[Genome] [Fwd: extracting human genes from mouse expression arrays]

[Kayla Smith]

Zhaodong,

The hg18.mmBlastTab (and mm8.hgBlastTab) tables will be of interest to 
you.  They connect human UCSC ids with mouse accession names.

Please see this previously answered mailinglist question which asks a 
similar question to yours:

https://www.soe.ucsc.edu/pipermail/genome/2007-March/013096.html

Also since your college mentions expression data in the email you 
attached below, I want to point out a useful resource available that is 
available.  We display some expression data in both our human and mouse 
browsers which you may be interested in.  When in the Genome Browser, 
scroll down to the "Expression and Regulation" track controls.  The GNF 
Atlas 2 tracks are popular.

I hope this information is helpful to you.  Please don't hesitate to 
contact us again if you require further assistance.

Kayla Smith
UCSC Genome Bioinformatics Group




Zhaodong Xu wrote:
> hi,
> 
> my collegue want to extract the accession data from the mouse data and
> convert them to human accession numbers, what kind of Table should I
> query to?
> 
> thanks
> 
> 
> zhaodong
> 
> -------- Original Message --------
> Subject: extracting human genes from mouse expression arrays
> Date: Mon, 30 Apr 2007 16:21:26 -0400
> From: izhar livnebar <i.livne at utoronto.ca>
> To: zxu at uhnres.utoronto.ca
> 
> Hello Zhadong, Rod wants me to generate heat maps from the expression  
> array of retinoblastoma samples. the heat maps should be of functional  
> groups that are active in the retina (Cell cycle, RNA metabolism  
> etc.). Can you find a way to extract the accession data for these  
> groups from the mouse papers below and convert them to human accession  
> numbers so I can import it into the my array analysis ?
> thanks, Izzy
> 
> Samuel Shao-Min Zhang,1,5 Xuming Xu,1 Mu-Gen Liu,1 Hongyu Zhao,2  
> Marcelo Bento Soares,3 Colin J Barnstable,1,5 and Xin-Yuan Fu4
> BMC Dev Biol. 2006; 6: 48.
> A biphasic pattern of gene expression during mouse retina development
> 
> Blackshaw S, Fraioli RE, Furukawa T, Cepko CL. Comprehensive analysis  
> of photoreceptor gene expression and the identification of candidate  
> retinal disease genes. Cell. 2001;107:579?589. doi:  
> 10.1016/S0092-8674(01)00574-8. [PubMed]
> 
> Blackshaw S, Harpavat S, Trimarchi J, Cai L, Huang H, Kuo WP, Weber G,  
> Lee K, Fraioli RE, Cho SH, et al. Genomic analysis of mouse retinal  
> development. PLoS Biol. 2004;2:E247. doi:  
> 10.1371/journal.pbio.0020247. [PubMed]
> Zhaodong Xu <zxu at uhnres.utoronto.ca>, Zuyao <zni at uhnres.utoronto.ca>
> 
> 
> ------------------------------------------------------------------------
> 
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