Tag Archives: GeneMANIA

What’s the Answer? Open Thread (gene networks)

BioStar is a site for asking, answering and discussing bioinformatics questions. We are members of thecommunity and find it very useful. Often questions and answers arise at BioStar that are germane to our readers (end users of genomics resources). Every Thursday we will be highlighting one of those questions and answers here in this thread. You can ask questions in this thread, or you can always join in at BioStar.

Question of the week:

I have 10 genes linked to a particular disease (for the sake of example say cancer).
I want to build a gene network for these 10 genes.
Any web based tools available which can do the job?

I immediately thought of GeneMania (publicly available OpenHelix tutorial) and STRING (tutorial, by subscription) . The best answer beat me too it, with a lot of other excellent tools. Go check it out.





Friday SNPpets

Welcome to our Friday feature link collection: SNPpets. During the week we come across a lot of links and reads that we think are interesting, but don’t make it to a blog post. Here they are for your enjoyment…

FYI – New version of GeneMANIA is now available

I recently got an email the the new release of GeneMANIA has gone public. You can read the announcement here, or see all of GeneMANIA’s past announcements here. You may remember our recent post announcing our new GeneMANIA tutorial, which is currently sponsored and free.

According to GeneMANIA’s developers at the Donnelly Centre for Cellular and Biomolecular Research at the University of Toronto:

“GeneMANIA helps you predict the function of your favourite genes and gene sets.”

I’ve posted tips on how older versions of GeneMANIA worked, and recently I’ve had access to GeneMANIA’s development site. I watched the great changes and updates as they occurred, occasionally chimed in with ‘user feedback’, and MOST IMPORTANTLY got to develop our tutorial on the new version! So what you see at GeneMANIA is what we explain in our tutorial. They also recently published an article in the web server issue of Nucleic Acids Research that you might want to check out. Please check all these resources out for your gene relationship and functional research needs.

The University of Toronto Announces Free OpenHelix Tutorial and Training Materials for GeneMANIA, a Gene Function Prediction Tool

Quote startThe OpenHelix tutorial suite is sure to help current and new users to get up to speed on our site and its new features, and therefore get their results more quickly to support their research.Quote end

Bellevue, WA (PRWEB) August 11, 2010

The creators of GeneMANIA have contracted with OpenHelix to provide comprehensive online training for the gene function prediction tool (http://genemania.org ).

GeneMANIA is a free public resource that offers a simple, intuitive web interface that shows the relationships between genes in a list and analyzes and extends the list to include other related genes. The web interface is backed by powerful analysis software and a large data warehouse containing extensive amounts of existing functional genomics data, and also includes Cytoscape Web, a web based advanced visualization tool to enable browsing of query results and creation of publication-ready figures.

“GeneMANIA will soon be updated to include significantly increased functionality,” according to Gary Bader and Quaid Morris, assistant professors in the Donnelly Centre (http://tdccbr.med.utoronto.ca/) and co-principal investigators for GeneMANIA. “OpenHelix based their tutorial on our development site, and even provided user feedback on our new features that resulted in improvements to our system. OpenHelix had very strong understanding of the GeneMANIA interface, which then translated into a powerful learning resource. The OpenHelix tutorial suite is sure to help current and new users to get up to speed on our site and its new features, and therefore get their results more quickly to support their research.”

The new training initiatives include a free online tutorial suite on GeneMANIA. The online narrated tutorial (http://www.openhelix.com/genemania ), which runs in just about any browser, can be viewed from beginning to end or navigated using chapters and forward and backward sliders. The approximately 60 minute tutorial highlights and explains the features and functionality needed to start using GeneMANIA effectively. The tutorial can be used by new users to introduce them to GeneMANIA, for previous users to view new features and functionality, or simply as a reference tool to understand specific features.

In addition to the tutorial, GeneMANIA users can also access useful training materials including the animated PowerPoint slides used as a basis for the tutorial, a suggested script for the slides, slide handouts, and exercises. This can save a tremendous amount time and effort for teachers and professors to create classroom content.

“GeneMANIA is an innovative, hypothesis generating tool that can be used to extend a given gene list to find related genes sharing similar functions,” said OpenHelix founder and President Dr. Mary Mangan. “OpenHelix is excited to contribute to furthering the field of gene function prediction by assisting researchers in effectively and efficiently using such a critical tool.”

Users can view the tutorials and download the free materials at www.openhelix.com .

In addition to the GeneMANIA tutorial suite, OpenHelix offers over 90 tutorial suites on some of the most powerful and popular bioinformatics and genomics tools available on the web. Some of the tutorials suites are freely available through support from the resource providers. The whole catalog of tutorials suites is available through a subscription. Users can view the tutorials and download the free materials at www.openhelix.com .

About GeneMANIA
GeneMANIA (www.genemania.org ) is a free web-based prediction tool that finds other genes that are related to a set of input genes, using a very large set of functional association data. Association data include protein and genetic interactions, pathways, co-expression, co-localization and protein domain similarity. You can use GeneMANIA to find new members of a pathway or complex, find additional genes you may have missed in your screen or find new genes with a specific function, such as protein kinases. Your question is defined by the set of genes you input. If members of your gene list make up a protein complex, GeneMANIA will return more potential members of the protein complex. If you enter a gene list, GeneMANIA will return connections between your genes, within the selected datasets.

GeneMANIA is actively developed at the University of Toronto, in the Donnelly Centre for Cellular and Biomolecular Research, in the labs of Gary Bader and Quaid Morris, with input from an independent scientific advisory board. GeneMANIA development is funded by Genome Canada, through the Ontario Genomics Institute (2007-OGI-TD-05).

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.

Tip of the Week: YeastMine

For this week’s tip I would like to take you over to the Saccharomyces Genome Database (SGD) & from there try out the beta release of YeastMine. YeastMine is based on the InterMine open source data warehouse system. We’ve featured other incarnations of InterMine, such as RatMine from RGD in this tip and modMine (associated with the modENCODE project) in this tip, so you’ve already seen some of its capabilities. The aspect that I want to focus on when we look at YeastMine is the interoperability of InterMine resources.

Mary noticed the beta YeastMine release notice first & mentioned it to me. When I got over to SGD, not only did I see the notice on YeastMine, but also noticed that they are now linking to GeneMANIA in some of their interaction resources. I think that’s cool because soon we will be releasing a new GeneMANIA-sponsored tutorial. I’ll head back over to SGD & maybe do a tip on that too, some other day, but for now enjoy today’s tip on how to make a gene list and then link to gene homolog information on FlyMine, the FlyBase/Drosophila version of InterMine.

Tip of the Week: GeneMANIA for Fast Gene Function Predictions

I am happily the lucky scientist here at OpenHelix who has been selected to create a full tutorial on a network resource named GeneMANIA, but I just couldn’t wait to share some of the details about this resource’s great features. GeneMANIA stands for Multiple Association Network Integration Algorithm. Users can either input a single gene and see interaction networks associated with the gene, or (more powerfully) to enter a list of related genes and use GeneMANIA’s ‘state-of-the-art analysis algorithm’ to quickly and easily find additional related genes.

GeneMANIA allows a  scientist with no prior training in computational bioinformatics to easily use their gene list of interest to search a customized list of published functional genomics publications, as well as a wide variety of public databases, and receive the results of their analysis in an easy to interpret PDF report. Users can even upload their own important datasets and affect how the algorithm scores each gene and dataset. I  cannot cover all this functionality in this short tip – you’ll have to see our tutorial for that – but here I will show you how to do a basic search and some of the display features of GeneMANIA.

GeneMANIA stands for Multiple Association Network Integration Algorithm. For more information about it, please see this 2008 GeneMANIA publication, or the GeneMANIA documentation.