The OpenHelix Blog

About 6-7 months ago, Mary mentioned that R-Genetics analysis was coming to Galaxy. Well, it has now and is available at the public Galaxy site. The old Rgenetics site links to the new one and the information about using Galaxy as a wrap around interface for the Rgenetics project tools. Today’s tip just points you to the tool and gives you a quick overview of what is there. You’ll need to do some exploring to learn to use it! Of course, we have our publicly available Galaxy tutorial to get you started.

(oh, and I point you to this tutorial on analyzing Desmond Tutu’s SNPs using Galaxy that I thought was interesting)

Today’s tip is the continuation of researching a single SNP in an individual genome. Trey will use a dbSNP RS ID to find linkage disequilibrium information between a SNP of interest and SNPs in the region easily and quickly. GVS, the Genome Variation Server at the University of Washington to analyze a dbSNP rs ID of your choice. This 3 minute screencast will show you how to use the GVS tool to quickly get this information for a wide range of populations.

The last tip of the week I did was Genome Variation Tour I where we started our journey following one SNP in an individual’s genome through various databases to see what we can find out about that variation. In that tip we started out by looking at a SNP in the CYP4F2 gene in the UCSC Genome Browser and followed it to dbSNP. Today’s tip will continue our journey to OMIM to see what information we can find there. We’ll find this variation is clinically associated with Warfarin dosage effects and specifically this individual’s C/T heterozygosity indicates an intermediate dosage for effectiveness if indeed he ever needed this drug.  In some ways, your guess is as good as mine as to what we will find and what avenues we will be taking in the next few tips I’ll be doing. I’m am discovering information as I go along too. I can tell you though that the next installment of the genome variation tour will take us to PubMed, and a few not particularly well known but gem databases perhaps and probably back to the UCSC Genome Browser to expand our look at the interactions of several variations in this individuals genome.

Today’s Tip of the Week is a short introduction to WAVe, or the Web Analysis of the Variome. The tool was recently introduced to us, and I’ve found it a welcome introduction to the tools available to the researcher to analyze human variation. This is apropos considering the recent paper we’ve been discussing on the clinical assessment of a personal genome (here, here and here) and that papers implications for personalized medicine and the use of online variation resources. WAVe also has introduced me to some additional tools I’ve either not been aware of, or haven’t used, which might be of use such as: LOVD (Leiden Open Variation Database), QuExT (Query Expansion Tool, also from the same developers as WAVe), and others. Of course there are also database information pulled in from Ensembl, Reactome, KEGG, InterPro, PDB, UniProt, NCBI and many others. Take some time to check it out.

Today’s tip is on a new genotype/phenotype resource from the Swiss Institute of Bioinformatics, or SIB. I was already a fan of many SIB tools and resources, and was using one (ENZYME) when I found a notice about SwissVar. SwissVar is described as ‘a portal to Swiss-Prot diseases and variants.’ It includes information about genotype-phenotype relationships for each specific variant, manually annotated from literature. Manual annotation adds a level of quality and believability to this data. The SwissVar portal also contains various pre-computed information that may aid in determining the effect of the variant. Genotype-phenotype searches can begin with either Medical Subject Headings, or MeSH terms (Disease), gene or protein names (General characteristics) or variants (Functional/structural features). There are multiple ways to modify your searches, and results are clean tables of data including gene/protein accessions, names, links to MeSH definitions and links to variation reports.

If your research could benefit from high quality, manually curated genotype/phenotype information, I suggest you watch this tip, and then explore SwissVar according to your own interests.

SwissVar – a Portal to Swiss-Prot Diseases and Variants: http://www.expasy.ch/swissvar/

Comprehensive tutorials on the publicly available dbGaP, GAD, and DGV databases enable researchers to quickly and effectively use these invaluable resources.

Seattle, WA: July 16, 2009 — OpenHelix today announced the availability of new tutorial suites on dbGaP, Genetic Assocation Database (GAD) and Database of Genomic Variants (DGV). The dbGaP resource is a database of genotypes and phenotypes with extensive variation data and clinical details GAD is an annotated resource connecting human genes and polymorphisms to diseases and traits, and DGV or Database of Genomic Variants, catalogs and displays structural variation in the human genome. These three new tutorials in conjunction with additional OpenHelix tutorials on dbSNP, VISTA, HapMap, GeneSNPs, SeattleSNPs, Genome Variation Server and many others, give the researcher an excellent set of training resources to assist in their genetic association and variation research.

The tutorial suites, available for single purchase or through a low- priced yearly subscription to all OpenHelix tutorials, contain an online, narrated, multi-media tutorial, which runs in just about any browser connected to the web, along with slides with full script, handouts and exercises. These tutorials will teach users:

dbGaP

GAD

DGV

With the tutorials, researchers can quickly learn to effectively and efficiently use these resources. The scripts, handouts and other materials can also be used as a reference or for training others. To find out more about these and over 70 other tutorial suites visit the OpenHelix Catalog and OpenHelix. Or visit the OpenHelix Blog for up-to-date information on genomics and genomics resources.

About OpenHelix:
OpenHelix, LLC, (www.openhelix.com) provides the genomics knowledge you need when you need it. OpenHelix provides online self-run tutorials and on-site training for institutions and companies on the most powerful and popular free, web-based, publicly accessible bioinformatics resources. In addition, OpenHelix is contracted by resource providers to provide comprehensive, long-term training and outreach programs.

(click either graphic to see the tip of the week movie) It’s not Halloween yet, but thought I’d get us started in the mood by introducing you to a database that has some obvious references to the movie “The Fly” (the 1958 version is the only really worth watching . Ok, so the database doesn’t actually help you turn humans into flies, that’s a few years away (that’s a joke of course). No, this is one of those resources that does one thing and does it well. It’s very straightforward and simple… it takes human disease genes and sequences found in OMIM and finds the homologs in the Drosophila melanogaster genome. The name of the database is Homophila. From the results you can find the links to the data and go from there. Simple function that can be very useful. Give it a try.

We go through the thousands of resources and databases available online in our search to do tutorials we found many that are great resources but for one or more reasons we don’t or can’t do a tutorial for. Yet they are great resources. So, we occasionally do “Tip of the Week” on some, but even those are not enough to at least touch on all the great resources out there, so occasionally I we are going to give a quick “shout out” to some of these resources occasionally.

So today it’s F-SNP.

As genome-wide association studies (GWAS) become much more widespread and useful, the genome browsers are finding ways to incorporate these data and to allow you to view the published data or your own.

The UCSC team has already developed a useful interface in their “Genome Graphs” tool which allows you to view and compare disease studies (9 diseases so far), browse regions in the genome browser, sort genes and more. It also allows you to import your own GWAS data.

The Ensembl blog has just announced that Ensembl too has now incorporated genome-wide association studies into their database (7 so far). You can access these in the DAS Sources menu  in the ContigView (in detailed view section as shown here, click to enlarge) and CytoView pages. These are listed as “WTCCC” and then disease initials (BD, CAD, CD, HT, RA, T1D, T2D) in the menu. I don’t yet see a way to easily upload and view your own data, but I’ll double check as I play around with it.

I see a blog post and  tip-of-the-week comparing these two in more detail coming! For now, just letting you know they are there.

This is another tutorial at SciVee (click on image to go to SciVee and watch movie), but this time it’s one of mine I did earlier. I’m on vacation (in Germany, were we used to live in Heidelberg while I worked at EMBL) so I’m pointing you to this short intro I did earlier so I can get back to my weiss wurst). Of course, I’ve also done a tip on one specific aspect of GVS before that you might want to check out. This is a general introduction to the Genome Variation Server at the University of Washington. Additionally, you can get more freely available training materials on GVS including a longer introductory tutorial (40 minutes), slides, handouts and exercises at OpenHelix GVS Tutorial or visit the resource at GVS.