Question: What Is The Best Resource For Protein/Genetic Interactions?
11
gravatar for Steven Williams
6.5 years ago by
Steven Williams110 wrote:

I'm about to start a new project, and I wanted to get some opinions on the different protein/genetic interaction databases such as IntAct, BioGRID, MINT, etc. What do you guys think of them and are there any advantages/disadvantages to using each one?

ADD COMMENTlink written 6.5 years ago by Steven Williams110

Do you have a specific organism in mind ?

ADD REPLYlink written 6.5 years ago by Khader Shameer17k

Perhaps if you can say a bit more about the general goals of your project, it might help people direct you to the right resource.

ADD REPLYlink written 6.5 years ago by Casey Bergman17k
8
gravatar for Qdjm
6.5 years ago by
Qdjm1.9k
Toronto
Qdjm1.9k wrote:

Do you want protein or genetic interactions, or both? Some databases focus only on molecular interactions and, strictly speaking, genetic interactions are not molecular interactions.

Protein interactions: If you are interested primary in protein interactions, look first at the IMEx consortium; all of the databases that you mention are a part of it. Their interactions are available through PSICQUIC web services, described here: http://code.google.com/p/psicquic/

Some websites combine data from multiple molecular interaction databases, e.g., Pathway Commons and IRefWeb. I know you can download a combined dataset of interactions from Pathway Commons but I haven't tried doing this with IRefWeb.

Genetic interactions: I think that BioGRID is the only major database that currently curates genetic interactions.

ADD COMMENTlink written 6.5 years ago by Qdjm1.9k
8
gravatar for Ian
6.5 years ago by
Ian4.9k
University of Manchester, UK
Ian4.9k wrote:

My favourite free offering to date is STRING.

ADD COMMENTlink written 6.5 years ago by Ian4.9k
1

I think STRING for interface simplicity alone is a great tool...

ADD REPLYlink written 6.5 years ago by Daniel Swan13k
1

Yeah, I'm going to second STRING. It was developed (and still maintained) by my colleagues in Peer Bork's lab when I was there earlier last decade. So I can vouch for it's brilliance ;-). Seriously though, it's a great prediction tool.

ADD REPLYlink written 6.5 years ago by Treylathe940
1

Not sure how this is relevant -- STRING doesn't contain genetic interactions, nor is it really a protein interaction database -- it predicts interactions.

ADD REPLYlink written 6.5 years ago by Qdjm1.9k

+1 for STRING. Recently they added actions to track the type of interactions. I am using it for various PPI related data mining projects.

ADD REPLYlink written 6.5 years ago by Khader Shameer17k
4
gravatar for Mary
6.5 years ago by
Mary11k
Boston MA area
Mary11k wrote:

Oooh...have I seen flamewars over this topic! Like all projects, it depends what what you need. But I thought the folks at iRefWeb made a good case for their tool in their paper that I talked about here: Tip of the Week: iRefWeb + protein interaction curation.

Check out both that paper and their site, and the previous paper on the topic that Mike Cusick et al wrote. Those offer some data on the underlying data sets, or ways to think about them at least.

ADD COMMENTlink written 6.5 years ago by Mary11k

iRefWeb is also an aggregation of many datasources, so you have all the data in one place, along with many filters to help you select just what you're looking for. http://wodaklab.org/iRefWeb

ADD REPLYlink written 6.5 years ago by Starheight0
0
gravatar for Casey Bergman
6.5 years ago by
Casey Bergman17k
Manchester, UK
Casey Bergman17k wrote:

Picking up on Khader's comment and qdjm's response, FlyBase curates Drosophila genetic interactions from the literature (see dump and description), and there are many large-scale PPI datasets generated for this species as well. All of these data are integrated into a nice interface in DroID, The Drosophila Interactions Database, which has it's own viewer and a cytoscape plugin as well. So if you are organism-agnostic and want to explore the effects of different data sources, DroID might be a good resources to check out.

ADD COMMENTlink written 6.5 years ago by Casey Bergman17k
0
gravatar for Andra Waagmeester
6.5 years ago by
Maastricht, the Netherlands
Andra Waagmeester3.2k wrote:

Pathguide might have some interesting resources for you as well.

ADD COMMENTlink written 6.5 years ago by Andra Waagmeester3.2k
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