Using bioinformatics to screen common key genes in hepatocellular carcinoma in human and rat / 中华肝胆外科杂志

ABSTRACT

Objective To use bioinformatics methods to analyze large amounts of data generated by gene chips and to screen common key genes in hepatocellular carcinoma in human and rat.Methods For search of the medical literature,3 sets of gene chip with data which met our predetermined criteria were downloaded from the GEO database.The data were standardized by using the bioconductor and R version of the 2.10.1 version.The original data of the affymetrix platform were normalized with background correction,standardized and transformed into log2 by using the algorithm of the affy packages RMA.The TTEST function of the excel was then used to calculate the significance of each gene.The DAVID was used for gene ID conversion and a table was established for samples and the corresponding gene expression data.A meta analysis was performed to calculate the common genes of human and rat.An enrichment regulation pathway was gained with the KEGG in the DAVID library. Results There were 26 common expression genes in the development process of hepatocellular carcinoma in human and rat.Five of these genes were up-regulation genes,while twenty-one were down-regulation genes.An enrichment pathway,which is a focal adhesion pathway,was found and this pathway has been reported to be associated with development of hepatocellular carcinoma.Conclusion With bioinformatics,we were able to screen common key genes and a pathway which were closely related to development of hepatocellular carcinoma in human and rat.