Hi, Recently, I would like to use the mRNA expression information to analyze AD. I have downloaded the gene expression table here Data Download :: Allen Brain Atlas: Aging, Dementia and TBI Study. However, it only provides the name of cortexs and hemisphere where the gene expressed. The corresponding MNI coordinate of the cortex was miss. Since I would like to use YEO, or other functional parcellations to split the whole brain. Therefore, it is helpful to get the MNI coordinate of the brain tissue where the RNA extract to align location of the genes to the parcellation I used. Therefore, is there any information or links to get the MNI information of brain tissue where genes are extracted?
Thanks for your interest in this project. We do not have MNI coordinates collected for this project, although all data comes from temporal cortex (grey matter), parietal cortex (grey matter and white matter), and hippocampus. There are two ways where you might be able to align to MNI coordinates (although I don’t know if either would work):
- We have MNI coordinates for the Allen Human Brain Atlas, so you could compare the TBI study RNA-seq data to the microarray data from HBA to find the nearest sample (either via correlation or via some other method) and then take the MNI coordinates for the relevant HBA sample as a proxy for the TBI section.
- You could attempt to align the pathology tissue sections from the TBI study to the Allen Brain Reference Atlases for adult human and derive MNI coordinates from there. I’m not sure how to go about this, but I have seen some previous Community Forum posts about this topic (for mouse).
All of this said, given that there were only four regions profiled in this study, I’m not sure whether either method for attempting to derive MNI coordinates would be worthwhile.
I appreciate your suggestions. Yes, I noticed, no whole-brain expression mRNA information for this cohort. I can try the methods you mention to assign the MNI coordinates if I can not find other brain mRNA datasets to reproduce my findings.