運用R及Bioconductor篩選差異性表達基因及探討相關之miRNAs-以前列腺癌為例

Using R and Bioconductor to identify differentially expressed genes and investigate related miRNAs –Prostate Cancer as a study case

陳順宗(Shun-Tsung Chen)

指導教授 ： 吳家樂 博士

亞洲大學/資訊學院/生物資訊學系碩士在職專班/碩士(2010年)

摘要

微陣列實驗可以一次記錄上萬個基因的表達，並可經由資料分
析，從中篩選差異性表達基因。但是微陣列的數據有多種背景雜訊，
因此ㄧ種能從微陣列中擷取差異性表達基因的分析方法便非常重要。
R為整合型資料處理及統計軟體；Bioconductor是以R為基礎的應
用軟體集，可分析不同的基因微陣列資料。本研究以R及Bioconductor
篩選前列腺癌微陣列的差異性表達基因(differentially expressed genes,
DEGs)，再利用TAG, ncRNAppi及miR2Disease等三個資料庫，探討調
控DEGs之相關miRNAs及其與人類癌症之關係。
經分析後，得出如下的結果：(1)前100名差異性表達基因之調整p
值皆小於5 1.9 10  ，其中有16個與癌症相關、(2) FOS, AXL及TGFBR2
分別受到miR-101, miR-1及miR-20a調控，PLP2, CD59受到miR-124調
控，而GJA1則受到miR-206及miR-1調控、(3) miR-101與包括前列腺
癌在內的六種癌症有關；miR-1與四種癌症有關；miR-20a與包括前列
腺癌在內的八種癌症有關；miR-124與一種癌症有關；miR-206與二種
癌症有關、(4) TGFBR2受miR-20a調控而影響前列腺癌的發生。
最後建立網頁將結果提供查詢， 網址為：
http://ppi.bioinfo.asia.edu.tw/R_prostate_cancer/index.htm

關鍵字

微陣列 ； 差異性表達基因 ； 前列腺癌 ； 微型核糖核酸

並列摘要

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.

並列關鍵字

microarray ； differentially expressed genes ； R cancer, microRNAs ； Bioconductor ； prostate cancer ； microRNAs

參考文獻

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