Video Tip of the Week: Digital Expression Explorer for RNA-seq

DEE_posterComing over my digital transom in a couple of different ways recently, the Digital Expression Explorer caught my attention. I have a soft spot for expression. It’s the business end of what’s going on, not just the archives of genomic info stored up in the nucleus, you know? Heh.

Anyway–I saw the poster via email from ResearchGate (yeah, I know, but a couple of interesting things have come to me from there). It was authored by someone that I’ve been on a paper with, so it notified me. And the volume of expression data and challenges for users definitely hits on a problem that I think about a lot. There’s such great detail underneath the surface in so many of these repositories we have, but few people have the tools to mine them. They specifically note the GEO and SRA in this case. Digital Expression Explorer (DEE) sits on top of them and provides a new way in, after standardizing the data. I think that’s worthwhile.

There’s no need for me to provide a more details here–the lead author Mark Ziemann has done a great job in this blog post: Introducing “Digital Expression Explorer”. He provides the background to the problem of re-using the data, and what they’ve done to solve it. And you can see the poster online. But better still, check out this quick intro video from Mark that is this week’s Video Tip of the Week:

So you can see how to pull out some data and begin to explore it with DEE. Then there’s a piece that illustrates taking this newly mined set and evaluating it with Degust. This quickly shows what you can get and what you can do next. It will give you an idea of the benefits (and the speed).

And, may I say, nice job on outreach! Poster, tweets, blog, and video. Many ways to reach potential users. Moar like this, plz, for all you folks with software tools.

Try it out, and see if it saves you time and delivers you more than you might have been able to mine out of the repositories so quickly in the past.

Quick link:

Digital Expression Explorer:


Ziemann M., Kaspi A., Lazarus R., & El-Osta A. (2015). Digital Expression Explorer: A user-friendly repository of uniformly processed RNA-seq data. ComBio2015 : 10.13140/RG.2.1.1707.5926