In a KEGG pathway, some nodes have more than 1 gene/protein associated with them. For instance in pathway hsa04022 (cGMP-PKG signaling pathway), the entity IRS maps to 3 ids - hsa:3667, hsa:8471, and hsa:8660; these 3 ids are IRS1, IRS4, and IRS2, respectively.
Does it mean that all 3 of them are an active part of the pathway or it is something else?
From my RNA seq data I see different expression profiles for all 3 of them viz.
IRS1 goes up by log2fc of 1.1, IRS2 down by -0.8 and IRS4 up by 2.1.
What should be infered from such a thing - is this node going up or down or it's unclear from such a study?
What does it mean to have more than 1 gene/protein (may be homologs) associated with one node in a KEGG pathway?
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Rajinder Gupta •
You can't necessarily tell what the node is doing from the information you provided. There are multiple proteins (3 of them) that can serve that role. Those proteins will all have different expression profiles (e.g., tissue of expression) and regulating proteins, to what's actually happening will depend on the underlying levels of those proteins in whatever cell type you're working on.
Thanks Devon But given the cell line and the expression profiles of these proteins; can I say that the step is fullfilled as 2 of the protein IRS1 and 4 are significantly up regulated.
By the term step is fulfilled, I mean that the function is carried on at or above as in control samples.
If you happen to have prior information about the system then yes you might be able to reliably draw that conclusion.
Thank you very much for your help
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