Imagine that there is a conserved pathway between animals and plants. But there is some differences. We have performed network analysis for each one. How we can compare them against each other to find differences? Or you have studied two similar disease and have its network. How you can find similarities and differences?
Start with a table of orthlogs of genes in both species... Then check how the pathways look like once translated from one to another - and which genes are up/downregulated in your conditions for both species. Then you can find a common part of both pathways (conserved part) and the differences. An example on close species is described here: http://www.ncbi.nlm.nih.gov/pubmed/23077551
@ Michal
Thank you. Very interesting reference. Can someone analyze two pathway, one normal and the other dysfunctioned? for e.g. normal cell and cancer cell to find similarities and differences without applying expression level. I mean we download most updated path or network for normal cell cycle and what we see in cancer. Can we use this method?
We have two pathway normal and not normal.
I think you can... and it would be a nice result if you prove the pathway "overlap" somehow - eg with expression data.
For your own knowledge, you can find the common part in the cancer/normal pathway and this way find the targets (eg key switches) for further study. Probably no standards and not much ready software tools there, so some "manual work" on your favourite pathways may be needed.
I just noticed from your paper on CElegans pathway that you do similar things already... This is an interesting reference for me too :)
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