What is the best tool to visualize linkage data for a set of genes in the mouse genome? E.g. two genes that are on some chromosome, and you want to get a chromosomal and genetic map of these two genes... how far they are apart on the chromosome, and what the relevant recombination frequencies/centimorgans are for them. What is the right tool for this? Thank you.
3 answers
You may want to look at Circos. Even tough its suitable for visualizing data within whole genome it also accommodates visualization of data by chromosomes and its associated features. Usually you do this by providing a data file and associating them together through Circos's configuration files (*.conf).
It may seem daunting at first to configure. Obviously, it has a high learning curve and requires considerable time to learn to output the desired images. However, such round plots seem favorable when wanting to publishing complex data.
In general this kind of information does not exist for each pair of genes. A genetic map is built form a set of markers, and from this you build a map that estimates the genetic distance between two points by summation (with the caveat that in reality AtoB + BtoC != AtoC because of interference).
For mouse, you can use Table S1 from Shifman et al (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1635748/) to find genetic distances that have been generated for the entire mouse genome. One way to solve your problem would be to find the cooridante of the SNP closet to each gene first and then use the SNP-to-SNP distances as a proxy for gene-to-gene distances.
@Casey: is there no tool that does this? I cannot figure out MapViewer which was the obvious choice in my mind... I can hack a script to take any two genes, look for nearest SNP based on this table, but it seems like there ought to be a better solution. Especially since that script would be basing it all on one data set from one paper
Have you tried the linkage map tools at Jax? I'm not sure they'll do what you want, but have a look:
http://www.informatics.jax.org/searches/linkmap_form.shtml
You can enter your own markers at the bottom.
You can also do maps in Map Viewer that might offer what you want: http://www.ncbi.nlm.nih.gov/projects/mapview/ But you'd have to go in and set the "maps and options" to show the specific sets of maps that you need. It won't be on display by default.
With which tool? If you mean MapViewer, I'd try find your region of interest and try several. All you have to do is add them with the +, and then drag the order. See what shows what you want. I agree that the information on which map is which isn't easy to find there. My personal favorite is "Genes_seq" which is written as "Genes" in the pick list, because it shows the gene, structure, and links to NCBI other stuff. You may want the RH or Genetic Maps though.
WHen I try typing multiple gene names (comma separated) at Jax or use multiple genomic coordinates in the markers box at the end of the form, it just fails with an IndexError or says that no hits match my query. I don't see the "+" button in MapViewer... I have a hard time getting both genes in the same view in Mapviewer. If you can say more on how to add two genes in the same map in MapViewer that would really help.. I find the interface very hard to use
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