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    Results: 1 to 20 of 111

    1.

    Methods for analyzing deep sequencing expression data: constructing the human and mouse promoterome with deepCAGE data.

    Balwierz PJ, Carninci P, Daub CO, Kawai J, Hayashizaki Y, Van Belle W, Beisel C, van Nimwegen E.

    Genome Biol. 2009;10(7):R79. Epub 2009 Jul 22.

    PMID:
    19624849
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    2.

    Deep cap analysis gene expression (CAGE): genome-wide identification of promoters, quantification of their expression, and network inference.

    de Hoon M, Hayashizaki Y.

    Biotechniques. 2008 Apr;44(5):627-8, 630, 632. Review.

    PMID:
    18474037
    [PubMed - indexed for MEDLINE]
    Free Article
    3.

    Genome-wide detection and analysis of hippocampus core promoters using DeepCAGE.

    Valen E, Pascarella G, Chalk A, Maeda N, Kojima M, Kawazu C, Murata M, Nishiyori H, Lazarevic D, Motti D, Marstrand TT, Tang MH, Zhao X, Krogh A, Winther O, Arakawa T, Kawai J, Wells C, Daub C, Harbers M, Hayashizaki Y, Gustincich S, Sandelin A, Carninci P.

    Genome Res. 2009 Feb;19(2):255-65. Epub 2008 Dec 11.

    PMID:
    19074369
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    4.

    Large-scale clustering of CAGE tag expression data.

    Shimokawa K, Okamura-Oho Y, Kurita T, Frith MC, Kawai J, Carninci P, Hayashizaki Y.

    BMC Bioinformatics. 2007 May 21;8:161.

    PMID:
    17517134
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    5.

    Genome-wide analysis reveals strong correlation between CpG islands with nearby transcription start sites of genes and their tissue specificity.

    Yamashita R, Suzuki Y, Sugano S, Nakai K.

    Gene. 2005 May 9;350(2):129-36. Epub 2005 Mar 19.

    PMID:
    15784181
    [PubMed - indexed for MEDLINE]
    6.

    Genome-wide analysis of alternative promoters of human genes using a custom promoter tiling array.

    Singer GA, Wu J, Yan P, Plass C, Huang TH, Davuluri RV.

    BMC Genomics. 2008 Jul 25;9:349.

    PMID:
    18655706
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    8.

    Analysis of promoter regions of co-expressed genes identified by microarray analysis.

    Veerla S, Höglund M.

    BMC Bioinformatics. 2006 Aug 17;7:384.

    PMID:
    16916454
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    9.

    Genome-wide analysis of factors regulating gene expression in liver.

    Teufel A, Weinmann A, Krupp M, Budinger M, Galle PR.

    Gene. 2007 Mar 15;389(2):114-21. Epub 2006 Nov 7.

    PMID:
    17174484
    [PubMed - indexed for MEDLINE]
    10.

    Genesis: cluster analysis of microarray data.

    Sturn A, Quackenbush J, Trajanoski Z.

    Bioinformatics. 2002 Jan;18(1):207-8.

    PMID:
    11836235
    [PubMed - indexed for MEDLINE]
    Free Article
    11.

    Identification of estrogen-responsive genes using a genome-wide analysis of promoter elements for transcription factor binding sites.

    Kamalakaran S, Radhakrishnan SK, Beck WT.

    J Biol Chem. 2005 Jun 3;280(22):21491-7. Epub 2005 Mar 24.

    PMID:
    15790569
    [PubMed - indexed for MEDLINE]
    Free Article
    12.

    Clustering and re-clustering for pattern discovery in gene expression data.

    Ma PC, Chan KC, Chiu DK.

    J Bioinform Comput Biol. 2005 Apr;3(2):281-301.

    PMID:
    15852506
    [PubMed - indexed for MEDLINE]
    13.

    Development of a DNA barcode tagging method for monitoring dynamic changes in gene expression by using an ultra high-throughput sequencer.

    Maeda N, Nishiyori H, Nakamura M, Kawazu C, Murata M, Sano H, Hayashida K, Fukuda S, Tagami M, Hasegawa A, Murakami K, Schroder K, Irvine K, Hume D, Hayashizaki Y, Carninci P, Suzuki H.

    Biotechniques. 2008 Jul;45(1):95-7.

    PMID:
    18611171
    [PubMed - indexed for MEDLINE]
    Free Article
    14.

    Mass distributed clustering: a new algorithm for repeated measurements in gene expression data.

    Matsumoto S, Aisaki K, Kanno J.

    Genome Inform. 2005;16(2):183-94.

    PMID:
    16901101
    [PubMed - indexed for MEDLINE]
    15.

    Combined analysis of expression data and transcription factor binding sites in the yeast genome.

    Nagaraj VH, O'Flanagan RA, Bruning AR, Mathias JR, Vershon AK, Sengupta AM.

    BMC Genomics. 2004 Aug 26;5(1):59.

    PMID:
    15331021
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    16.

    Oligonucleotide DNA chips are useful adjuncts in epigenetic studies of glioblastomas.

    Kim B, Kim H, Song BJ, Cha SH, Lee MO, Park SH.

    Neuropathology. 2006 Oct;26(5):409-16.

    PMID:
    17080717
    [PubMed - indexed for MEDLINE]
    17.

    Genome-wide profiling of DNA methylation reveals a class of normally methylated CpG island promoters.

    Shen L, Kondo Y, Guo Y, Zhang J, Zhang L, Ahmed S, Shu J, Chen X, Waterland RA, Issa JP.

    PLoS Genet. 2007 Oct;3(10):2023-36. Epub 2007 Sep 10.

    PMID:
    17967063
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    18.

    Tissue-specific transcript annotation and expression profiling with complementary next-generation sequencing technologies.

    Hestand MS, Klingenhoff A, Scherf M, Ariyurek Y, Ramos Y, van Workum W, Suzuki M, Werner T, van Ommen GJ, den Dunnen JT, Harbers M, 't Hoen PA.

    Nucleic Acids Res. 2010 Sep;38(16):e165. Epub 2010 Jul 7.

    PMID:
    20615900
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    19.

    Identification and quantification of disease-related gene clusters.

    Firneisz G, Zehavi I, Vermes C, Hanyecz A, Frieman JA, Glant TT.

    Bioinformatics. 2003 Sep 22;19(14):1781-6.

    PMID:
    14512349
    [PubMed - indexed for MEDLINE]
    Free Article
    20.

    Defining transcriptional networks through integrative modeling of mRNA expression and transcription factor binding data.

    Gao F, Foat BC, Bussemaker HJ.

    BMC Bioinformatics. 2004 Mar 18;5:31.

    PMID:
    15113405
    [PubMed - indexed for MEDLINE]
    Free PMC Article

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