How to get mouse-human homologues table from UCSC?
4
1
Entering edit mode
9.4 years ago

Hello,

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

genome gene alignment sequence • 6.1k views
ADD COMMENT
0
Entering edit mode

@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

ADD REPLY
0
Entering edit mode

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.

ADD REPLY
2
Entering edit mode
9.4 years ago
Sej Modha 5.3k

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/

ADD COMMENT
2
Entering edit mode
9.4 years ago

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.

ADD COMMENT
1
Entering edit mode
9.4 years ago
Lesley Sitter ▴ 610

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

Image not available

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

Image not available

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?

ADD COMMENT
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode
7.8 years ago
macmath ▴ 170

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

ADD COMMENT

Login before adding your answer.

Traffic: 1390 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6