation by microRNAs: are the answers in sight?
    • Filipowicz W, Bhattacharyya S, Sonenberg N. Mechanisms of post-transcriptional regulation by microRNAs: are the answers in sight?. Nat Rev Genet 2008, 9(2):102-114.
    • (2008) Nat Rev Genet , vol.9 , Issue.2 , pp. 102-114
    • Filipowicz, W.1    Bhattacharyya, S.2    Sonenberg, N.3
  • 31
    • 49949116902 scopus 로고    scopus 로고
    • The impact of microRNAs on protein output
    • 10.1038/nature07242, 2745094, 18668037
    • Baek D, Villén J, Shin C, Camargo F, Gygi S, Bartel D. The impact of microRNAs on protein output. Nature 2008, 455(7209):64-71. 10.1038/nature07242, 2745094, 18668037.
    • (2008) Nature , vol.455 , Issue.7209 , pp. 64-71
    • Baek, D.1    Villén, J.2    Shin, C.3    Camargo, F.4    Gygi, S.5    Bartel, D.6
  • 32
    • 49949117302 scopus 로고    scopus 로고
    • Widespread changes in protein synthesis induced by microRNAs
    • 10.1038/nature07228, 18668040
    • Selbach M, Schwanhausser B, Thierfelder N, Fang Z, Khanin R, Rajewsky N. Widespread changes in protein synthesis induced by microRNAs. Nature 2008, 455(7209):58-63. 10.1038/nature07228, 18668040.
    • (2008) Nature , vol.455 , Issue.7209 , pp. 58-63
    • Selbach, M.1    Schwanhausser, B.2    Thierfelder, N.3    Fang, Z.4    Khanin, R.5    Rajewsky, N.6
  • 33
    • 28044457883 scopus 로고    scopus 로고
    • MicroRNAs control translation initiation by inhibiting eukaryotic initiation factor 4E/cap and poly (A) tail function
    • 10.1073/pnas.0506482102, 1287990, 16287976
    • Humphreys D, Westman B, Martin D, Preiss T. MicroRNAs control translation initiation by inhibiting eukaryotic initiation factor 4E/cap and poly (A) tail function. Proc Natl Acad Sci USA 2005, 102(47):16961. 10.1073/pnas.0506482102, 1287990, 16287976.
    • (2005) Proc Natl Acad Sci USA , vol.102 , Issue.47 , pp. 16961
    • Humphreys, D.1    Westman, B.2    Martin, D.3    Preiss, T.4
  • 34
    • 67149115119 scopus 로고    scopus 로고
    • Transfection of small RNAs globally perturbs gene regulation by endogenous microRNAs
    • 2782465, 19465925
    • Khan A, Betel D, Miller M, Sander C, Leslie C, Marks D. Transfection of small RNAs globally perturbs gene regulation by endogenous microRNAs. Nat Biotechnol 2009, 27(6):549-555. 2782465, 19465925.
    • (2009) Nat Biotechnol , vol.27 , Issue.6 , pp. 549-555
    • Khan, A.1    Betel, D.2    Miller, M.3    Sander, C.4    Leslie, C.5    Marks, D.6
  • 35
    • 84894378829 scopus 로고    scopus 로고
    • Identification of microRNA-mRNA modules using microarray data
    • 12
    • Vivek J, David M, Yee Y. Identification of microRNA-mRNA modules using microarray data. BMC Genomics 12.
    • BMC Genomics
    • Vivek, J.1    David, M.2    Yee, Y.3
  • 36
    • 79951751828 scopus 로고    scopus 로고
    • Identifying functional miRNA-mRNA regulatory modules with correspondence latent dirichlet allocation
    • 10.1093/bioinformatics/btq576, 2995118, 20956247
    • Liu B, Liu L, Tsykin A, Goodall G, Green J, Zhu M, Kim C, Li J. Identifying functional miRNA-mRNA regulatory modules with correspondence latent dirichlet allocation. Bioinformatics 2010, 26(24):3105-3111. 10.1093/bioinformatics/btq576, 2995118, 20956247.
    • (2010) Bioinformatics , vol.26 , Issue.24 , pp. 3105-3111
    • Liu, B.1    Liu, L.2    Tsykin, A.3    Goodall, G.4    Green, J.5    Zhu, M.6    Kim, C.7    Li, J.8
  • 38
    • 84894337504 scopus 로고    scopus 로고
    • Correlation of expression profiles between microRNAs and mRNA targets using NCI-60 data
    • 10
    • Yu-Ping W, Kuo-Bin L. Correlation of expression profiles between microRNAs and mRNA targets using NCI-60 data. BMC Genomics 10.
    • BMC Genomics
    • Yu-Ping, W.1    Kuo-Bin, L.2
  • 39
    • 65849340430 scopus 로고    scopus 로고
    • Identification of microRNAs with regulatory potential using a matched microRNA-mRNA time-course data
    • 10.1093/nar/gkp153, 2677888, 19295134
    • Jayaswal V, Lutherborrow M, Ma D, Yang Y. Identification of microRNAs with regulatory potential using a matched microRNA-mRNA time-course data. Nucleic Acids Res 2009, 37(8):e60-e60. 10.1093/nar/gkp153, 2677888, 19295134.
    • (2009) Nucleic Acids Res , vol.37 , Issue.8
    • Jayaswal, V.1    Lutherborrow, M.2    Ma, D.3    Yang, Y.4
  • 41
    • 79955983466 scopus 로고    scopus 로고
    • Modeling microRNA-mRNA interactions using PLS regression in human colon cancer
    • Li X, Gill R, Cooper N, Yoo J, Datta S. Modeling microRNA-mRNA interactions using PLS regression in human colon cancer. BMC Med Genom 2011, 4:44.
    • (2011) BMC Med Genom , vol.4 , pp. 44
    • Li, X.1    Gill, R.2    Cooper, N.3    Yoo, J.4    Datta, S.5
  • 43
    • 79959997653 scopus 로고    scopus 로고
    • MirConnX: condition-specific mRNA-microRNA network integrator
    • 3125733, 21558324
    • Huang G, Athanassiou C, Benos P. mirConnX: condition-specific mRNA-microRNA network integrator. Nucleic Acids Res 2011, 39(suppl 2):W416-W423. 3125733, 21558324.
    • (2011) Nucleic Acids Res , vol.39 , Issue.SUPPL. 2
    • Huang, G.1    Athanassiou, C.2    Benos, P.3
  • 44
    • 67849101186 scopus 로고    scopus 로고
    • MicroRNA and mRNA integrated analysis (MMIA): a web tool for examining biological functions of microRNA expression
    • 2703907, 19420067
    • Nam S, Li M, Choi K, Balch C, Kim S, Nephew K. MicroRNA and mRNA integrated analysis (MMIA): a web tool for examining biological functions of microRNA expression. Nucleic Acids Res 2009, 37(suppl 2):W356-W362. 2703907, 19420067.
    • (2009) Nucleic Acids Res , vol.37 , Issue.SUPPL. 2
    • Nam, S.1    Li, M.2    Choi, K.3    Balch, C.4    Kim, S.5    Nephew, K.6
  • 45
    • 79951882529 scopus 로고    scopus 로고
    • Prediction of associations between microRNAs and gene expression in glioma biology
    • 10.1371/journal.pone.0014681, 3040173, 21358821
    • Wuchty S, Arjona D, Li A, Kotliarov Y, Walling J, Ahn S, Zhang A, Maric D, Anolik R, Zenklusen J, et al. Prediction of associations between microRNAs and gene expression in glioma biology. PLoS One 2011, 6(2):e14681. 10.1371/journal.pone.0014681, 3040173, 21358821.
    • (2011) PLoS One , vol.6 , Issue.2
    • Wuchty, S.1    Arjona, D.2    Li, A.3    Kotliarov, Y.4    Walling, J.5    Ahn, S.6    Zhang, A.7    Maric, D.8    Anolik, R.9    Zenklusen, J.10
  • 47
    • 33745765418 scopus 로고    scopus 로고
    • Detecting microRNA targets by linking sequence, microRNA and gene expression data
    • Springer
    • Huang J, Morris Q, Frey B. Detecting microRNA targets by linking sequence, microRNA and gene expression data. Research in Computational Molecular Biology 2006, 114-129. Springer.
    • (2006) Research in Computational Molecular Biology , pp. 114-129
    • Huang, J.1    Morris, Q.2    Frey, B.3
  • 49
    • 57049175013 scopus 로고    scopus 로고
    • Detecting microRNA binding and siRNA off-target effects from expression data
    • 10.1038/nmeth.1267, 2635553, 18978784
    • van Dongen S, Abreu-Goodger C, Enright A. Detecting microRNA binding and siRNA off-target effects from expression data. Nat Methods 2008, 5(12):1023-1025. 10.1038/nmeth.1267, 2635553, 18978784.
    • (2008) Nat Methods , vol.5 , Issue.12 , pp. 1023-1025
    • van Dongen, S.1    Abreu-Goodger, C.2    Enright, A.3
  • 52
    • 77951092180 scopus 로고    scopus 로고
    • Targeting of mRNAs by multiple miRNAs: the next step
    • 10.1038/onc.2010.59, 20190803
    • Peter M. Targeting of mRNAs by multiple miRNAs: the next step. Oncogene 2010, 29(15):2161-2164. 10.1038/onc.2010.59, 20190803.
    • (2010) Oncogene , vol.29 , Issue.15 , pp. 2161-2164
    • Peter, M.1
  • 54
    • 77950537175 scopus 로고    scopus 로고
    • Regularization paths for generalized linear models via coordinate descent
    • Friedman J, Hastie T, Tibshirani R. Regularization paths for generalized linear models via coordinate descent. J Stat Soft 2010, 33:1.
    • (2010) J Stat Soft , vol.33 , pp. 1
    • Friedman, J.1    Hastie, T.2    Tibshirani, R.3
  • 55
    • 58149203235 scopus 로고    scopus 로고
    • The database of experimentally supported targets: a functional update of TarBase
    • 2686456, 18957447
    • Papadopoulos G, Reczko M, Simossis V, Sethupathy P, Hatzigeorgiou A. The database of experimentally supported targets: a functional update of TarBase. Nucleic Acids Res 2009, 37(suppl 1):D155-D158. 2686456, 18957447.
    • (2009) Nucleic Acids Res , vol.37 , Issue.SUPPL. 1
    • Papadopoulos, G.1    Reczko, M.2    Simossis, V.3    Sethupathy, P.4    Hatzigeorgiou, A.5
  • 56
    • 77956117850 scopus 로고    scopus 로고
    • Towards computational prediction of microRNA function and activity
    • 10.1093/nar/gkq570, 2926627, 20576699
    • Ulitsky I, Laurent L, Shamir R. Towards computational prediction of microRNA function and activity. Nucleic Acids Res 2010, 38(15):e160-e160. 10.1093/nar/gkq570, 2926627, 20576699.
    • (2010) Nucleic Acids Res , vol.38 , Issue.15
    • Ulitsky, I.1    Laurent, L.2    Shamir, R.3
  • 57
    • 34447288056 scopus 로고    scopus 로고
    • Bayesian inference of microRNA targets from sequence and expression data
    • 10.1089/cmb.2007.R002, 17683260
    • Huang JC, Morris QD, Frey BJ. Bayesian inference of microRNA targets from sequence and expression data. J Comput Biol 2007, 14:550-563. 10.1089/cmb.2007.R002, 17683260.
    • (2007) J Comput Biol , vol.14 , pp. 550-563
    • Huang, J.C.1    Morris, Q.D.2    Frey, B.J.3
  • 59
    • 43149084575 scopus 로고    scopus 로고
    • Large-scale mutagenesis in ip19ARFi and ip53i deficient mice identifies cancer genes and their collaborative networks
    • 10.1016/j.cell.2008.03.021, 2405818, 18485879
    • Uren A, Kool J, Matentzoglu K, De Ridder J, Mattison J, Van Uitert M, Lagcher W, Sie D, Tanger E, Cox T, et al. Large-scale mutagenesis in ip19ARFi and ip53i deficient mice identifies cancer genes and their collaborative networks. Cell 2008, 133(4):727-741. 10.1016/j.cell.2008.03.021, 2405818, 18485879.
    • (2008) Cell , vol.133 , Issue.4 , pp. 727-741
    • Uren, A.1    Kool, J.2    Matentzoglu, K.3    De Ridder, J.4    Mattison, J.5    Van Uitert, M.6    Lagcher, W.7    Sie, D.8    Tanger, E.9    Cox, T.10
  • 60
    • 75349100888 scopus 로고    scopus 로고
    • MimiRNA: a microRNA expression profiler and classification resource designed to identify functional correlations between microRNAs and their targets
    • 10.1093/bioinformatics/btp649, 19933167
    • Ritchie W, Flamant S, Rasko J. mimiRNA: a microRNA expression profiler and classification resource designed to identify functional correlations between microRNAs and their targets. Bioinformatics 2010, 26(2):223-227. 10.1093/bioinformatics/btp649, 19933167.
    • (2010) Bioinformatics , vol.26 , Issue.2 , pp. 223-227
    • Ritchie, W.1    Flamant, S.2    Rasko, J.3
  • 61
    • 36849079370 scopus 로고    scopus 로고
    • Hoshino Si: Mechanism of mRNA deadenylation: evidence for a molecular interplay between translation termination factor eRF3 and mRNA deadenylases
    • 10.1101/gad.1597707, 2081979, 18056425
    • Funakoshi Y, Doi Y, Hosoda N, Uchida N, Osawa M, Shimada I, Tsujimoto M, Suzuki T, Katada T. Hoshino Si: Mechanism of mRNA deadenylation: evidence for a molecular interplay between translation termination factor eRF3 and mRNA deadenylases. Genes Dev 2007, 21(23):3135-3148. 10.1101/gad.1597707, 2081979, 18056425.
    • (2007) Genes Dev , vol.21 , Issue.23 , pp. 3135-3148
    • Funakoshi, Y.1    Doi, Y.2    Hosoda, N.3    Uchida, N.4    Osawa, M.5    Shimada, I.6    Tsujimoto, M.7    Suzuki, T.8    Katada, T.9
  • 62
    • 1642374097 scopus 로고    scopus 로고
    • Specificity of microRNA target selection in translational repression
    • 10.1101/gad.1184404, 374233, 15014042
    • Doench JG, Sharp PA. Specificity of microRNA target selection in translational repression. Genes Dev 2004, 18(5):504-511. 10.1101/gad.1184404, 374233, 15014042.
    • (2004) Genes Dev , vol.18 , Issue.5 , pp. 504-511
    • Doench, J.G.1    Sharp, P.A.2
  • 63
    • 79958250243 scopus 로고    scopus 로고
    • Computational prediction of intronic microRNA targets using host gene expression reveals novel regulatory mechanisms
    • 10.1371/journal.pone.0019312, 3111417, 21694770
    • Radfar M, Wong W, Morris Q. Computational prediction of intronic microRNA targets using host gene expression reveals novel regulatory mechanisms. PLoS One 2011, 6(6):e19312. 10.1371/journal.pone.0019312, 3111417, 21694770.
    • (2011) PLoS One , vol.6 , Issue.6
    • Radfar, M.1    Wong, W.2    Morris, Q.3
  • 64
    • 44349128983 scopus 로고    scopus 로고
    • Inferring microRNA activities by combining gene expression with microRNA target prediction
    • 10.1371/journal.pone.0001989, 2291556, 18431476
    • Cheng C, Li L. Inferring microRNA activities by combining gene expression with microRNA target prediction. PLoS One 2008, 3(4):e1989. 10.1371/journal.pone.0001989, 2291556, 18431476.
    • (2008) PLoS One , vol.3 , Issue.4
    • Cheng, C.1    Li, L.2
  • 65
    • 76249103552 scopus 로고    scopus 로고
    • MRNA expression profiles show differential regulatory effects of microRNAs between estrogen receptor-positive and estrogen receptor-negative breast cancer
    • 10.1186/gb-2009-10-9-r90, 2768979, 19723326
    • Cheng C, Fu X, Alves P, Gerstein M, et al. mRNA expression profiles show differential regulatory effects of microRNAs between estrogen receptor-positive and estrogen receptor-negative breast cancer. Genome Biol 2009, 10(9):R90. 10.1186/gb-2009-10-9-r90, 2768979, 19723326.
    • (2009) Genome Biol , vol.10 , Issue.9
    • Cheng, C.1    Fu, X.2    Alves, P.3    Gerstein, M.4
  • 66
    • 79960028760 scopus 로고    scopus 로고
    • MirAct: a web tool for evaluating microRNA activity based on gene expression data
    • 3125759, 21596785
    • Liang Z, Zhou H, He Z, Zheng H, Wu J. mirAct: a web tool for evaluating microRNA activity based on gene expression data. Nucleic acids Res 2011, 39(suppl 2):W139-W144. 3125759, 21596785.
    • (2011) Nucleic acids Res , vol.39 , Issue.SUPPL. 2
    • Liang, Z.1    Zhou, H.2    He, Z.3    Zheng, H.4    Wu, J.5
  • 67
    • 77949430343 scopus 로고    scopus 로고
    • The DIANA-mirExTra web server: from gene expression data to microRNA function
    • 10.1371/journal.pone.0009171, 2820085, 20161787
    • Alexiou P, Maragkakis M, Papadopoulos G, Simmosis V, Zhang L, Hatzigeorgiou A. The DIANA-mirExTra web server: from gene expression data to microRNA function. PLoS One 2010, 5(2):e9171. 10.1371/journal.pone.0009171, 2820085, 20161787.
    • (2010) PLoS One , vol.5 , Issue.2
    • Alexiou, P.1    Maragkakis, M.2    Papadopoulos, G.3    Simmosis, V.4    Zhang, L.5    Hatzigeorgiou, A.6
  • 68
    • 79951730858 scopus 로고    scopus 로고
    • MiRonTop: mining microRNAs targets across large scale gene expression studies
    • 10.1093/bioinformatics/btq589, 2995122, 20959382
    • Le Brigand K, Robbe-Sermesant K, Mari B, Barbry P. MiRonTop: mining microRNAs targets across large scale gene expression studies. Bioinformatics 2010, 26(24):3131-3132. 10.1093/bioinformatics/btq589, 2995122, 20959382.
    • (2010) Bioinformatics , vol.26 , Issue.24 , pp. 3131-3132
    • Le Brigand, K.1    Robbe-Sermesant, K.2    Mari, B.3    Barbry, P.4
  • 69
    • 75249096480 scopus 로고    scopus 로고
    • Identification of microRNA activity by Targets' Reverse EXpression
    • 10.1093/bioinformatics/btp598, 2796810, 19897564
    • Volinia S, Visone R, Galasso M, Rossi E, Croce C. Identification of microRNA activity by Targets' Reverse EXpression. Bioinformatics 2010, 26:91-97. 10.1093/bioinformatics/btp598, 2796810, 19897564.
    • (2010) Bioinformatics , vol.26 , pp. 91-97
    • Volinia, S.1    Visone, R.2    Galasso, M.3    Rossi, E.4    Croce, C.5
  • 70
    • 47149088851 scopus 로고    scopus 로고
    • Individual mRNA expression profiles reveal the effects of specific microRNAs
    • 10.1186/gb-2008-9-5-r82, 2441468, 18485210
    • Arora A, Simpson D. Individual mRNA expression profiles reveal the effects of specific microRNAs. Genome Biol 2008, 9(5):R82. 10.1186/gb-2008-9-5-r82, 2441468, 18485210.
    • (2008) Genome Biol , vol.9 , Issue.5
    • Arora, A.1    Simpson, D.2
  • 71
    • 33846675660 scopus 로고    scopus 로고
    • Global analysis of microRNA target gene expression reveals that miRNA targets are lower expressed in mature mouse and Drosophila tissues than in the embryos
    • 1802562, 17158157
    • Yu Z, Jian Z, Shen S, Purisima E, Wang E. Global analysis of microRNA target gene expression reveals that miRNA targets are lower expressed in mature mouse and Drosophila tissues than in the embryos. Nucleic Acids Res 2007, 35:152-164. 1802562, 17158157.
    • (2007) Nucleic Acids Res , vol.35 , pp. 152-164
    • Yu, Z.1    Jian, Z.2    Shen, S.3    Purisima, E.4    Wang, E.5
  • 72
    • 80052862997 scopus 로고    scopus 로고
    • Expression levels of microRNAs are not associated with their regulatory activities
    • 10.1186/1745-6150-6-1, 3043529, 21199581
    • Liang Z, Zhou H, Zheng H, Wu J, Liang Z, Zhou H, Zheng H, Wu J, et al. Expression levels of microRNAs are not associated with their regulatory activities. Biol Direct 2011, 6:1-4. 10.1186/1745-6150-6-1, 3043529, 21199581.
    • (2011) Biol Direct , vol.6 , pp. 1-4
    • Liang, Z.1    Zhou, H.2    Zheng, H.3    Wu, J.4    Liang, Z.5    Zhou, H.6    Zheng, H.7    Wu, J.8
  • 73
    • 84855658374 scopus 로고    scopus 로고
    • Measures of association for identifying MicroRNA-mRNA pairs of biological interest
    • 10.1371/journal.pone.0029612, 3256172, 22253745
    • Jayaswal V, Lutherborrow M, Yang Y. Measures of association for identifying MicroRNA-mRNA pairs of biological interest. PloS one 2012, 7:e29612. 10.1371/journal.pone.0029612, 3256172, 22253745.
    • (2012) PloS one , vol.7
    • Jayaswal, V.1    Lutherborrow, M.2    Yang, Y.3
  • 74
    • 77149153066 scopus 로고    scopus 로고
    • Structure and activity of putative intronic miRNA promoters
    • 10.1261/rna.1731910, 2822915, 20075166
    • Monteys A, Spengler R, Wan J, Tecedor L, Lennox K, Xing Y, Davidson B. Structure and activity of putative intronic miRNA promoters. RNA 2010, 16(3):495. 10.1261/rna.1731910, 2822915, 20075166.
    • (2010) RNA , vol.16 , Issue.3 , pp. 495
    • Monteys, A.1    Spengler, R.2    Wan, J.3    Tecedor, L.4    Lennox, K.5    Xing, Y.6    Davidson, B.7
  • 75
    • 56549129538 scopus 로고    scopus 로고
    • Chromatin structure analyses identify miRNA promoters
    • 10.1101/gad.1706508, 2593607, 19056895
    • Ozsolak F, Poling L, Wang Z, Liu H, Liu X, Roeder R, Zhang X, Song J, Fisher D. Chromatin structure analyses identify miRNA promoters. Genes Dev 2008, 22(22):3172. 10.1101/gad.1706508, 2593607, 19056895.
    • (2008) Genes Dev , vol.22 , Issue.22 , pp. 3172
    • Ozsolak, F.1    Poling, L.2    Wang, Z.3    Liu, H.4    Liu, X.5    Roeder, R.6    Zhang, X.7    Song, J.8    Fisher, D.9
  • 76
    • 57149116346 scopus 로고    scopus 로고
    • Genome-scale spatiotemporal analysis of Caenorhabditis elegans microRNA promoter activity
    • 10.1101/gr.083055.108, 2593583, 18981266
    • Martinez N, Ow M, Reece-Hoyes J, Barrasa M, Ambros V, Walhout A. Genome-scale spatiotemporal analysis of Caenorhabditis elegans microRNA promoter activity. Genome Res 2008, 18(12):2005. 10.1101/gr.083055.108, 2593583, 18981266.
    • (2008) Genome Res , vol.18 , Issue.12 , pp. 2005
    • Martinez, N.1    Ow, M.2    Reece-Hoyes, J.3    Barrasa, M.4    Ambros, V.5    Walhout, A.6
  • 77
    • 84863555312 scopus 로고    scopus 로고
    • Impact of microRNA regulation on variation in human gene expression
    • 10.1101/gr.132514.111, 3396366, 22456605
    • Lu J, Clark A. Impact of microRNA regulation on variation in human gene expression. Genome Res 2012, 22(7):1243-1254. 10.1101/gr.132514.111, 3396366, 22456605.
    • (2012) Genome Res , vol.22 , Issue.7 , pp. 1243-1254
    • Lu, J.1    Clark, A.2
  • 79
    • 34250729886 scopus 로고    scopus 로고
    • Origin and evolution of human microRNAs from transposable elements
    • 1894593, 17435244
    • Piriyapongsa J, Mariño-Ramírez L, Jordan I. Origin and evolution of human microRNAs from transposable elements. Genetics 2007, 176(2):1323-1337. 1894593, 17435244.
    • (2007) Genetics , vol.176 , Issue.2 , pp. 1323-1337
    • Piriyapongsa, J.1    Mariño-Ramírez, L.2    Jordan, I.3
  • 81
    • 0001677717 scopus 로고
    • Controlling the false discovery rate: a practical and powerful approach to multiple testing
    • Benjamini Y, Hochberg Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc Ser B (Methodological) 1995, 289-300.
    • (1995) J R Stat Soc Ser B (Methodological) , pp. 289-300
    • Benjamini, Y.1    Hochberg, Y.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.