Tag Archives: genes

What’s the Answer? (genes in a region)

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.

This question is asked periodically at our workshops or at Biostar:

Find out the genes that correspond to my coordinates. 

There are several answers, some computational. I’ve added a simple Table Browser search that I think answers the problem with just a few steps. We recently had a question of how to use Galaxy to obtain gene names and locations within a certain distance up and downstream of a short region. It was a bit more involved, but still possible.

What’s the Answer? (what is a canonical transcript in UCSC?)

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.

This week’s highlighted question:

What is the rationale behind UCSC canonical transcripts?

Several good answers. The short of it is “The canonical transcript is defined as either the longest CDS, if the gene has translated transcripts, or the longest cDNA.” from the UCSC mailing list.

If you want to retrieve the canonical transcripts, you can check out our tip from a little over a year ago, still valid :D.

Video Tips of the Week: Annual Review IV, 2nd half

As you may know, we’ve been doing these video tips-of-the-week for FOUR years now. We have completed around 200 little tidbit introductions to various resources from last year, 2011 (yep, it’s 2012 now). At the end of the year we’ve established a sort of holiday tradition: we are doing a summary post to collect them all. If you have missed any of them it’s a great way to have a quick look at what might be useful to your work.

You can see past years’ tips here: 2008 I2008 II2009 I2009 II2010 I2010 II. The summary of the first half of 2011 is available from last week.

July 2011

July 6: Prioritizing genes using the Gene Prioritization Portal

July 13: PolySearch, searching many databases at once

July 20: Human Epigenomics Visualization Hub

July 27: The new SIB Bioinformatics Resource Portal

 

August 2011

August 3: SNPexp, correlation between SNPs and gene expression 

August 10: CompaGB for comparing genome browser software

August 17: CoGe, comparing genomes revisited

August 24: Domain Draw for quick motif diagrams

August 31: From UniProt to the PSI SBKB and back again

 

September 2011

September 7: Plant comparative genomics using Plaza

September 14: phiGENOME for bacteriophage genome exploration

September 21: Getting flanking sequences of genomic locations

September 28: Introduction to R statistical software 

 

October 2011

October 5: VnD resource for genetic variation and drug information

October 12: Track Hubs in UCSC Genome Browser

October 19: Mitochondrial Transcriptome GBrowser 

October 26: Variation data from Ensembl

 

November 2011

November 2: MizBee Synteny Browser

November 9: The new database of genomic variants: DGV2

November 16: MapMi, automated mapping of microRNA loci

November 23: BioMart’s new central portal

November 30: Phosphida, a post-translational modification database

December 2011

December 7: VarSifter, for identifying key sequence variations

December 14: Big changes to NCBI’s genome resources

December 21: eggNOG for the Holidays (or to explore orthologous genes)

December 28: Video Tips of the Week: Annual Review IV (first half of 2011)

Tip of the Week: Prioritizing Genes

Many types of experiments today return large lists of genes, association studies, expression arrays, linkage analysis and more. The researcher needs to determine which of those genes are of most interest and promising so the next step in the analysis is to prioritize the list and find the method to do so.

There are a lot of methods and tools to prioritize a list of genes and getting a handle on which tool to use can be a bit of a daunting task. The Gene Prioritization Portal is an excellent resource to find the right tool. It’s a bit more than just a database of databases or tools. it’s a regularly updated list with detailed information about the tools (there are 25 at the moment), stats about what the data sources of the tools are, the outputs and references. There is also a nice search tool to find the tool that most fits your needs.

Today’s tip will introduce the site and perform a quick search. Future tips might be highlighting some of these tools.

Update: due to technical difficulties either in recording or the upload/processing the audio isn’t working. I’m trying to fix this. In the meantime, you can get a basic overview watching, but I’ll get a new version up as soon as I’m able to fix this.

Tip of the Week: Getting the canonical gene info

We went to ASHG last week. In addition to having lunch at my favorite cafeteria on the mall, we learned a lot at the 1000 Genomes workshop and helped out at the UCSC and Galaxy workshops there on Wednesday and Thursday. Both those resources are extensive (and developing) enough that no matter how many times I use or teach on them, I learn something. Well, one thing I learned at the workshop is how to view the ‘canonical’ gene in the Genome Browser (instead of all the splice variants, and how to get the canonical gene data out from the Table Browser. Simple bits of function that could come in handy. Today’s tip goes through those.

(We have several tutorials on the Genome and Table Browsers to get deeper if you wish. These are free to the user as they are sponsored by UCSC.)

HT to Bob Kuhn at UCSC for the Table Browser how-to!

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: Homophila

homophilahomophila2(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.

Tip of the Week: Clock Gene Music

gene2music

If you didn’t know it already, there is an entire community out there, having noted the similarity between biological sequences and music, that has been working out methods to convert DNA and protein sequences into music using the properties/differences in the bases and amino acids. Some of the results of this fiddling have created some interesting, and often haunting and beautiful, music. One such site is Gene2Music. Here, several people (Rie Takahashi, Jeffery Miller et. al) have created an algorithm to translate gene sequences into music. In this tip of the week we’ll show you the site and how to take a gene of interest and create your own piece. Take a quick listen to Human ThyA (audio) and then listen to a piece composed by Rie Takahashi based on the themes of ThyA. Impressive. Maybe the next Mozart will do a series of compositions based on the human genome (that will be one long concert).