You Are Here

While bemoaning Led Zeppelin's location on the Map of Rock in my lab I made note of the fact that where you start will greatly influence what your map ends up looking like (the map, by the way, has expanded to 150 edges. This additional exploration resulted in the loss of considerable sleep, the depletion of valuable rum stores and the discovery of the Bakerloo Blues Line). We want to think that whatever's in the center of a picture has a great deal of importance, which is why we had beautiful, detailed and utterly wrong maps like this:

You just don't get factual inaccuracy this pretty anymore.

That is a geocentric model of the universe by Bartolomeu Velho. You know it's classy because it uses text figures instead of lining figures. I have a hard-on for text figures. They do to documents the same thing a good dress does to an escort. I'm going to take an educated guess that the heliocentric model is pretty widely accepted by my readers. Lets not completely discount the geocentric model though: its picture of the earth itself is pretty much the same as the new (if you ignore its lack of Australia): in fact, accompanied by some pretty wild orbital gymnastics, the geocentric model would even tell you where our celestial neighbors were in the night sky. Where the two differ deeply is in their idea of where we sit relative to the rest of the universe.

You are here.

Which brings us back to protein interactions. If you're interested in how a protein behaves, one standard is to look it up in a database and find out what it interacts with. Take PKACA for example. According to IntAct it has 17 interactors. According to MINT, 15. According to DIP, 1. The word on the street says that there are 1532 of these if you want to amalgamate all the databases supporting the PSICQUIC interface. Thanks by the way, for generating countless competing standards for what constitutes a protein interaction. I really needed to be that insecure about the most basic level of my research.

So that's one way of looking at a protein. The issue I have with this view is that the protein then becomes a prima donna; everything you see revolves around it.

Another way, is to look at metabolic pathways. These reach far deeper into the interactome than just a single degree, but more importantly, they represent a functional unit of the cell. If you're looking at how PKACA actually does stuff, you can see it here, here and... in fact, here's the whole list of 27 places it is according to KEGG and another 5 from the Pathway Interaction Database. It's no longer the center of its own little world, it's situated

All snarky quips about competing standards aside, which view do you think represents more usable information about the protein? My money is riding on the second representation right now, which is a major shift in the way I've been designing my products so far. Stay tuned for a prototype, and maybe a downloadable version of the Map of Rock.