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

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

ppi network cytoscape protein
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updated by Ibrahim Tanyalcin Ibrahim Tanyalcin • written by Ivy Ng • Ivy Ng

1 answer

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,

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written by Ibrahim Tanyalcin Ibrahim Tanyalcin

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?

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written by Ivy Ng • Ivy Ng

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

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written by Ibrahim Tanyalcin Ibrahim Tanyalcin

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