Wednesday, April 22, 2020

Protein-protein binary maps covering 53,000 interactions in humans!

When I started grad school I had to shift gears a lot and learn a lot of molecular biology. I didn't retain any of it, but I do remember a lot about yeast 2 hybrid assays and how methodical and painful those sounded. Express one protein as a bait? Locate it's interactors one at a time, in one system? It's something like that. I think I maybe thought that mass spectrometry and big interactome studies completely negated those technologies.

Okay -- but what if someone started doing these around the turn of the century and then just kept going? Obviously, the systems work, but the only way to get all the data is to do ALL OF THE PROTEINS. Then you'd end up with a binary map of all of them. And that's what we've got here.

What would you need to do this, outside of a decade or two?

175 people helping you? That's a decent start.

I bet the reviewers at Nature were just like " deserve to be here because I am SO glad that I didn't have to do this....."

Now -- I get a little fuzzy on the numbers here. And probably on the details. To be honest, I'm paywalled but I can still explore the output of this research. It's called HURI and you can access the portal here. 

The numbers get fuzzy because it appers that around 9,000 proteins were done by the Yeast 2 Hybrid thingy, but HuRI also curates "high quality interactions" from the literature. Also, some mass spectrometry is also pulled in because there is a small set of data from ProteomeXchange that is referenced (PXD012321) but this looks a bit like a validation set.

As much as it seems like I'm poking fun at the method, this is obviously valuable. When you're trying to work out the biological implications of the proteins you're seeing that are messed up where do you go from there? Personally, I send people right to BioPlex. However, BioPlex is an ongoing project that only just now deposited data from it's second cell line. If you're protein isn't there -- there is HuRI. Also -- I'm sure looking at the data in BioPlex (which is high quality AE-MS [IP-MS]) which might encompass a lot of secondary, and possibly tertiary interactions, might be aided by looking at binary interaction data, at least as a filter. (Not a biologist, but hey -- I'm adding it to my list for when people say "thanks for the list -- WTF do I do now?"

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