The OpenHelix Blog

Comprehensive tutorial on the publicly available GeneTests resource enable researchers to quickly and effectively use this invaluable resource.

Seattle, WA (PRWEB) May 25, 2010 – OpenHelix today announced the availability of an updated tutorial suite on GeneTests.

GeneTests is an integrated resource designed to provide access to current genetic testing and other clinical genetics information. The GeneTests resource includes the Laboratory Directory database, an international directory that identifies the location of clinical laboratories offering genetic testing; and GeneReviews, a collection of up-to-date, comprehensive disease-specific overviews which include clinical descriptions, diagnosis, management, molecular genetics, current genetic testing, and genetic counseling. This tutorials, in conjunction with OpenHelix tutorials on OMIM, dbSNP, GVS, HapMap and many others will give the medical researcher or clinician a set of training resources to help be efficient and effective at accessing and analyzing genomic variation and biomedical data.

The tutorial suites, available through an annual OpenHelix subscription, contain an online, narrated, multimedia tutorial, which runs in just about any browser connected to the web, along with slides with full script, handouts and exercises. 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.

This tutorials will teach users:
*to perform disease-specific searches and navigate the GeneTests site
*to understand the GeneReviews and Laboratory Directory Displays
*to access additional searches to query the GeneReviews and Laboratory Directory databases by disease feature, gene and protein specific searches, and more
*to identify U.S. and international laboratories offering molecular genetic testing for specific disorders, use the Clinical Directory to locate genetics professionals and services, and investigate additional educational and other resources

To find out more about these and over 90 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 a bioinformatics and genomics search and training portal, giving researchers one place to find and learn how to use resources and databases on the web. The OpenHelix Search portal searches hundreds of resources, tutorial suites and other material to direct researchers to the most relevant resources and OpenHelix training materials for their needs. Researchers and institutions can save time, budget and staff resources by leveraging a subscription to nearly 100 online tutorial suites available through the portal. More efficient use of the most relevant resources means quicker and more effective research.

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/

Ok, so we don’t have GWAS (Genome-wide Association Study) mondays, but we might as well have. The field of study seems to be growing hugely fast, especially when you consider one of the first major GWAS was published just a short 2 years ago (or 4 years ago, depending on how you define major, still… short time ago .  I read this post at Spittoon last month and thought I’d link to it (better late than never), but it appears now that there now over 328 GWAS published and many more coming. The post goes on to wonder “what next?” and summarizes some interesting articles at the New England Journal of Medicine from last month.

While I’m at it, let me point out some past recent posts on GWAS and tools here . Last summer I posted a note about Ensembl and UCSC Genome Browser’s GWAS viewers, in November Mary posted a link to a list of then complete GWAS, in January she also posted a Tip of the Week on visualizing GWAS using HapMap (where a commenter pointed to this useful paper), in February I posted a quick link to a new GWAS viewer, and you can find a few other posts on GWAS by doing a simple boolean search of the blog.

Well, as far as I can tell, read & do all the normal stuff for staying healthy (you know, all the stuff Mom used to say – wash your hands, drink plenty of liquids, eat right & get plenty of sleep.) I heard about swine flu as I woke up yesterday morning listening to NPR, and the coverage of the “outbreak” seems to be spreading more virally than the virus itself. PubMed already has a special section of their homepage dedicated to swine flu info, with links to recent PubMed articles,  a link to the swine flu sequence in NCBI’s Influenza Virus Resource, and a widget to CDC’s swine flu information page.  Through one of the PubMed references I found a resource I had not heard of before – ESNIP2 – the European Surveillance Network for Influenza in Pigs.  From the sequence report I could like to structures in NCBI’s MMDB and from there to structures in RCSB PDB.  From the CDC’s site I followed a link to an update from the World Health Organization which reported the number of cases and deaths in various world locations. I find it really cool to be able to link so freely between biological/health information resources, and be able to counter all the popular media frenzy with reports of real science. And the fear mongering seems to be just that, at least for now, because nothing that I’ve read so far indicates that swine flu is any more deadly or virulent than ‘normal’ seasonal flu – it is just a different virus than we normally see.

Yea, ok, we live in a small world where people move around and potentially spread diseases far and wide. But there is so much information at our finger tips – with an internet connection and a bit of knowledge where to look. I’ll continue to take my risks, travel, read science, and of course listen to Mom & wash my hands!

Addition (Trey): These are some great resources that Jennifer linked to. I’d like to include some additional general and genomic data too. I’ll add more as I find them:

Kristi at Bioinformatics@Becker (she’s here at Wash U where we are giving a seminar today) has a great post with links to many general and science links.

BioHealthBase has the swine flu strain genome details. BioHealthBase “provides a comprehensive genomic and proteomic data repository for five pathogenic organism groups that pose a threat to public health”

Effect Measure is a MUST read blog for anything public health policy and science related, and is a great read right now.

A short primer on the science of the swine flu.

  For today’s tip, I would like to introduce you to the TDR Targets Database, which seeks “… to exploit the availability of diverse datasets to facilitate the identification and prioritization of drug targets in pathogens causing neglected diseases.” I found out about this database this past weekend as I was catching up on my ’science reading’. The database was featured in an article published November of 2008 in Nature Reviews Drug Discover – if you have a subscription, I’ve cited it below. Even though the article is a bit old, it seems very timely for us here at OpenHelix right now since in February Trey participated in the first annual African Virtual Conference on Bioinformatics 2009, and later this week he is heading off to give a talk at the Genetics and Genomics of Infectious Diseases conference in Singapore. TDR Targets is a nice resource – here I show a few search options, but there is so much more here that you can explore on your own!

Agüero, F., Al-Lazikani, B., Aslett, M., Berriman, M., Buckner, F., Campbell, R., Carmona, S., Carruthers, I., Chan, A., Chen, F., Crowther, G., Doyle, M., Hertz-Fowler, C., Hopkins, A., McAllister, G., Nwaka, S., Overington, J., Pain, A., Paolini, G., Pieper, U., Ralph, S., Riechers, A., Roos, D., Sali, A., Shanmugam, D., Suzuki, T., Van Voorhis, W., & Verlinde, C. (2008). Genomic-scale prioritization of drug targets: the TDR Targets database Nature Reviews Drug Discovery, 7 (11), 900-907 DOI: 10.1038/nrd2684

Recently, we are learning a lot about the cold virus. The genomes of many have now been sequenced (that is a subscription-required Science report, you can read more about the report here).

You can find more genomic information at the picornaviridae.com at the NCBI’s Entrez Genomes and some structural information at MMDB. (just a side note, rhinovirus is now classified as enterovirus).

One of the most common questions we get when we are out doing software training is: what do I do with a list of genes? People generate lists from all sorts of biomedical research forays: microarray results, database searches, literature searches, library screens, etc. The source doesn’t matter much–in the end people have this list that they need to analyze, assess, categorize, group, filter, and manage.

We’ve been looking into some tools to accomplish this. We’ve already demonstrated a few of them already (Reactome SkyPainter, Gene Ontology Term Enrichment, MatchMiner…). But there are more that I want to explore. What I decided to do was to create a standard list that I’m going to use to explore and evaluate different tools. Today the tip is where I got this list and how I created it. I want to be able to refer back to this list in the upcoming “list” tips, and thought that if I explained that first it would help.

So today’s tip is obtaining a list of disease genes from UniProt. Now, you could just go to UniProt yourself and get this handy list. But I show you how to get there starting from the UniProt homepage, and what I did to filter this list to a set of unique gene symbols for disease genes in Excel. I end up with ~2500 unique symbols for disease genes that will be the input for upcoming tips.

The Comparative Toxicogenomics Database (or CTD) is an excellent database to find information on chemical-gene-disease interactions. It is a manually curated database of chemical-gene interactions, chemical-disease and gene-disease associations. At your fingertips you can find information about chemicals, interacting gnees, inferred diseases, pathways, references and news. It’s worth a look. And you can use Google to quickly search the database. Check out this week’s tip to find out more about the database and using Google to search it quickly.

(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.