I have a basic question, for which I don’t find a direct answer on line.
For any brain region, may the reported values be used to quantitatively compare the mRNA expression of two genes?
Hi @PZF, could you please be more specific about which atlas(es) you are referring to. Thanks!
Sorry, I was referring to the Allen Brain Atlas
Hi @PZF ! There are over a dozen types of Allen Brain Atlases; can you provide a URL or a description of which atlas you are using, so we can better address your question? For example, Adult Mouse Brain? Adult Human Brain? In situ Hybridization (ISH)? scRNA-Seq? Microarray? The ISH data is only semi-quantitative, for example.
Thanks for your answer.
It’s for the Adult Human Brain. I would like to be sure that I can quantitatively compare the mRNA transcripts of two different genes in the same region. I know these are normalized values, but if I want to compare, say, the Serotonin receptor A and the Serotonin receptor B in a given region, and I see that the transcripts of A have a value of 10 and the transcripts of B have a value of 5, can I conclude that in the region there are twice as many A receptors as B (assuming no post-transcriptional changes take place)?
Hi @PZF. The short answer is you can qualitatively, but not quantitatively compare these values (so you can believe obvious binary differences, but not subtle ones). You can do a semi-quantitative comparison by scaling expression of some probes based on RNAseq data. This topic has been addressed a bit more in this forum post.
Thanks for your answer. So if I understand correctly, I can quantitatively compare the same probe across different regions and across different brains, but I cannot compare probes for different genes, unless I normalize over RNAseq (which improves, but not entirely solves, the quantification problems). Am I right?
Hi. I’m using the Human Brain atlas and wondering what is the best way to find an average expression value of a certain tissue.
Each probe can give varying expression levels for a single structure, I want to know what is the best practice to find an average value among them.
Hi @LevelUpOrNot. Regarding your second point about which probe(s) to use for a given gene, this question was just addressed in another post. Regarding averaging values across a certain tissue, you can do this for three resolutions by setting the “Resolution” tab at the bottom of the heatmap:
This will average probe expression across all samples for a given structure. If you want to do anything more complicated, I would suggested downloading the data.