how to find a group of genes interactions they are involved in R

Question

[whocares21]

I have a set of genes (or probe id, I don't know exactly) as follows:

205242_at
208305_at
209138_x_at
209374_s_at
211430_s_at
211637_x_at
211644_x_at
211645_x_at
213915_at
214669_x_at
214777_at
215121_x_at
215176_x_at
215214_at
215379_x_at
216401_x_at
216491_x_at
216510_x_at
216560_x_at
216576_x_at
216984_x_at
217148_x_at
217235_x_at
217258_x_at
217281_x_at
217378_x_at
219768_at
221286_s_at

Now, first, I am very newbie about this kind of stuff.

I have found above genes as differentially expressed genes from a large databse after two days. Now I need to find their interactions with other genes. This is a HW, so I don't want you guys to do it for me. I need ideas, libraries and maybe some pseudocodes.

Here is the question from the hw page:

A text file containing the interactions that the genes you've identified are involved.

How can I do that? Thanks in advance.

[russhh]

There's lots of interaction datasets and datasets that can be used as such: co-expression, yeast-2-hybrid / affinity purification, orthology, co-mutation, functional annotations, synthetic lethality....

But if you don't unambiguously know which genes/proteins you are working with, they're largely useless to you

[whocares21]

Can u explain what did u mean for dummies? :) Currently, I have their Refseq IDs, enterzIDs, GO terms and kegg path ways. I don't know how I did, but I did. Are they useful to find out which gene/protein I am working with?

[russhh]

I'm not going to explain at a 'for dummies' level, since you're supposed to be a scientist now; and more pressingly, this is a homework assignment. Evidently you have more information to hand than you have mentioned in your question. So you're already further on than I thought you were

Answer 1

[Michael]

Trying to give you some hint for how to get something out of this task. Protein-protein interactions are a complex topic as russhh explained, to get a first impression of the topic you could look at StringDB http://string-db.org (and read some reviews ;), investigate the type of interactions it stores, play around with different queries and find the type of protein names it understands, and how the data can be queried (also programmatically?), and how the results can be viewed and exported. I think you won't need to code for a simple query.