Differentially expressed genes profiling in human esophageal squamous cell carcinoma: a small data of microarray and bioinformatics

Esophageal squamous cell carcinoma (ESCC) is the predominant histologic type of esophageal cancer with high incidence and poor prognosis in China. Multiple heterogeneous genetic and epigenetic changes are detected frequently in ESCC. The purpose of this study was to identify potential differentially expressed genes (DEGs) and molecular biological processes in the occurrence and development of ESCC. An integrated analysis of microarray and bioinformatics technologies was use in the study. First, we constructed a small cDNA microarray dataset in eight cases of ESCC tissues compared with matched normal esophageal epithelium. Then, we performed a bioinformatics analysis by ways of Gene Ontology (GO) analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, signal transduction pathways and gene co-expression networks. A total of 1208 genes DEGs including 529 up-regulated genes and 679 down-regulated genes were screened form this small microarray dataset. Gene function analysis showed that 347 of the functions of up-regulated DEGs and 203 down-regulated DEGs were explored, respectively. KEGG pathway analysis revealed that 52 and 51 signal transduction pathways were enriched in the up-regulated and down-regulated DEGs, respectively. Furthermore, some target DEGs (ie. PIK3R, JAM2, KIT, ITGA9, TJP1, ERBB3, PLCB4, ATCN1, FZD6 and HPGD) were examined which highly involved in ESCC tumorigenesis by the construction of gene-gene interaction network and gene co-expression network. Our findings provide the groundwork for understanding the molecular mechanism of ESCC with an integrated analysis of microarray and bioinformatics technologies.