I am going to evaluate the gene expression levels in the MKN45 cell line (gastric cancer). Before that, I want to identify critical differentially expressed genes obtained from tissues available on the GEO database because there are no datasets associated with the MKN45 cell line. My question is that is it reasonable to do that?
Hi Hossein,
a growing body of evidence shows that researchers identify differentially expressed genes (DEGs) in disease state vs. controls from GEO database and then validate the DEGs in another independent GEO dataset or in tissue samples of their own. I think it makes sense to mine the dataset and figure out DEGs for further validation in your cell lines. As in your case, the only concern is whether DEGs determined in silico would differ in the associated cell line you mentioned.
Best and good luck!
Hi, Hossein
In my opinion, it's make sense for your idea. Maybe the silico research could cover the tissue from the normal and tumor, and then the results of the wet lab study could be discussed in the variety way. Good luck to you.
Yi Yan Thanks for answering. In fact, we do not know whether a specific gene/protein is over/down expressed in cell lines. We want to examine the gene and protein expression levels of c-FLIP in only one type of gastric cancer cell line. Before that, I want to support our potential finding by knowing the gene expression level of c-FLIP (in silico) obtained from tissue samples of gastric cancer patients available on the GEO database. Now, my concern is that the in silico analysis is on tissue samples, but our wet experiments are on the specific cell line. Is it rational to do that?
Hi, Hossein
I think it's may depend on your final purpose of research. There are some elements affecting your thoughts for the study rationale, such as which control cell line do you choice or the MKN-45 cell line may possess the specific gene... so on. Therefor maybe re-design the process based on what you want to solve the question. Good luck.
Hi Hossein,
If gene expression of c-FLIP alters both in tumor tissue samples and the specific cells compared to corresponding controls, I think it is rational and would support your hypothesis in the research. Afterwards you can do more investigation on the mechanism how it was changed in tumor and to see whether intervention of target gene could alter the phenotype of tumor cells.
Best
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