Tag Archives: ArrayExpress

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/

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

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.