13 days ago by
Cambridge, United Kingdom
This is unlikely to be a meaningful comparison.
At the very least, you will have technical batch effects, e.g., differences in probe design/affinity between arrays, differences in RNA extraction/RT efficiency, variation in non-specific binding from the rest of the transcriptome. So, even if you had a homologous gene with the same abundance of transcript molecules in mouse and human, I would be amazed if you managed to obtain the same signal on the associated arrays. There is almost certainly a strong batch effect that will confound any comparison between species.
The other major problem is the biological interpretation of differences. Let's say that you did manage to somehow resolve the batch effects and get comparable intensities between species. Then what? If you say that gene X has higher intensity (i.e., more transcript molecules) in mouse compared to human, how would I even attempt to interpret that? Do 10 transcript molecules of gene X in mouse cells have the same effect as 10 molecules of gene X in human cells? Perhaps mice need 20 molecules of X to achieve the same biological activity as that in humans. Or 5. Or 100.
A more rigorous approach would be to compare within each species, then do a meta-analysis across species. You could ask things like "which genes are DE between A and B in mice, but not in humans" and vice versa. This also seems to answer a more relevant scientific question than a direct comparison between species.
modified 13 days ago
13 days ago by
Aaron Lun • 24k