How to get mouse-human homologues table from UCSC?

Question

[ifudontmind_plzz]

Hello,

How to get the mouse(mm10)-human(hg19) homologues gene table with its genomic coordinates from UCSC?

[ifudontmind_plzz]

@Sej Modha I am aware of how to get the list from ensembl. But I would like to have it from UCSC. There are some genes which are not found in ensembl but found in UCSC

[cyril-cros]

Best way is to get a list of homologues from Homologenes, and to use join(linux command or database operation) to merge it with the information you want.

Answer 1

[Sej Modha]

I'm not sure how you can do this in UCSC but you can use ensembl.

http://www.ensembl.info/blog/2009/01/21/how-to-get-all-the-orthologous-genes-between-two-species/

Answer 2

[David Langenberger]

You can use the NCBI HomoloGene database. You can download the homology file from their ftp and then parse this file to get the homologous genes (human<->mouse) you are interested in. To do so, you can use the Taxonomy IDs.

Answer 3

[Lesley Sitter]

I don't really know what you want, but if you are looking for all genes or just single ones I think I remember how you do it :P

If you know the name of a gene then you can use the Gene Sorter.

https://genome.ucsc.edu/cgi-bin/hgNear?hgsid=433420817_vXSSLyUGtSAroCeYQh6E7zrB5ExC

You select Human h19 as the genome, then go to Sort by and select Protein Homology and press configure

You then get a new window, here you select Mouse Orthologs, select it, and then submit it

Now back at the first screen you only have to add a name in the box and press GO!

This will give a table containing the names of the gene in both species (in case there is a ortholog) and also the location of the human genome. Is this what you were looking for?

[ifudontmind_plzz]

@tsr640 I am looking for the entire gene list from mouse genome (mm10 annotated) and its homologues human gene coordinates (hg19)

[Lesley Sitter]

Are you sure that they have it? When looking at their server I can't seem to find a hg19 - mm10 homology table that includes gene names etc :S

http://hgdownload.cse.ucsc.edu/goldenPath/hg19/vsMm10/

I think you might be better off picking one of the other methods that were posted here by Sej Modha or David Langenberger

Answer 4

[macmath]

Check this http://www.informatics.jax.org/homology.shtml and here you can find results for the following:

Find the mouse homolog of a human gene? http://www.informatics.jax.org/faq/ORTH_gene.shtml

Download all mouse and human homologs? http://www.informatics.jax.org/faq/ORTH_dload.shtml