Identification of genes related to nasopharyngeal carcinoma with the help of pathway-based networks.
cDNA microarray is a powerful tool to analyze simultaneously the expression levels of tens of thousands of genes. Compared with normal nasopharynx (NP) tissues, 2210 genes were highly differentially expressed in nasopharyngeal carcinoma (NPC) tissues detected by cDNA microarray. Since signal pathway is widely used to describe the complex relationship between genes, a pathway-based network was constructed to visualize the connection between the genes obtained from microarray data in this report. We analyzed the targeted genes that may have more important influence on this gene network with statistical methods and found that some genes might have significant influence on this network, especially Ras-related nuclear protein (RAN), carboxyl ester lipase (CEL), v-rel reticuloendotheliosis viral oncogene homolog A (RELA) genes. To verify the results from pathway-based selection, reverse transcription-polymerase chain reaction (RT-PCR) and real-time RT-PCR were performed to detect the expression levels of RAN, CEL and RELA genes and it was found that the RAN and CEL genes were significantly up-regulated in more than 80% of NPC tissues. To further elucidate the function of the RAN gene, RAN expression was specifically suppressed in a 5-8F NPC cell line by RNA interference (RNAi). As expected, the depletion of RAN could effectively block the proliferation of tumor cells. Therefore, our study may open up a new way to analyze the vast microarray data.
Li
Hui
H
Cancer Research Institute, Xiangya School of Medicine, Central South University, Changsha 410078, China.
Ren
Cai-Ping
CP
Tan
Xiao-Jun
XJ
Yang
Xu-Yu
XY
Zhang
Hong-Bo
HB
Zhou
Wen
W
Yao
Kai-Tai
KT
D001483:Base Sequence; D015153:Blotting, Western; D002277:Carcinoma / Q000235:genetics*; D002453:Cell Cycle; D045744:Cell Line, Tumor; D015972:Gene Expression Regulation, Neoplastic; D006801:Humans; D008954:Models, Biological; D008969:Molecular Sequence Data; D009303:Nasopharyngeal Neoplasms / Q000235:genetics*; D020411:Oligonucleotide Array Sequence Analysis; D034622:RNA Interference; D020133:Reverse Transcriptase Polymerase Chain Reaction; D013778:Tetrazolium Salts / Q000494:pharmacology; D013844:Thiazoles / Q000494:pharmacology; D014162:Transfection; D020931:ran GTP-Binding Protein / Q000235:genetics*
D013778:Tetrazolium Salts; D013844:Thiazoles; D020931:ran GTP-Binding Protein; C022616:thiazolyl blue