Tag Archives: expression data

DEE_poster

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: http://dee.bakeridi.edu.au/

Reference:

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

ncbi_logo_black

Video Tip of the Week: Explore Gene Pages at NCBI with Variation and Expression Information

NCBI has produced some of the most in-depth and reliable bioinformatic tools, in large part because they’ve been building them since the earliest days of the genomics era. ncbi_logo_black I once noted that I remember the oldest web interface, because it was one of the first places that I went for computational tools back in the day. Check out my post here with some of their older interfaces. I remember all of them.

But they don’t rest on their laurels. NCBI teams are always adding new tools, new features, and new data. Sometimes, though, I think that people take them for granted. Or they only keep re-visiting things they know. So recently they asked me to do a walk-through video about how I use the tools, so that I can show people ways they can go further than they might realize. This week’s Video Tip of the Week shows how I can add and explore a lot of data on a Gene page, to examine additional features: variations and expression data, right in the sequence viewer.  A lot of people may not even be aware these tracks exist.

This video provides a walk-through of how to explore variation data and expression data from Gene pages, using the sequence viewer that’s embedded right on the page. Enhance your understanding of your genes of interest quickly using these additional track options.

I hope this demonstrates how you can add more information to your genes of interest from gene pages, which you might already use. But now you can use them better. You can take advantage of the great depth at NCBI, while staying up-to-date on the tools.

Speaking of staying up-to-date, which is a big need in this field: you should definitely keep an eye out for new features from NCBI. My favorite way is the announcement mailing list, because it has details of new stuff, upcoming webinars, data releases, etc. But you can also watch their blog and twitter for new information all the time. They’ve been doing a lot of outreach–webinars, quick videos, and more. You should sign up to be notified, so you can stay current with the best data and tools. Check out their learning/webinars pages to see what I mean.

We are planning another video, and we’d love any feedback you have on this one.

Quick links:

NCBI Gene (subject of the video): https://www.ncbi.nlm.nih.gov/gene/

NCBI-announce mailing list: http://www.ncbi.nlm.nih.gov/mailman/listinfo/ncbi-announce

NCBI Insights blog: http://ncbiinsights.ncbi.nlm.nih.gov

NCBI twitter: @NCBI

Learn (see webinars link): https://www.ncbi.nlm.nih.gov/home/learn.shtml

NCBI YouTube channel: https://www.youtube.com/channel/UCvJHVo5xGSKejBbBj0A5AyQ

References:

NCBI Resource Coordinators (2014). Database resources of the National Center for Biotechnology Information Nucleic Acids Research, 43 (D1) DOI: 10.1093/nar/gku1130

Disclosure: This video was sponsored and completed under contract to NCBI. 

Tip of the Week: BioGPS for expression data and more

This week’s tip introduces BioGPS, or Gene Portal System. We get a lot of questions about two things that BioGPS can help you to tackle: what do I do with a list of genes to find out what they are? And the next question people have after that is: and where are they expressed? BioGPS can help you with both of those problems. It is a tool that integrates and displays many types of data that researchers would be interested in. It also allows you to customize your display with the types of data that are most relevant to you–using their extensive plug-in collection. And it can do so from your browser, or access the basic portal from your iPhone!

Recently there was a question at BioStar about ways to quickly access some human gene expression data. The top rated answer over there was BioGPS, so we thought we’d provide a look at the kinds of things available to users via BioGPS. This 5-minute movie introduces some of the features.

Basically you can search for a gene or a list of genes, you can search with various types of IDs, you can search by keyword, or you can even search by genomic intervals. Your resulting list will quickly link you to all kinds of information from expression data, to annotation details and wikis, and more.  The results are provided in a handy default view with panels of information which may offer what you are looking for.

But you can go further with BioGPS using their customization and plug-in features. You aren’t tied to the default view. The system offers plug-ins: other tools can pipe their information over to BioGPS so you can use it within that framework. You can  register/create a login and then store views that are suited to your research needs.

At the time they wrote the paper provided below, they already had over 150 plug-ins available. As I write this today there are nearly 400 things you could bring in to supplement the views of the genes you are interested in. And the range of plug-ins is tremendous: interaction data sets, SNPs, phylogenetic data… The Figure 2 in their paper gives a partial list of the plug-ins at that time, and the categories they highlight include: literature searching (such as PubMed, iHop, patents, more), gene portals (such as Entrez Gene, UniProt, Gene Cards, more), genetics (dbSNP, HapMap, HuGE, more), pathway tools (KEGG, Reactome, STRING, more) and even reagent providers. But there are more now, and it looks like more will continue to be developed and added. It really depends on what you need and want to display for your searches. You can browse around or search the plug-in collection to explore what’s available to view.

There are other tools you can use to explore expression data specifically. We like the UCSC Gene Sorter for some types of queries. Of course the large repositories of GEO and ArrayExpress can offer expression data as well. But for some users the BioGPS portal may offer integration and customization features that will suit their research needs. Go over and check it out. Register, set up some views, and you’ll be finding all sorts of useful annotations for your genes or regions of interest.

Just to also quickly mention: you can do searches from your lab bench, or from seminars, with the iPhone version of BioGPS as well. I didn’t have time to cover that in the movie but there’s more information over at their site about the tool. I’ve got mine installed and I’ve found it handy during talks!

Quick links:

BioGPS homepage: http://biogps.gnf.org/ EDIT: has moved: http://biogps.org/

BioGPS iPhone app: http://biogps.gnf.org/iphone/

Reference:
Wu, C., Orozco, C., Boyer, J., Leglise, M., Goodale, J., Batalov, S., Hodge, C., Haase, J., Janes, J., Huss, J., & Su, A. (2009). BioGPS: an extensible and customizable portal for querying and organizing gene annotation resources Genome Biology, 10 (11) DOI: 10.1186/gb-2009-10-11-r130

Cerebellar Development Transcriptome Database

Announcement today from the MGI-mailing list on the CDT-DB:

Updated: Cerebellar Development Transcriptome Database (CDT-DB)

Dear Colleagues,

We are pleased to announce the release of the updated CDT-DB version 4.2.

* CDT-DB ver4.2: www.cdtdb.brain.riken.jp

CDT-DB ver4.2 provides you with valuable information on spatiotemporal gene expression profiles during mouse cerebellar development.

You can download “User’s Guide” (provisional) by clicking “Download” tab menu.

We hope that you find the enhanced functions (including data search, data display, data analysis, ontology search, hyperlinks to various bioinformatics) and website design to be useful for your study.

We would be grateful for any feedback you have. [they offer an email address that I don’t want to offer to spammers–Mary]

Cheers.

CDT-DB

Looks like a nice resource, but I haven’t had a chance to go too deep at this point.  It also links to the Allen Brain Atlas data.  If you are interested in brain development, this looks like a resource you should know about.

Tip of the Week: Gene Expression Data by Condition at ArrayExpress

AE Atlas TipIn today’s tip, I want to show you how to use a great looking beta tool that I just found at EBI’s ArrayExpress Gene Expression repository (AE). The tool’s name is the ArrayExpress Atlas. You may have retrieved expression data from the ArrayExpress Warehouse, which is a carefully curated collection of expression data. The Warehouse is a wonderful resource, and a great way to obtain expression data sets, but the information retrieved is organized by gene name and sample values. The ArrayExpress Atlas appears to be the next generation of the Warehouse and it provides gene expression data as a table, with genes corresponding to rows and experimental conditions corresponding to columns. The tool is easy to use, provides easy to interpret results, and looks like its capabilities are growing fast. Check out this tip, check out the Atlas blog spot, check out the tool, and send any feedback for improving the tool to AE.