<p>Hi all,</p>

<p>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).</p>

<p>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.</p>

<p>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!</p>

<p>Thanks.</p>

**Signaling Pathway Impact Analysis** (<a href="http://www.ncbi.nlm.nih.gov/pubmed/18990722">SPIA</a>; 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**. <a href="http://www.ncbi.nlm.nih.gov/pubmed/22870252">NEXCADE</a> or your <a href="http://www.biostars.org/post/show/1650/library-module-for-network-analysis/">network library</a> of choice with a bit of scripting and stats could do such analysis. See related manuscripts <a href="http://www.biomedcentral.com/1752-0509/6/54">1</a> and <a href="http://www.ncbi.nlm.nih.gov/pubmed/20709523">2</a>