I’d like to find a straightforward way to access the “average” expression of a gene across the entire mouse brain, or at least the information that would enable me to calculate some statistic like that. The goal would be to normalize a gene’s “expression energy” for a particular region, obtained using Structure Unionization, in order to get a sense of region-specific enrichment or depletion for genes with very different abundances. Really appreciate the guidance!
Thanks for your question. Which data modality are you interested in using for your source? In situ hybridization (ISH) data from the Adult mouse brain atlas? And have you had a look at the API yet?
Yes, the adult mouse brain atlas. And I’ve taken a look – is the easiest way to pull expression statistics for all genes across the broadest ABA anatomical regions (e.g. for CH, CS, CB) and then average the values for each gene by combining the results from these queries? I’m just wondering if there is a more straightforward approach. Thanks for the help!
Hi @vbhave. I don’t think anyone has addressed the exact question you are referring to; however, for your more specific question of how to get gene expression values for all genes in a single anatomical region, this has been addressed in another thread (which it seems you were also a part of!). If you do find that this type of normalization improves your analysis of the Adult mouse brain atlas data, please let us know (for example, by posting a link to your future publication in this thread).