Identification of genetic markers for cortical areas using a Random Forest classification routine and the Allen Mouse Brain Atlas

The mammalian neocortex is subdivided into a series of ‘cortical areas’ that are functionally and anatomically distinct, and are often distinguished in brain sections using histochemical stains and other markers of protein expression. We searched the Allen Mouse Brain Atlas, a database of gene expression, for novel markers of cortical areas. We employed a random forest algorithm to screen for genes that change expression at area borders. We found novel genetic markers for 19 of 39 areas and provide code that quickly and efficiently searches the Allen Mouse Brain Atlas.