Video Tip of the Week: GWATCH, for flying over chromosomes

Ok, so it’s not *just* for flying over chromosomes. There’s more to it, of course. But that’s the part of GWATCH (Genome-Wide Association Tracks Chromosome Highway) that caught my attention. I’m always looking for different ideas and strategies to visualize data, and this was the first time I drove along the whole length of a human Chromosome 9 highway, seeing the various SNPs along the way.

A post on Google+ pointed me to the GWATCH paper and software, so hat tip to Taras Oleksyk. And I was pleased to see that they’ve done a video explaining their project and demonstrating the software, so that will be this week’s Tip of the Week.

It’s not the first time I’ve seen a 3D representation of SNPs. I remember seeing that from GeneSNPs in the past. But GeneSNPs visual option was a way to look at the features within a single gene–you could seen introns, exons, and choose to view SNPs by features like “non-synonymous”, and you could examine the frequency. It was an interesting way to combine a lot of data, but captured only one limited region. GWATCH goes much wider than that, letting you scan along whole chromosomes for patterns. That said–it would be very cool to have those features, and maybe a pointer to possible promoter regions, along the roadway as well. At first I didn’t notice the gene symbol track–er sidewalk?–along the edge of the view. But seemed to me you could add more sidewalk, a bike lane….Of course, then I want to add a domain bypass….Anyway–it’s got me thinking about ways to explore.

And I’ve focused on that unusual “moving browser” for this post, but there’s more to the tool that that. There are other ways to slice the data in 2D that can be helpful for your analyses. And it’s not limited to GWAS data either. But you can see more about that in both the video and it’s covered in their paper. So explore GWATCH more from their site, and you can load up their sample data and take it for a spin. You go to the site and click on the “Active Datasets” to see the ones they’ve provided. Open one, click on the “Highway Chromosome Browser” to select one. But you can also see the other types of tools they have from there.

Quick links:

GWATCH: http://gen-watch.org/ for taking it for a spin

Reference:

Svitin A., Sergey Malov, Nikolay Cherkasov, Paul Geerts, Mikhail Rotkevich, Pavel Dobrynin, Andrey Shevchenko, Li Guan, Jennifer Troyer, Sher Hendrickson & Holli Dilks & (2014). GWATCH: a web platform for automated gene association discovery analysis, GigaScience, 3 (1) 18. DOI: http://dx.doi.org/10.1186/2047-217x-3-18