Hi, I try to compare the expression of alpha5GABA subunit in mouse and in human, but the presentation of data in the 2 species are different. In mouse it looks obvious, but in human the colourcode is confusing, and I do not see 3D options. Would someone tell me the way I should look human data? Thanks, Bert
Hi. Could you please clarify which mouse and which human resources you are looking at? We have several of each and the answer will depend on the resource.
If you are talking about the original mouse and human brain atlases, the reasons they look different is because the mouse brain atlas is done using sequential ISH sections, aligned to a common coordinate framework, and has cellular resolution data. The human data is collected using microarray, which has the resolution of a dissected chunk of tissue, and therefore you get a single value for a relatively large tissue area (hence the patchy 3D images).
Hi,
so, Experiment Detail :: Allen Brain Atlas: Mouse Brain
and Microarray Gene Detail :: Allen Brain Atlas: Human Brain
So, I try to compare the data for alpha5GABA subunit presentation in the 2 species, but I cant read the human data? Green is the high density and dark red is the low or oposite? Can you help with it? thanks, Bert
In this case red is high expression and green is low expression, but you can change the color bar and units via the arrow (^) in the upper right of the images:
You can see the actual values underneath the images by clicking (“Selected Structure”) or hovering (“Structure”) over the image.
Excellent, and thanks. Bert
Hi Jeremy, some more question if I may? So, sometimes there are huge differences between donors? Like HTR2B on human, there is almost nothing on one donor, but lot in the other? Is it sensitivity issue, or individual differences? Can you explain what are the differences between A_number? and CUST_numbers ? Thanks a lot, Bert
If a gene has high expression it is usually well conserved between donors, and therefore high variability between donors usually means the gene generally has low expression (with some fluctuations). It can also be a real biological or technical result; for example, things like immediate early genes can vary substantially between donors, but this is less likely.
As for the A_number vs. CUST_numbers, the microarray used for this study had some standard Agilent (I think) probes (A_) as well as additional custom probes (CUST_) created to increase the number of genes and/or the number of probes per gene for specific genes of interest. There are many ways to decide which probes are most meaningful (I wrote a paper on the topic several years ago) but in most cases your best bet is to choose the gene with the highest expression, regardless of whether it starts with A_ or CUST_.
Thank you very much!
Hi Jeremy, I have a problem to interpret the differences is some cases, like in this one. Would you help me to understand, how to judge the expression of adrenoreceptor alpha 1B in human? There are 2 sets of data, like Microarray Gene Detail :: Allen Brain Atlas: Human Brain
and the A_23_P33326 has very different than A_23_P21929. One showed nice expression level in different region, the other shows almost nothing, so which one is right?
Thanks a lot, Bert
I’d use A_23_P33326 since it has highest expression. That said, these expression patterns are very similar, as you can see with this view. You can also click on Find Correlates and see the the other probe for ADRA1B is the most highly correlated probe on the whole microarray, confirming that these probes have similar patterns.
Thank you, Bert