Question: Estimating Pathway Inhibition
2
gravatar for miquelduranfrigola
6.6 years ago by
Barcelona
miquelduranfrigola760 wrote:

Hi all,

imagine that I have a pathway P (e.g. from KEGG). The only information I have is the topology of P (nodes, edges, and direction of the edges).

Say that now I want to inhibit (modulate, if you wish, for a more general case) P. I achieve my inhibitions by formally removing edges from P. Intuitively, removing an edge that is upstream should cause a higher degree of inhibition, and possibly the same would happen for edges that depart from central nodes, and so on. However, if you take a KEGG pathway you will soon realize that the casuistics are huge, and non-trivial.

Are you guys aware of some method or approach to account for all this? As I said, I only have the pathway topology, and I want to estimate the level of pathway inhibition I would achieve by removing certain edges. I'm not an expert on the field: is this what you call "network dynamics"? Any hints will be more than welcome!

Thanks.

pathway kegg • 1.3k views
ADD COMMENTlink modified 6.6 years ago by Khader Shameer18k • written 6.6 years ago by miquelduranfrigola760
2
gravatar for Khader Shameer
6.6 years ago by
Manhattan, NY
Khader Shameer18k wrote:

Signaling Pathway Impact Analysis (SPIA; see package here) could be an approach that could be similar to what you are looking for.

Another approach is to treat your pathway as a network and perform network level perturbation analysis. NEXCADE or your network library of choice with a bit of scripting and stats could do such analysis. See related manuscripts 1 and 2

ADD COMMENTlink written 6.6 years ago by Khader Shameer18k

Great! Thanks Khader.

ADD REPLYlink written 6.6 years ago by miquelduranfrigola760
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