Identification Key Genes of Hepatocellular Carcinoma Base on TCGA Database
Abstract: Objective: Hepatocellular carcinoma (HCC) is a common cancer of the digestive system, is the third cause of death worldwide and the second cause of death in China. The Cancer Genome Atlas (TCGA) aims to better understand the molecular mechanisms of cancer by using a large-scale genome se-quencing-based analysis techniques and extensive cooperation. This study introduces TCGA data-base to find key genes of HCC events. Materials and Methods: The data from TCGA were processed, integrated according to the standard procedure of TCGA, data types and levels were carefully as-sessed. Bioinformatics analysis was done using the DESeq and edgeR package of R language (3.1.1 version). Results were showed as pheatmap, VennDiagram, hist, PlotMA etc. Differences were de-fined as follows: expression increased more than two folds; P <0.05; gene ranked in the top 10%. Results: 17 mRNA chips of HCC and 9 mRNA chips of normal tissue were collected from TCGA data- base. Hist figure reflected the number of different gene was large. PLotMA map showed the distribu-tion of gene expression, suggesting most genes of different expression were increased. 719 diffe-rentially expressed genes were found by DESeq, while 4413 by edger, among which 713 were com-mon different genes. Conclusion: Compared to conventional microarray, TCGA method has its own advantages such as larger number of samples, less cost and easier for analyzing, offering opportuni-ty for large-scale genomic studies of HCC and subsequent functional genomics-based research.
文章引用: 贾俊君 , 何 宁 , 张 静 , 姜 骊 , 周燕飞 , 周 琳 , 郑树森 (2015) 基于TCGA数据库的肝癌发生关键基因筛选。 外科， 4， 1-8. doi: 10.12677/HJS.2015.41001
 Pang, R.W., Joh, J.W., Johnson, P.J., Monden, M., Pawlik, T.M., et al. (2008) Biology of hepatocellular carcinoma. Annals of Surgical Oncology, 15, 962-971.
 He, J., Gu, D., Wu, X., Reynolds, K., Duan, X., et al. (2005) Major causes of death among men and women in China. New England Journal of Medicine, 353, 1124-1134.
 Oshlack, A., Robinson, M.D. and Young, M.D. (2010) From RNA-seq reads to differential expression results. Genome Biology, 11, 220.
 Venook, A.P., Papandreou, C., Furuse, J. and de Guevara, L.L. (2010) The incidence and epidemiology of hepatocellular carcinoma: A global and regional perspective. Oncologist, 15, 5-13.
 Sanyal, A.J., Yoon, S.K. and Lencioni, R. (2010) The etiology of hepatocellular carcinoma and consequences for treatment. Oncologist, 15, 14-22.
 Trevisani, F., Cantarini, M.C., Wands, J.R. and Bernardi, M. (2008) Recent advances in the natural history of hepatocellular carcinoma. Carcinogenesis, 29, 1299-1305.
 Alexandrov, L.B., Nik-Zainal, S., Wedge, D.C., Aparicio, S.A., Behjati, S., et al. (2013) Signatures of mutational pro- cesses in human cancer. Nature, 500, 415-421.
 Hoadley, K.A., Yau, C., Wolf, D.M., Cherniack, A.D., Tamborero, D., et al. (2014) Multiplatform analysis of 12 cancer types reveals molecular classification within and across tissues of origin. Cell, 158, 929-944.
 Barrio-Real, L., Benedetti, L.G., Engel, N., Tu, Y., Cho, S., et al. (2014) Subtype-specific overexpression of the Rac- GEF P-REX1 in breast cancer is associated with promoter hypomethylation. Breast Cancer Research, 16, 441.
 Yang, D., Sun, Y., Hu, L., Zheng, H., Ji, P., et al. (2013) Integrated analyses identify a master microRNA regulatory network for the mesenchymal subtype in serous ovarian cancer. Cancer Cell, 23, 186-199.
 Brennan, C.W., Verhaak, R.G., McKenna, A., Campos, B., Noushmehr, H., et al. (2013) The somatic genomic landscape of glioblastoma. Cell, 155, 462-477.