Mapping Mouse Genes To Human Genes (Using Pwms)

Question

[Alex Reynolds]

What might be some strategies for mapping genes from mouse (say, mm9) to human (hg18 or hg19) using UniPROBE PWMs? While PWMs map to gene records, the gene names themselves do not map to orthologs between species. Is using a PWM-to-gene mapping a sensible idea or would you recommend alternative approaches?

[Qdjm]

Hi Alex, Could you please clarify what you want to do? You seem to be saying that you have a Uniprobe PWM that is associated with a mouse gene/protein, and you want to know the corresponding PWM for the human ortholog of that gene. Or are you using the PWM to scan the mouse genome for likely targets of the associated transcription factor and are trying to map these predicted targets to their human orthologs?

Answer 1

[David Quigley]

For suggestions on the general problem of mapping orthologs between species, you might try the responses to this question: How Do I Match Orthologues In One Species To Another, Genome Scale?