Title page for 962211001


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Student Number 962211001
Author Yi-An Ko(¬_©É¦w)
Author's Email Address No Public.
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Department Graduate Institute of Systems Biology and Bioinformatics
Year 2008
Semester 2
Degree Master
Type of Document Master's Thesis
Language English
Title Development of a Non-Restricted Functional Elements Assay Method for Identifying Genome-Wide Regulatory Elements
Date of Defense 2009-07-02
Page Count 57
Keyword
  • Colorectal Cancer
  • DNase
  • Pair-wise Gaussian
  • Promoter Array
  • Abstract A major challenge for post-genomics research is the integration gene expressions with their corresponding regulatory elements and chromatin architectures on a genome-wide scale. Regulatory elements exert diverse mechanisms to regulate the expression of genes through protein-protein or protein-DNA interactions, while chromatin structures act in the upstream of the regulatory cascade and have a broad effect on the expression of multiple genes. Here, we developed a novel method, denoted as genome-wide non-restricted functional elements assay (NOFEE), to identify changes of regulatory elements and to pursue a more comprehensive characterization of the gene expression profile of HCT-116 colorectal cancer cell line in response to the treatment of a Pt-based compound. Our experiments integrate high-resolution promoter tiling arrays and exon arrays on samples that were treated with optimized concentration of DNase I. Data were subsequently analyzed with ¡¥Partek¡¦ software package, which is a commercial product based on pair-wise Gaussian merging method. A total of 12,117 regions in the promoter array and 3,043 differentially expressed genes in the exon array were used in our experiment. By integrating these datasets, we show that 61% of the exon expression profile can be associated with promoter regulatory regions suggesting that promoters in these regions may be directly involved in the transcriptional regulation of in response to Pt-compound treatment. Our results also suggest that the NOFEE approach can be a powerful method for genome-wide investigations of cis-acting regulatory elements.
    Table of Content Abstracti
    ºK­nii
    Chapter 1 Introduction1
    1-1CURRENT STUDIES OF GENE REGULATORY ELEMENTS1
    1-2DNASE-CHIP4
    1-3CHIP-CHIP7
    1-4NOFEE-CHIP9
    1-5ANALYSIS11
    1-6COLORECTAL CANCER AND OXALIPLATIN¡ÐTHE PT-BASED COMPOUND12
    Chapter 2Materials and Methods15
    2-1MATERIALS15
    2-2METHODS18
    Chapter 3Results35
    3-1 EXPERIMENTAL RESULTS35
    3-2 PARTEK ANALYSIS37
    3-3 INTEGRATION OF PROMOTER ARRAY AND EXON ARRAY39
    3-4 GENE ONTOLOGY BY DAVID41
    3-5 PATHWAY MAPPINGS44
    3-6 NETWORK ANALYSIS47
    3-7 VALIDATION ON B_1_55433149
    Chapter 4Discussion50
    Chapter 5Conclusion54
    References:55
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    Advisor
  • Qing-Dong Ling(­â¼yªF)
  • Sun-Chong Wang(¤ý®]±R)
  • Files
  • 962211001.pdf
  • disapprove authorization
    Date of Submission 2009-07-30

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