Tag Archives: KOMP

Video Tip of the Week: A Mouse for All Reasons

At first the title of this paper made laugh, as I am a major fan of Paul Scofield’s performance in A Man for All Seasons.  And then I remembered what happened to Thomas More.  Well, the analogy drops away for me there…. A Mouse for All Reasons by the International Mouse Knockout Consortium presented the framework and foundations of the project to knock out every single protein-coding gene in mice, generate the corresponding ES (embryonic stem) cells, and make them available for development of subsequent transgenic mice.  Some of these mice will go on to give their life for science in a noble manner, I guess–so maybe the analogy picks back up :)

The project has made tremendous progress since that paper was published, and there are a lot of knockouts you should know about if you are interested in using mouse as a model organism.

For this tip of the week we’ll explore the new portal for the International Mouse Knockout Consortium (IMKC), which used to be at the URL for the KOMP, or Knock Out Mouse Project. It appears that the groups referenced in the Mouse for All Reasons paper have now harmonized on to the knockoutmouse.org site, and use a single portal for access to the information and reagents.  There are a variety of ways to search: browsing genes, specific text searching, and even a BioMart interface for the portal.  This short movie takes a look at those pieces to introduce you to the site.

The announcement for this came over the MGI mailing list as this:

The IKMC web portal

The International Knockout Mouse Consortium (IKMC) has launched its official web site at www.knockoutmouse.org, formerly the URL for the Knockout Mouse Project (KOMP). This extended site, supported by the NIH and EU, now serves as the common web portal for access to information on knockout vectors, ES cells and mice available from the international high-throughput knockout projects: KOMP, EUCOMM, NorCOMM and TIGM. Stay tuned for future enhancements as the content continues to evolve. We welcome your comments and feedback. (Please email to contact@knockoutmouse.org).

This site is maintained by the I-DCC and the KOMP-DCC

(http://www.knockoutmouse.org/about) . Supported by the European Union (Project number: 223592) and the National Institutes of Health (Grant number: NIH HG004074).

The International Mouse Knockout Consortium (2007). A Mouse for All Reasons Cell, 128 (1), 9-13 DOI: 10.1016/j.cell.2006.12.018

Mouse KOMP, all over the browsers

An email from the MGI mailing list alerted me to some interesting new data on the browsers. The mouse KOMP project is generating knock-out mouse ES cells for every gene in the genome (well, that’s the goal anyway). This means you will be able to buy off-the-shelf mouse knockout cells for lots of regions you might want to study. You can grow ‘em up, and then breed ‘em with other mutants. You can characterize them in your favorite developmental stages and tissues. What a terrific reagent collection. In fact, if I was a post-doc, I would be looking for very interesting genes in this data set to pursue. You could start a whole career characterizing some of these beasts.

The email from MGI says:

The NIH funded Knockout Mouse Project (KOMP) is in full swing and reagents (vectors, ES cells, mice) from this project are becoming available to the research community.

Find out more about the KOMP project, which genes are being targeted, and which genes have reagents available for distribution by visiting the Knockout Mouse Project Data Coordination Center at http://www.knockoutmouse.org.

The UCSC genome browser (http://genome.ucsc.edu) now has a “KOMP Gene” track that shows which mouse genes are being targeted by the KOMP project. The tracks are linked to the KOMP Data Coordination Center site for the most recent information on project status and reagent availability.

KOMP gene information is also available in the Ensembl genome browser for mouse (http://www.ensembl.org/Mus_musculus/index.html) and will soon be available on the MGI Mouse Genome Browser (http://gbrowse.informatics.jax.org/cgi-bin/gbrowse/mouse_current/).

Of course I went looking for some examples. I found a couple to show you on the UCSC Genome Browser and I created sessions to share. If you would like to look at tracks that indicate the region of the knockout you can see this one that indicates the gene Xpr1 is knocked out and ready for you–see the bright green bar track in about the center of the page.

Another example is March4. Here blue and yellow tracks indicate a different status at the 2 groups performing the knockouts. Blue is “not started/on hold” and yellow is “in progress” according to the code on the details page (click the blue or yellow track to see that color code info on the description page).

Although it says the data is also in Ensembl I couldn’t find it–I have a query in to the help desk on that. Will let you know what I learn.

Edit: word back from ensembl = “KOMP data is in a track along with other KO alleles (EUCOMM and NorCOMM). In Ensembl it is called “Alleles”, available in the drop-down list in contigview.” But I’m looking in those same regions as I know data exists from the UCSC stuff and I still don’t see anything. You can go to those URLs but you’ll have to open the DAS sources menu and check the “alleles” box. March4 in ensembl. Xpr1 gives me an error message in the track (Error retrieving KO_vectors features (Can’t connect to the host!). Second attempt said No KO alleles in that section.

And it will be on the MGI GBrowse soon, too. I’ll try to find a sample of that when it is available too.