how to compare the expression of homology genes between different organisms?

Question

[wuzongze001]

I have the RNA-seq data for human and mouse and want to compare the expression of homologous gene. I can run TopHat and Cufflink for those two datasets independently, but because I do not have the mapping file for human and mouse(human gene id and corresponding mouse gene id), so I do not know which genes are homologous and can not compare. Is there any way I can solve this problem?

Answer 1

[pld]

You can either carry this out yourself using BLAST (or BRBH), or you can check out databases like ENSEMBL that already store this type of information. You can use BioMart to download lists of homologs/orthologs from there.