I was writing to ask about how we might obtain a full gene expression dataset for a handful of brain regions from the adult mouse (e.g. the DR and PAG). We’re interested in getting data by anatomical region as opposed to voxel. Because the ABA interface already permits looking at differentially exp…

A good starting point would be Structure Unionization (see this post ). This gets the converse of what you want: all regions for one gene, but does wrap up by region as requested. I’m not sure about getting all gene data for a few regions, but maybe someone else on here knows.

Here is the API call that would get you structure unionization data by region. http://api.brain-map.org/api/v2/data/query.json?criteria=model::StructureUnionize,rma::criteria,structure[acronym$eq'DR'] This returns an entry for each of the tens of thousands of section data sets (experiments) in the…

Thank you! In this JSON, is there information about the gene being looked at in each section dataset? Or am I misunderstanding what you’re doing here? Really appreciate the help.

No, as it is written that information is not there, but it could be. Perhaps you can more explicitly describe what it is you need. So far we have identified expression per structure with gene information added. Anything else?

[image] wayne: http://api.brain-map.org/api/v2/data/query.json?criteria=model::StructureUnionize,rma::criteria,structure[acronym$eq'DR'] This is very close! The last step would be find out what gene is being assayed in each of the thousands of “section_data_set_ids” (and perhaps other informa…

How about this one? http://api.brain-map.org/api/v2/data/query.json?criteria=model::SectionDataSet,rma::criteria,structure_unionizes(structure[acronym$eq'DR']),genes,rma::include,genes,structure_unionizes

So this seems great! I’m assuming these are the Structure Unionize attributes for all the experiments specifically in DR? Just a couple of quick q’s: I appended “rma::options[num_rows$eqall]” to the end of that last query, but both the max number of displayed rows (25971) and total rows (26038) are…

Adding these additional fields is the equivalent of doing a database “INNER JOIN”. It is likely that not every record will have a corresponding record in another table. If you are really interested in tracking it down further, I am going to refer you to the API documentation to write queries that r…

Is there a working solution for this, for the developing mouse brain? (I want to do something similar: All genes, organized by region, and all time points)

Extracting data for all genes from an ROI

Technical

danielsf August 4, 2025, 6:52pm 11

I have tried to provide an example in the response on this thread.

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Extracting data for all genes from an ROI

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