Reproducing "differential gene search" via API for mouse brain ISH data


I am in love with the “Differential search” function for the ISH data of the mouse brain and I wish to write a Python script that reproduces the search (eg) below programmatically.

I then found this very helpful doc that allows me to do so, but my results are not consistent with the website (I find more genes than when I query via the Allen website, although structures and dataset are the same).

I think that this is due to the threshold parameters: in the query to system :: mouse_differential I have 4 different thresholds: start/end threshold for either target or contrast. In the website, I only have one slider that controls one expression threshold that ranges from 0 to 7.

  1. Could you please tell me how to reproduce differential gene search via URL/API that are consistent with Allen website?
  2. I guess that means, could you tell me the 4 values of the thresholds that you use in Allen website ?
  3. Would you recommend any particular threshold value to get biological significant results?

Thank you very much,


Actually I found the answer (and that was simple). By clicking the button I realized that the URL,50&domain2_threshold=1,50&image_set=P56&search_type=differential

contains the thresholds. The default values are:
target: start 0, end 50
contrast: start 1, end 50.

Thank you!


Thanks a lot for following up with the solution!

I’m sure it will be appreciated by anyone else digging into the API.