Identifi cation of Rectal Cancer Genes by Microarray Analysis
Keywords:
Rectal cancer, Gene expression, MicroarrayAbstract
In northern part of Thailand, cancer is a leading cause of death and colorectal cancer is ranked the third among different fatalities in this region. The purpose of this study is to use a cDNA microarray to analyze the difference in gene expression profi les between normal and tumor tissue in 6 stage III rectal cancer patients who were treated at Maharaj Nakorn Chiang Mai Hospital (Suandok) between December 2009 - April 2010. Microarray analysis for rectal cancer genes was completed using the R program, which is a program for statistical and graphical computation. To measure gene expression we used the linear model statistics function provided by the limma package in R. This approach included three main steps. First, the cDNA microarray data was imported into R. cDNA preprocessing steps including background correction, normalization and summarization were performed. Normalization involved both within-array and between-array normalization. Second, the linear model function was used to analyze the cDNA gene expression and classify different gene expressions of rectal cancer. Using fold change value of 2 (=2) and a p-value less than 0.005 (<0.005) for t-test, the differences in the gene expressions between normal and tumor tissue were obtained. Finally, from TNM staging we found common rectal cancer genes in T3 stage differentiated from normal tissue. After intensive analysis, three genes were identifi ed, named CDC4 gene, placenta growth factor precursor (PlGF) and CD27-binding protein.
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