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Volumn 4, Issue 10, 2008, Pages

Removal of AU bias from microarray mRNA expression data enhances computational identification of active microRNAs

Author keywords

[No Author keywords available]

Indexed keywords

DATA VISUALIZATION; GENE EXPRESSION; RNA;

EID: 55449117619     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1000189     Document Type: Article
Times cited : (8)

References (29)
  • 1
    • 33344477448 scopus 로고    scopus 로고
    • Genomics of microRNA
    • Kim VN, Nam JW (2006) Genomics of microRNA. Trends Genet 22: 165-173.
    • (2006) Trends Genet , vol.22 , pp. 165-173
    • Kim, V.N.1    Nam, J.W.2
  • 2
    • 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
  • 3
    • 18044377963 scopus 로고    scopus 로고
    • Principles of microRNA-target recognition
    • doi:10.1371/journal.pbio.0030085
    • Brennecke J, Stark A, Russell RB, Cohen SM (2005) Principles of microRNA-target recognition. PLoS Biol 3: e85. doi:10.1371/journal.pbio.0030085.
    • (2005) PLoS Biol , vol.3
    • Brennecke, J.1    Stark, A.2    Russell, R.B.3    Cohen, S.M.4
  • 4
    • 33745248430 scopus 로고    scopus 로고
    • MicroRNA target predictions in animals
    • Rajewsky N (2006) MicroRNA target predictions in animals. Nat Genet 38: S8-S13.
    • (2006) Nat Genet , vol.38
    • Rajewsky, N.1
  • 5
    • 0038444122 scopus 로고    scopus 로고
    • Genome-wide in silico identification of transcriptional regulators controlling the cell cycle in human cells
    • Elkon R, Linhart C, Sharan R, Shamir R, Shiloh Y (2003) Genome-wide in silico identification of transcriptional regulators controlling the cell cycle in human cells. Genome Res 13: 773-780.
    • (2003) Genome Res , vol.13 , pp. 773-780
    • Elkon, R.1    Linhart, C.2    Sharan, R.3    Shamir, R.4    Shiloh, Y.5
  • 6
    • 0034785443 scopus 로고    scopus 로고
    • Identifying regulatory networks by combinatorial analysis of promoter elements
    • Pilpel Y, Sudarsanam P, Church GM (2001) Identifying regulatory networks by combinatorial analysis of promoter elements. Nat Genet 29: 153-159.
    • (2001) Nat Genet , vol.29 , pp. 153-159
    • Pilpel, Y.1    Sudarsanam, P.2    Church, G.M.3
  • 7
    • 2442446708 scopus 로고    scopus 로고
    • Genome-wide discovery of transcriptional modules from DNA sequence and gene expression
    • Segal E, Yelensky R, Koller D (2003) Genome-wide discovery of transcriptional modules from DNA sequence and gene expression. Bioinformatics 19: i273-i282.
    • (2003) Bioinformatics , vol.19
    • Segal, E.1    Yelensky, R.2    Koller, D.3
  • 8
    • 33646029456 scopus 로고    scopus 로고
    • Stability regulation of mRNA and the control of gene expression
    • Cheadle C, Fan J, Cho-Chung YS, Werner T, Ray J, et al. (2005) Stability regulation of mRNA and the control of gene expression. Ann N Y Acad Sci 1058: 196-204.
    • (2005) Ann N Y Acad Sci , vol.1058 , pp. 196-204
    • Cheadle, C.1    Fan, J.2    Cho-Chung, Y.S.3    Werner, T.4    Ray, J.5
  • 9
    • 29144505309 scopus 로고    scopus 로고
    • The widespread impact of mammalian microRNAs on mRNA repression and evolution
    • Farh KK, Grimson A, Jan C, Lewis BP, Johnston WK, et al. (2005) The widespread impact of mammalian microRNAs on mRNA repression and evolution. Science 310: 1817-1821.
    • (2005) Science , vol.310 , pp. 1817-1821
    • Farh, K.K.1    Grimson, A.2    Jan, C.3    Lewis, B.P.4    Johnston, W.K.5
  • 10
    • 13944282215 scopus 로고    scopus 로고
    • Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs
    • Lim LP, Lau NC, Garrett-Engele P, Grimson A, Schelter JM, et al. (2005) Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs. Nature 433: 769-773.
    • (2005) Nature , vol.433 , pp. 769-773
    • Lim, L.P.1    Lau, N.C.2    Garrett-Engele, P.3    Grimson, A.4    Schelter, J.M.5
  • 12
    • 34249819336 scopus 로고    scopus 로고
    • MicroRNA-mediated feedback and feedforward loops are recurrent network motifs in mammals
    • Tsang J, Zhu J, van Oudenaarden A (2007) MicroRNA-mediated feedback and feedforward loops are recurrent network motifs in mammals. Mol Cell 26: 753-767.
    • (2007) Mol Cell , vol.26 , pp. 753-767
    • Tsang, J.1    Zhu, J.2    van Oudenaarden, A.3
  • 13
    • 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
  • 15
    • 0346727524 scopus 로고    scopus 로고
    • MicroRNAs modulate hematopoietic lineage differentiation
    • Chen CZ, Li L, Lodish HF, Bartel DP (2004) MicroRNAs modulate hematopoietic lineage differentiation. Science 303: 83-86.
    • (2004) Science , vol.303 , pp. 83-86
    • Chen, C.Z.1    Li, L.2    Lodish, H.F.3    Bartel, D.P.4
  • 16
    • 29144440077 scopus 로고    scopus 로고
    • MicroRNAs 221 and 222 inhibit normal erythropoiesis and erythroleukemic cell growth via kit receptor down-modulation
    • Felli N, Fontana L, Pelosi E, Botta R, Bonci D, et al. (2005) MicroRNAs 221 and 222 inhibit normal erythropoiesis and erythroleukemic cell growth via kit receptor down-modulation. Proc Natl Acad Sci U S A 102: 18081-18086.
    • (2005) Proc Natl Acad Sci U S A , vol.102 , pp. 18081-18086
    • Felli, N.1    Fontana, L.2    Pelosi, E.3    Botta, R.4    Bonci, D.5
  • 17
    • 33847304124 scopus 로고    scopus 로고
    • CD34+ hematopoietic stem-progenitor cell microRNA expression and function: A circuit diagram of differentiation control
    • Georgantas RW 3rd, Hildreth R, Morisot S, Alder J, Liu CG, et al. (2007) CD34+ hematopoietic stem-progenitor cell microRNA expression and function: a circuit diagram of differentiation control. Proc Natl Acad Sci U S A 104: 2750-2755.
    • (2007) Proc Natl Acad Sci U S A , vol.104 , pp. 2750-2755
    • Georgantas 3rd, R.W.1    Hildreth, R.2    Morisot, S.3    Alder, J.4    Liu, C.G.5
  • 18
    • 28344438648 scopus 로고    scopus 로고
    • A minicircuitry comprised of microRNA-223 and transcription factors NFI-A and C/EBPalpha regulates human granulopoiesis
    • Fazi F, Rosa A, Fatica A, Gelmetti V, De Marchis ML, et al. (2005) A minicircuitry comprised of microRNA-223 and transcription factors NFI-A and C/EBPalpha regulates human granulopoiesis. Cell 123: 819-831.
    • (2005) Cell , vol.123 , pp. 819-831
    • Fazi, F.1    Rosa, A.2    Fatica, A.3    Gelmetti, V.4    De Marchis, M.L.5
  • 19
    • 9144226389 scopus 로고    scopus 로고
    • Molecular signatures of self-renewal, differentiation, and lineage choice in multipotential hemopoietic progenitor cells in vitro
    • Bruno L, Hoffmann R, McBlane F, Brown J, Gupta R, et al. (2004) Molecular signatures of self-renewal, differentiation, and lineage choice in multipotential hemopoietic progenitor cells in vitro. Mol Cell Biol 24: 741-756.
    • (2004) Mol Cell Biol , vol.24 , pp. 741-756
    • Bruno, L.1    Hoffmann, R.2    McBlane, F.3    Brown, J.4    Gupta, R.5
  • 20
    • 25444531992 scopus 로고    scopus 로고
    • Evaluation of the similarity of gene expression data estimated with SAGE and Affymetrix GeneChips
    • van Ruissen F, Ruijter JM, Schaaf GJ, Asgharnegad L, Zwijnenburg DA, et al. (2005) Evaluation of the similarity of gene expression data estimated with SAGE and Affymetrix GeneChips. BMC Genomics 6: 91.
    • (2005) BMC Genomics , vol.6 , pp. 91
    • van Ruissen, F.1    Ruijter, J.M.2    Schaaf, G.J.3    Asgharnegad, L.4    Zwijnenburg, D.A.5
  • 21
    • 1342294092 scopus 로고    scopus 로고
    • Normalization for cDNA microarray data: A robust composite method addressing single and multiple slide systematic variation
    • Yang YH, Dudoit S, Luu P, Lin DM, Peng V, et al. (2002) Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation. Nucleic Acids Res 30: e15.
    • (2002) Nucleic Acids Res , vol.30
    • Yang, Y.H.1    Dudoit, S.2    Luu, P.3    Lin, D.M.4    Peng, V.5
  • 22
    • 45249111019 scopus 로고    scopus 로고
    • Affymetrix Whole-Transcript Human Gene 1.0 ST array is highly concordant with standard 3′ expression arrays
    • Pradervand S, Paillusson A, Thomas J, Weber J, Wirapati P, et al. (2008) Affymetrix Whole-Transcript Human Gene 1.0 ST array is highly concordant with standard 3′ expression arrays. Biotechniques 44: 759-762.
    • (2008) Biotechniques , vol.44 , pp. 759-762
    • Pradervand, S.1    Paillusson, A.2    Thomas, J.3    Weber, J.4    Wirapati, P.5
  • 23
    • 34247584465 scopus 로고    scopus 로고
    • Requirement of bic/microRNA-155 for normal immune function
    • Rodriguez A, Vigorito E, Clare S, Warren MV, Couttet P, et al. (2007) Requirement of bic/microRNA-155 for normal immune function. Science 316: 608-611.
    • (2007) Science , vol.316 , pp. 608-611
    • Rodriguez, A.1    Vigorito, E.2    Clare, S.3    Warren, M.V.4    Couttet, P.5
  • 24
  • 25
    • 33947721625 scopus 로고    scopus 로고
    • miR-181a is an intrinsic modulator of T cell sensitivity and selection
    • Li QJ, Chau J, Ebert PJ, Sylvester G, Min H, et al. (2007) miR-181a is an intrinsic modulator of T cell sensitivity and selection. Cell 129: 147-161.
    • (2007) Cell , vol.129 , pp. 147-161
    • Li, Q.J.1    Chau, J.2    Ebert, P.J.3    Sylvester, G.4    Min, H.5
  • 26
    • 34250879111 scopus 로고    scopus 로고
    • Oncogenic potential of the miR-106-363 cluster and its implication in human T-cell leukemia
    • Landais S, Landry S, Legault P, Rassart E (2007) Oncogenic potential of the miR-106-363 cluster and its implication in human T-cell leukemia. Cancer Res 67: 5699-5707.
    • (2007) Cancer Res , vol.67 , pp. 5699-5707
    • Landais, S.1    Landry, S.2    Legault, P.3    Rassart, E.4
  • 28
    • 33747885673 scopus 로고    scopus 로고
    • Bioconductor: An open source framework for bioinformatics and computational biology
    • Reimers M, Carey VJ (2006) Bioconductor: an open source framework for bioinformatics and computational biology. Methods Enzymol 411: 119-134.
    • (2006) Methods Enzymol , vol.411 , pp. 119-134
    • Reimers, M.1    Carey, V.J.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.