Re: [genome] Human-Mouse and Human-Rat orthologs

[Steve Heitner]

Hello, Natalie.

It is possible to do this by using our Table Browser and BlastTab tables which cross-reference IDs between two organisms.  In human (hg19), the tables are named mmBlastTab for mouse and rnBlastTab for rat.  The only caveat here is that in hg19, the BlastTab tables are organized by UCSC Genes IDs rather than RefSeq IDs.  If your genes are in RefSeq ID or gene name format, you will need to convert those to UCSC Genes IDs before you can cross-reference the mouse and rat IDs.  Also, once cross-referenced, the mouse results are given in UCSC Genes ID format and the rat results are given in RGD Genes ID format.  If you want those in any other format, you will need to convert again.

If you are unfamiliar with the Table Browser, please see the User’s Guide at http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html.

The following are instructions on how to convert from RefSeq ID or gene name to UCSC Genes ID:

1. Navigate to http://genome.ucsc.edu/cgi-bin/hgTables

2. Select the following options:
Clade: Mammal
Genome: Human
Assembly: Feb. 2009 (GRCh37/hg19)
Group: Genes and Gene Prediction Tracks
Track: UCSC Genes
Table: knownGene
Region: genome
Output format: selected fields from primary and related tables

3. On the “identifiers” line, click the “paste list” or “upload list” button to enter your list of IDs/gene names.  Note that when you click these buttons, you will also be shown an example of the format that your identifiers are expected to be in.

4. Click the “get output” button

5. In the “hg19.kgXref fields” section, check the “kgID” checkbox

6. Click the “get output” button

Now you can use the above output and enter it into a new Table Browser query using the mmBlastTab table to get the corresponding mouse IDs.

7. From the main Table Browser page, change the following options:
Group: All Tables
Table: mmBlastTab

8. On the “identifiers” line, click the “paste list” or “upload list” button to use your output from the previous Table Browser query

9. Click the “get output” button

10. In the “Select Fields from hg19.mmBlastTab” section, check the “target” checkbox

11. Click the “get output” button

Now, if you want to convert your mouse UCSC Genes IDs into any other format, you can follow the steps in the first Table Browser query with a couple of modifications:

In step 2, change “Genome” from “Human” to “Mouse”

In step 5, check the checkbox corresponding to whichever data format you want (i.e., check the “refseq” box for the RefSeq ID; check the “geneSymbol” box for the gene name)

If you are trying to convert from Rat SGD Genes ID format to RefSeq Genes, there are a couple of additional steps to replace step 5 with:

5.1: Scroll down to the “Linked Tables” section and check the rn4.rgdGene2ToRefSeq checkbox

5.2: Click the “allow selection from checked tables” button

5.3: In the “rn4.rgdGene2ToRefSeq fields” section, check the “value” checkbox

Please contact us again at gen...@soe.ucsc.edu if you have any further questions.

---
Steve Heitner
UCSC Genome Bioinformatics Group

-----Original Message-----
From: Natalie Dror <nd...@selventa.com>
Date: Wed, 19 Dec 2012 10:40:15 +0000

Dear Donna ,
I am trying to find the mouse and rat orthologs to a long list of human genes.
Is there a way to do this in any online tool?
Thanks a lot,
Natalie Dror

[Natalie Dror]

Thanks a lot, Steve.