Intro Figuring out how one group’s brain is different from another’s is a big part of neuroscience. MRI-neuroanatomy – the study of the sizes of brain regions – is a wonderful tool for this job and makes up a sizeable chunk of what we study. MRI operates in a lovely middle ground in the scales of neuroscience. It is strongly related to macroscale features of the organism, including sex, behaviour, etc; but can also inform us about the effects of microscale factors – such as gene expression.

Intro In this post I will demonstrate how to use my package ABIgeneRMINC to download, read and analyze mouse brain gene expression data from the Allen Brain Institute. The Allen Brain Institute (ABI) has acquired and released genome-wide spatial gene expression maps for the mouse brain. The data is generated using in situ hybridization experiments (ISH), where nucleotide probes for specific genes bind directly to mouse brain tissue. The probe binding is then marked with a biotin label that can be used to locate regions where a gene is expressed.

Why co-clinical trials? Here at the Mouse Imaging Centre, a large portion of our research is related to neurodevelopmental disorders. Ultimately the goal of such research is to improve health outcomes for individuals with these disorders. One clear way to impact health outcomes for individuals with neurodevelopmental disorders is to develop new medicines. Part of my research has been on the animal side of a project aimed at using matched human and animal trials to expedite drug development for autism spectrum disorders.