What's the difference between Biological process and pathway when analyzing group of protein under different conditions, which one to choose?

Question

[Ivy Ng]

Hi there,

I have a group of protein under different treatments, and we are try to compare their functional difference (binding), which one shall I use, biological process or pathway analysis?

Also, I am new to this area, anyone could kindly tell me that if I want to compare the differences in Cytoscape, what is the best way? I have 4-5 groups, and we are try to find the common and different expressed protein and their function regards binding.

Thank you so much!!

Best, Ivy

Answer 1

[Ibrahim Tanyalcin]

Dear Ivy,

I would suggest you keep an eye on both biological process (from this I guess you mean binding affinity under different conditions) and pathway analysis. If you think about them separately than you would miss the point that throughout evolution, they sort of co-evolved together. If the binding affinity of a protein is changed to its ligand under a treatment condition, than the whole pathway(s) involving these two proteins are (possibly) altered. First try to assess the minimal common members of the different pathways.

Regards,

[Ivy Ng]

Hi, Thank you so much for the suggestions, they are quite helpful! In that case I think I should also distinguish pathways from biological process in the network?

[Ibrahim Tanyalcin]

Yes, I think you should distinguish them but nonetheless keep an eye an both. Because they covariate.