Transcriptome analysis of highly metastatic cell line

A prediction of peritoneal recurrence is of significance using metastasis-related biomarker. This work describes a combined analysis of proteome and transcriptome data for biomarker discovery in highly metastatic cell line. We used nano-flow liquid chromatography (LC) linear ion trap time-of-flight mass spectrometry (LIT-TOF MS) and cDNA microarray to identify specific protein differentially expressed between a highly metastatic stomach cancer cell line MKN-45-P and its parental cell line MKN-45. In total, 240 proteins were found to be expressed between the two cell lines. Of these, 75 proteins (31%) and 49 proteins (20%) were only identified from MKN-45-P and MKN-45 respectively. An mRNA expression of 1533 genes was up-regulated in MKN-45-P compared with MKN-45. No close correlation was found between proteomic and transcriptomic analysis. Interestingly, 4 of 240 proteins (1.6%) were involved in the up-regulated mRNA expression. Comparison analysis of gene expression between highly metastatic gastric cancer cell line MKN-45-P and its parental cell line MKN-45.