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.

2 thoughts on “Mouse KOMP, all over the browsers

  1. Xose

    Mary,
    As you probably are aware, the Distributed Annotation System (DAS) allows Ensembl to display information which is not stored in our databases, and therefore we get information stored in servers elsewhere. This is the beauty of DAS, we don’t own your data, you can ‘control’ your datasets and share them, but at the same time, we have no control whatsoever over the server, if for whatever reason that server is down (perhaps scheduled maintenance), we cannot reboot it… If you check now, you should be able to see those KO vectors and follow the link to the Sanger Institute for additional information about what you see:
    http://www.sanger.ac.uk/htgt/report/gene_report?gene_id=20376

    Regards,
    Xose (from Ensembl)

  2. Mary

    Hi Xose–yes, I know what DAS sources are. But we must be looking in different places. I was told to look for these on ContigView in Ensembl.

    This is what I saw the day I wrote this:
    http://screencast.com/t/mg1mfsn8Yv and that’s what I’m seeing today with the same choices.

    That’s fine–I understand it may be out of your control.

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