Entering edit mode
9.3 years ago
Deepak Tanwar
★
4.2k
Hi,
I have a gene list. I want to find out all the possible interaction of the genes and their position of interaction.
Example: Suppose- CCNE1 reacts with CCNE2, MFN1, BLCA1, etc. It reacts in a manner like: CCNE1 ---> CCNE2 -------> MFN1 ---> BLCA1
So, here CCNE1 reacts with CCNE2 and interaction site is 1 and with BLCA1, the interaction site is 3.
I hope that this information would be present in the bioconductor package "reactome.db". Am I right?
How to find this out, as I tried to described in the example?
It could be I used wrong words to describe. Please correct me.
Thank you
It is not quite clear what you are looking for. Do you want to find out which domains in the proteins are interacting, or just if the proteins are interacting? If you just google database of interacting protein domain there are plenty of options, and this covers the first option. If you would like to just find interactions, and not necessarily the domain, you will have to ask yourself if you are interested in physical or functional annotations.
Actually, I am using the Gene sets derived from the Reactome pathway database, from http://www.broadinstitute.org/gsea/msigdb/collections.jsp
I have a set of 50 genes. Not from any GE data or so, just a list of 50 genes. I wanted to know, how is it possible to check that which genes belongs to which pathway?
Secondly, Suppose- CCNE1 reacts with CCNE2, MFN1, BLCA1, etc. It reacts in a manner like: CCNE1 reacts on first site with CCNE2 and then to MFN1 (like a chemical reaction). So how to find this?
If I am still unable to make it clear, please let me know.