Hi all
I found that my target gene expression (consistent in mRNA level and protein level) is different in a cell line against different stimuli. So I want to know why this phenomenon happened.
After search on some websites of bioinformatics, there are about 20 candidates of transcription factors or signal pathways might be involved. It's too hard and expensive for me to screen them one by one using WB or inhibitors.
Could anyone give me some suggestions about the strategy?
I also found some investigators recommend using co-expressed or co-regulated genes but I don't know what does that mean and how to do it.
Any suggestions would be greatly appreciated.
Hi Zhang,
Isolate total phospho-proteome of different stimuli conditions and go for mass spectrometer acquisition and after getting the results search for candidate transcription factor levels. I think this may help you.
instead of Mass Spec., you can do RNA-seq of the different stimuli conditions. It is not cheap but I find MS to be quit noisy and it may be hard to infer data from it.
Once you have you RNA-seq analysis you can look for pathways that have significantly changed in a specific condition, or in all conditions, and further investigate it.
Dear Girish and Nitsan
Thank you for your suggestions and I am studying these techniques to decide which one we should choose.
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