Question: How to find the neighbors of a sparce network using PPI network??
gravatar for Chaimaa
21 months ago by
Chaimaa150 wrote:

Dear all, I want to make my sparse network more dense by finding the neighbors of each gene contain in this network using any human PPI networks .

Could anyone tell me how to do that? whether automatically or programmatically , and i appreciate anyhelp!!

ppi network sparce network • 491 views
ADD COMMENTlink modified 21 months ago by ivivek_ngs4.7k • written 21 months ago by Chaimaa150
gravatar for Jean-Karim Heriche
21 months ago by
EMBL Heidelberg, Germany
Jean-Karim Heriche18k wrote:

For the naive approach of going for neighbours, have a look at the ego_graph() function of the igraph R package. Alternatively, given a list of genes (e.g. those in your network) and an interaction graph, you could extract the relevant subgraph as described here. The method is implemented as get_relevant_subgraph() in my perl Graph module. Depending on your objective, this may give you a more meaningful graph.

ADD COMMENTlink written 21 months ago by Jean-Karim Heriche18k
gravatar for ivivek_ngs
21 months ago by
Seattle,WA, USA
ivivek_ngs4.7k wrote:

Apart from what @Jean-Karim Heriche suggested, I would also ask the OP to take a look at this paper that uses an integrated approach of SWC, DECOMP and SSS. Might be worth taking a shot since it works on sparsely PPI network connections.

Another thing which I have recently come across while I was working on gene regulatory network with VIPER was the use of leading edge analysis that uses the GSEA on the gene expression signature. This work was first shown by Subramanium et. al and the paper can be found here. Take a look at both and see which fits well.

There is apparently a new paper as well published a year back based on transcriptome studies. But I am sure it can be used for your own purposes as well.

ADD COMMENTlink modified 21 months ago • written 21 months ago by ivivek_ngs4.7k
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