Predicted protein protein interaction FREE tool, insert list of genes and relate to a Single pathway of my interest

Question

[MrT11]

Hi All,

I have a list of 2000 genes which I need to relate to the Nfkb pathway, to find if there's any predicted interaction between my target genes and the pathway itself. What I am doing at the moment is using STRING, I insert some genes up- and down-stream of the nfkb pathway and my genes of interesting. Unfortunately this is too tedious and not so accurate, does anybody know a FREE software OR ONLINE tool/plug in which would allow me to upload a longer list of genes and check their relevance in my pathway of interest?

I also tried to use Ingenuity but I'd like a free-easy version

Thanks in advance

Answer 1

[Jean-Karim Heriche]

I would propose to turn the query around. Find genes related to the NF-kB pathway using available data and find if your genes of interest are in there. This can easily by done using FUN-L or GeneMANIA: input a list of known NF-kB pathway genes and you'll get back the rest of the genome ranked by relevance to the NF-kB pathway as represented by your query genes.