Monday, September 8, 2014

Bulk mapping of human protein-protein interactions

How do we normally figure out protein-protein interactions?  I think, normally, it goes this way:  Grad student studies one protein and over the course of his/her Ph.D., he/she identifies 1-10 proteins that aid the protein of interest in that protein's function.  Ingenuity and Protein Centre collect the publications and add these links to their databases.

This approach is extremely thorough, and all of a sudden we have a Ph.D. level scientist out there in the world who knows this protein and its interactors inside and out.  This person is a resource that couldn't really be replaced by anything.  There are down-sides, however.  The first is that this approach is slow.  The second is that not every study can be reproduced by everyone.  Experimental designs vary a lot over time.  The third is that we tend to bias the proteins that we are studying to whatever the funding agencies happen to find interesting at any particular point in time.  Not exactly the most democratic method of expanding our knowledge of the Universe.

So...what if someone were to systematically take human proteins and, using the same exact method, just go right through and map what proteins they interact with?  That would be immeasurably valuable, right?  What if this study isn't even published yet, and this group has already mapped over 27,000 protein-protein interactions?  Would that be enough for you to Tweet "Holy Shit!" on Twitter?

In case you hadn't guessed, this resource is real.  And it is amazing!  The bulk of the work appears to stem from the Gygi lab and Biogen IDEC in Cambridge.  They have been using HA-Tags (an awesome, relatively easy to pull down glyco tag from the flu virus) and have been just going through proteins and mapping who that protein is friends with.

The website says that the current dataset will be continually updated -- until they finish the ORFeome!  What's that mean?  They aren't going to stop until they catch them all!

Ugh...I did seem funny for a's like 4am, give me a break....

Anyway!  You can check out this awesome resource here!

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