메뉴 건너뛰기




Volumn 38, Issue 7, 2010, Pages

Impact of probe annotation on the integration of miRNA-mRNA expression profiles for miRNA target detection

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA; MICRORNA;

EID: 77954097757     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkp1239     Document Type: Article
Times cited : (8)

References (68)
  • 1
    • 0038343499 scopus 로고    scopus 로고
    • MicroRNA pathways in flies and worms: growth, death, fat, stress, and timing
    • Ambros, V. (2003) MicroRNA pathways in flies and worms: growth, death, fat, stress, and timing. Cell, 113, 673-676.
    • (2003) Cell , vol.113 , pp. 673-676
    • Ambros, V.1
  • 2
    • 0037418839 scopus 로고    scopus 로고
    • bantam encodes a developmentally regulated microRNA that controls cell proliferation and regulates the proapoptotic gene hid in Drosophila
    • Brennecke, J., Hipfner, D.R., Stark, A., Russell, R.B. and Cohen, S.M. (2003) bantam encodes a developmentally regulated microRNA that controls cell proliferation and regulates the proapoptotic gene hid in Drosophila. Cell, 113, 25-36.
    • (2003) Cell , vol.113 , pp. 25-36
    • Brennecke, J.1    Hipfner, D.R.2    Stark, A.3    Russell, R.B.4    Cohen, S.M.5
  • 3
    • 0035955374 scopus 로고    scopus 로고
    • Identification of novel genes coding for small expressed RNAs
    • Lagos-Quintana, M., Rauhut, R., Lendeckel, W. and Tuschl, T. (2001) Identification of novel genes coding for small expressed RNAs. Science, 294, 853-858.
    • (2001) Science , vol.294 , pp. 853-858
    • Lagos-Quintana, M.1    Rauhut, R.2    Lendeckel, W.3    Tuschl, T.4
  • 4
    • 0027751663 scopus 로고
    • The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14
    • Lee, R.C., Feinbaum, R.L. and Ambros, V. (1993) The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell, 75, 843-854.
    • (1993) Cell , vol.75 , pp. 843-854
    • Lee, R.C.1    Feinbaum, R.L.2    Ambros, V.3
  • 9
    • 39749110083 scopus 로고    scopus 로고
    • Small non-coding RNAs in animal development
    • Stefani, G. and Slack, F.J. (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
  • 10
    • 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
  • 12
    • 34848922072 scopus 로고    scopus 로고
    • miRNAs play a tune
    • Hobert, O. (2007) miRNAs play a tune. Cell, 131, 22-24.
    • (2007) Cell , vol.131 , pp. 22-24
    • Hobert, O.1
  • 14
    • 0347444723 scopus 로고    scopus 로고
    • MicroRNAs: genomics, biogenesis, mechanism, and function
    • Bartel, D.P. (2004) MicroRNAs: genomics, biogenesis, mechanism, and function. Cell, 116, 281-297.
    • (2004) Cell , vol.116 , pp. 281-297
    • Bartel, D.P.1
  • 16
    • 26944498633 scopus 로고    scopus 로고
    • Prediction and validation of microRNAs and their targets
    • Bentwich, I. (2005) Prediction and validation of microRNAs and their targets. FEBS Lett., 579, 5904-5910.
    • (2005) FEBS Lett , vol.579 , pp. 5904-5910
    • Bentwich, I.1
  • 21
    • 34748821761 scopus 로고    scopus 로고
    • The role of site accessibility in microRNA target recognition
    • Kertesz, M., Iovino, N., Unnerstall, U., Gaul, U. and 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
  • 22
    • 33747849920 scopus 로고    scopus 로고
    • RNAhybrid: microRNA target prediction easy, fast and flexible
    • Kruger, J. and Rehmsmeier, M. (2006) RNAhybrid: microRNA target prediction easy, fast and flexible. Nucleic Acids Res., 34, W451-W454.
    • (2006) Nucleic Acids Res , vol.34
    • Kruger, J.1    Rehmsmeier, M.2
  • 25
    • 33745248430 scopus 로고    scopus 로고
    • microRNA target predictions in animals
    • Rajewsky, N. (2006) microRNA target predictions in animals. Nat. Genet., 38(Suppl.), S8-S13.
    • (2006) Nat. Genet. , vol.38 , Issue.SUPPL
    • Rajewsky, N.1
  • 26
    • 45749154794 scopus 로고    scopus 로고
    • Molecular architecture of a miRNA-regulated 3′ UTR
    • Didiano, D. and Hobert, O. (2008) Molecular architecture of a miRNA-regulated 3′ UTR. Rna, 14, 1297-1317.
    • (2008) Rna , vol.14 , pp. 1297-1317
    • Didiano, D.1    Hobert, O.2
  • 28
    • 41349096445 scopus 로고    scopus 로고
    • Gene regulation by transcription factors and microRNAs
    • Hobert, O. (2008) Gene regulation by transcription factors and microRNAs. Science, 319, 1785-1786.
    • (2008) Science , vol.319 , pp. 1785-1786
    • Hobert, O.1
  • 30
    • 34447288056 scopus 로고    scopus 로고
    • Bayesian inference of MicroRNA targets from sequence and expression data
    • Huang, J.C., Morris, Q.D. and Frey, B.J. (2007) Bayesian inference of MicroRNA targets from sequence and expression data. J. Comput. Biol., 14, 550-563.
    • (2007) J. Comput. Biol. , vol.14 , pp. 550-563
    • Huang, J.C.1    Morris, Q.D.2    Frey, B.J.3
  • 31
    • 60149084355 scopus 로고    scopus 로고
    • Computational analysis of microRNA profiles and their target genes suggests significant involvement in breast cancer antiestrogen resistance
    • Xin, F., Li, M., Balch, C., Thomson, M., Fan, M., Liu, Y., Hammond, S.M., Kim, S. and Nephew, K.P. (2009) Computational analysis of microRNA profiles and their target genes suggests significant involvement in breast cancer antiestrogen resistance. Bioinformatics, 25, 430-434.
    • (2009) Bioinformatics , vol.25 , pp. 430-434
    • Xin, F.1    Li, M.2    Balch, C.3    Thomson, M.4    Fan, M.5    Liu, Y.6    Hammond, S.M.7    Kim, S.8    Nephew, K.P.9
  • 32
    • 66349119276 scopus 로고    scopus 로고
    • Correlation of expression profiles between microRNAs and mRNA targets using NCI-60 data
    • Wang, Y.P. and Li, K.B. (2009) Correlation of expression profiles between microRNAs and mRNA targets using NCI-60 data. BMC Genomics, 10, 218.
    • (2009) BMC Genomics , vol.10 , pp. 218
    • Wang, Y.P.1    Li, K.B.2
  • 34
    • 33646947554 scopus 로고    scopus 로고
    • Differential repression of alternative transcripts: a screen for miRNA targets
    • Legendre, M., Ritchie, W., Lopez, F. and Gautheret, D. (2006) Differential repression of alternative transcripts: a screen for miRNA targets. PLoS Comput. Biol., 2, e43.
    • (2006) PLoS Comput. Biol. , vol.2
    • Legendre, M.1    Ritchie, W.2    Lopez, F.3    Gautheret, D.4
  • 35
    • 33748486517 scopus 로고    scopus 로고
    • AceView: a comprehensive cDNA-supported gene and transcripts annotation
    • Thierry-Mieg, D. and Thierry-Mieg, J. (2006) AceView: a comprehensive cDNA-supported gene and transcripts annotation. Genome Biol., 7(Suppl. 1), S12 11-14.
    • (2006) Genome Biol , vol.7 , Issue.SUPPL. 1 , pp. 11-14
    • Thierry-Mieg, D.1    Thierry-Mieg, J.2
  • 36
    • 31444431754 scopus 로고    scopus 로고
    • Reliability and reproducibility issues in DNA microarray measurements
    • Draghici, S., Khatri, P., Eklund, A.C. and Szallasi, Z. (2006) Reliability and reproducibility issues in DNA microarray measurements. Trends Genet., 22, 101-109.
    • (2006) Trends Genet , vol.22 , pp. 101-109
    • Draghici, S.1    Khatri, P.2    Eklund, A.C.3    Szallasi, Z.4
  • 37
    • 2442691827 scopus 로고    scopus 로고
    • Sequence-matched probes produce increased cross-platform consistency and more reproducible biological results in microarray-based gene expression measurements
    • Mecham, B.H., Klus, G.T., Strovel, J., Augustus, M., Byrne, D., Bozso, P., Wetmore, D.Z., Mariani, T.J., Kohane, I.S. and Szallasi, Z. (2004) Sequence-matched probes produce increased cross-platform consistency and more reproducible biological results in microarray-based gene expression measurements. Nucleic Acids Res., 32, e74.
    • (2004) Nucleic Acids Res , vol.32
    • Mecham, B.H.1    Klus, G.T.2    Strovel, J.3    Augustus, M.4    Byrne, D.5    Bozso, P.6    Wetmore, D.Z.7    Mariani, T.J.8    Kohane, I.S.9    Szallasi, Z.10
  • 40
    • 34247349497 scopus 로고    scopus 로고
    • Transcript-based redefinition of grouped oligonucleotide probe sets using AceView: high-resolution annotation for microarrays
    • Lu, J., Lee, J.C., Salit, M.L. and Cam, M.C. (2007) Transcript-based redefinition of grouped oligonucleotide probe sets using AceView: high-resolution annotation for microarrays. BMC Bioinformatics, 8, 108.
    • (2007) BMC Bioinformatics , vol.8 , pp. 108
    • Lu, J.1    Lee, J.C.2    Salit, M.L.3    Cam, M.C.4
  • 41
    • 62849085777 scopus 로고    scopus 로고
    • Transcript-specific expression profiles derived from sequence-based analysis of standard microarrays
    • Moll, A.G., Lindenmeyer, M.T., Kretzler, M., Nelson, P.J., Zimmer, R. and Cohen, C.D. (2009) Transcript-specific expression profiles derived from sequence-based analysis of standard microarrays. PLoS ONE, 4, e4702.
    • (2009) PLoS ONE , vol.4
    • Moll, A.G.1    Lindenmeyer, M.T.2    Kretzler, M.3    Nelson, P.J.4    Zimmer, R.5    Cohen, C.D.6
  • 42
    • 11844278458 scopus 로고    scopus 로고
    • Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets
    • Lewis, B.P., Burge, C.B. and Bartel, D.P. (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
  • 46
    • 61449172037 scopus 로고    scopus 로고
    • Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources
    • Huang da, W., Sherman, B.T. and Lempicki, R.A. (2009) Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat. Protoc., 4, 44-57.
    • (2009) Nat. Protoc. , vol.4 , pp. 44-57
    • Huang da, W.1    Sherman, B.T.2    Lempicki, R.A.3
  • 48
    • 12744278777 scopus 로고    scopus 로고
    • Comparison of the current RefSeq Ensembl and EST databases for counting genes and gene discovery
    • Larsson, T.P., Murray, C.G., Hill, T., Fredriksson, R. and Schioth, H.B. (2005) Comparison of the current RefSeq, Ensembl and EST databases for counting genes and gene discovery. FEBS Lett., 579, 690-698.
    • (2005) FEBS Lett , vol.579 , pp. 690-698
    • Larsson, T.P.1    Murray, C.G.2    Hill, T.3    Fredriksson, R.4    Schioth, H.B.5
  • 49
    • 0035930903 scopus 로고    scopus 로고
    • Distinctive tissue distribution and phosphorylation of IRSp53 isoforms
    • Okamura-Oho, Y., Miyashita, T. and Yamada, M. (2001) Distinctive tissue distribution and phosphorylation of IRSp53 isoforms. Biochem. Biophys. Res. Commun., 289, 957-960.
    • (2001) Biochem. Biophys. Res. Commun. , vol.289 , pp. 957-960
    • Okamura-Oho, Y.1    Miyashita, T.2    Yamada, M.3
  • 50
    • 1342323632 scopus 로고    scopus 로고
    • ErbB receptors: directing key signaling networks throughout life
    • Holbro, T. and Hynes, N.E. (2004) ErbB receptors: directing key signaling networks throughout life. Annu. Rev. Pharmacol. Toxicol., 44, 195-217.
    • (2004) Annu. Rev. Pharmacol. Toxicol. , vol.44 , pp. 195-217
    • Holbro, T.1    Hynes, N.E.2
  • 51
    • 0031671617 scopus 로고    scopus 로고
    • Expression of gonadotropin-releasing hormone (GnRH) and GnRH receptor mRNA in prostate cancer cells and effect of GnRH on the proliferation of prostate cancer cells
    • Bahk, J.Y., Hyun, J.S., Lee, H., Kim, M.O., Cho, G.J., Lee, B.H. and Choi, W.S. (1998) Expression of gonadotropin-releasing hormone (GnRH) and GnRH receptor mRNA in prostate cancer cells and effect of GnRH on the proliferation of prostate cancer cells. Urol. Res., 26, 259-264.
    • (1998) Urol. Res. , vol.26 , pp. 259-264
    • Bahk, J.Y.1    Hyun, J.S.2    Lee, H.3    Kim, M.O.4    Cho, G.J.5    Lee, B.H.6    Choi, W.S.7
  • 52
    • 0027941068 scopus 로고
    • Antiproliferative effects of luteinizing hormone-releasing hormone (LHRH) agonists on human androgen-independent prostate cancer cell line DU 145 evidence for an autocrine-inhibitory LHRH loop
    • Dondi, D., Limonta, P., Moretti, R.M., Marelli, M.M., Garattini, E. and Motta, M. (1994) Antiproliferative effects of luteinizing hormone-releasing hormone (LHRH) agonists on human androgen-independent prostate cancer cell line DU 145: evidence for an autocrine-inhibitory LHRH loop. Cancer Res., 54, 4091-4095.
    • (1994) Cancer Res , vol.54 , pp. 4091-4095
    • Dondi, D.1    Limonta, P.2    Moretti, R.M.3    Marelli, M.M.4    Garattini, E.5    Motta, M.6
  • 53
    • 0033963203 scopus 로고    scopus 로고
    • High incidence of receptors for luteinizing hormone-releasing hormone (LHRH) and LHRH receptor gene expression in human prostate cancers
    • Halmos, G., Arencibia, J.M., Schally, A.V., Davis, R. and Bostwick, D.G. (2000) High incidence of receptors for luteinizing hormone-releasing hormone (LHRH) and LHRH receptor gene expression in human prostate cancers. J. Urol., 163, 623-629.
    • (2000) J. Urol. , vol.163 , pp. 623-629
    • Halmos, G.1    Arencibia, J.M.2    Schally, A.V.3    Davis, R.4    Bostwick, D.G.5
  • 56
    • 34548168073 scopus 로고    scopus 로고
    • miR-221 and miR-222 expression affects the proliferation potential of human prostate carcinoma cell lines by targeting p27Kip1
    • Galardi, S., Mercatelli, N., Giorda, E., Massalini, S., Frajese, G.V., Ciafre, S.A. and Farace, M.G. (2007) miR-221 and miR-222 expression affects the proliferation potential of human prostate carcinoma cell lines by targeting p27Kip1. J. Biol. Chem., 282, 23716-23724.
    • (2007) J. Biol. Chem. , vol.282 , pp. 23716-23724
    • Galardi, S.1    Mercatelli, N.2    Giorda, E.3    Massalini, S.4    Frajese, G.V.5    Ciafre, S.A.6    Farace, M.G.7
  • 57
    • 40749090479 scopus 로고    scopus 로고
    • Widespread deregulation of microRNA expression in human prostate cancer
    • Ozen, M., Creighton, C.J., Ozdemir, M. and Ittmann, M. (2008) Widespread deregulation of microRNA expression in human prostate cancer. Oncogene, 27, 1788-1793.
    • (2008) Oncogene , vol.27 , pp. 1788-1793
    • Ozen, M.1    Creighton, C.J.2    Ozdemir, M.3    Ittmann, M.4
  • 62
    • 33646157967 scopus 로고    scopus 로고
    • Comprehensive analysis of microRNA expression patterns in hepatocellular carcinoma and non-tumorous tissues
    • Murakami, Y., Yasuda, T., Saigo, K., Urashima, T., Toyoda, H., Okanoue, T. and Shimotohno, K. (2006) Comprehensive analysis of microRNA expression patterns in hepatocellular carcinoma and non-tumorous tissues. Oncogene, 25, 2537-2545.
    • (2006) Oncogene , vol.25 , pp. 2537-2545
    • Murakami, Y.1    Yasuda, T.2    Saigo, K.3    Urashima, T.4    Toyoda, H.5    Okanoue, T.6    Shimotohno, K.7
  • 65
    • 33846188098 scopus 로고    scopus 로고
    • microRNAs as oncogenes and tumor suppressors
    • Zhang, B., Pan, X., Cobb, G.P. and Anderson, T.A. (2007) microRNAs as oncogenes and tumor suppressors. Dev. Biol., 302, 1-12.
    • (2007) Dev. Biol. , vol.302 , pp. 1-12
    • Zhang, B.1    Pan, X.2    Cobb, G.P.3    Anderson, T.A.4
  • 66
    • 40449131878 scopus 로고    scopus 로고
    • Loss of mir-146a function in hormone-refractory prostate cancer
    • Lin, S.L., Chiang, A., Chang, D. and Ying, S.Y. (2008) Loss of mir-146a function in hormone-refractory prostate cancer. Rna, 14, 417-424.
    • (2008) Rna , vol.14 , pp. 417-424
    • Lin, S.L.1    Chiang, A.2    Chang, D.3    Ying, S.Y.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.