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    Please use this identifier to cite or link to this item: http://asiair.asia.edu.tw/ir/handle/310904400/10914


    Title: Using R and Bioconductor to identify differentially expressed genes and investigate related miRNAs –Prostate Cancer as a study case
    Authors: Shun-Tsung Chen
    Contributors: Department of Bioinformatics
    Keywords: microarray;differentially expressed genes;R cancer, microRNAs;Bioconductor;prostate cancer;microRNAs
    Date: 2010
    Issue Date: 2010-11-08 10:33:09 (UTC+8)
    Publisher: Asia University
    Abstract: Microarray experiment enables us to record the expression levels of
    thousands of genes at one time and identify differentially expressed
    genes(DEGs). Microarray technology involves many steps and for each
    step there may introduce background noises, so an effective way of
    identifying DEGs from microarray becomes very important.
    The R is a kind of integrated data processing and statistical software, and
    the Bioconductor is a R-based application software of analying genomic
    information that can be used to analyze microarray data.
    In this study, the R and Bioconductor are used to screen and analyze
    DEGs of microarray of prostate cancer data. By integrating the Tumor
    Associated Gene (TAG), ncRNAppi and miR2Disease databases, it is
    found that certain DEGs are regulated by microRNAs.
    The findings are as follows: (1) the adjusted p-values of the top 100
    DEGs are less than 5 1.9 10  , and there are 16 cancer-related genes among
    the top 100 DEGs, (2) three genes, FOS, AXL and TGFBR2, are regulated
    by the microRNA miR-101, miR-1 and miR-20a, respectively, and two
    genes, the PLP2 and CD59, are regulated by the microRNA miR-124, and
    GJA1, is regulated by both miR-206 and miR-1, (3) miR-101 is related
    with six types of cancers, including prostate cancer, and miR-1 is related
    with four types of cancers, and the miR-20a is related with eight types of
    cancers, including prostate cancer, and the miR-124 is related with one
    type of cancer, and the miR-206 is related with two types of cancers, and
    (4) TGFBR2 is regulated by miR-20a inducing prostate cancer.
    The web site of studying results is available at
    http://ppi.bioinfo.asia.edu.tw/R_prostate_cancer/index.htm.
    Appears in Collections:[生物資訊與醫學工程學系 ] 博碩士論文

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