Allen Human Brain Atlas data

We used the brain-wide microarray gene expression data generated by the Allen Institute for Brain Science (downloaded from http://human.brain-map.org/) (Hawrylycz et al., 2012, 2015). The dataset consists of a total of 3702 microarray samples from six donors (one female). Each sample comprised 58 692 gene probes and provides coordinates in MNI152 space. The gene expression data have been normalized and corrected for batch effects by the Allen Institute (TECHNICAL WHITE PAPER: MICROARRAY DATA NORMALIZATION, 2013). We first restricted the set of samples to the left hemisphere (six in total) and to cortical regions based on the provided slab type (‘cortex’), retaining only samples with a maximal distance of 3 mm to a cortical region of interest obtained by a parcellation (Cardoso et al., 2015) of the study template used in Cash et al. (2018). After additionally removing samples being annotated by the Allen Institute as non-cortical samples (e.g. CA1 field), 1248 microarray samples were available in total. Next, as previously described (Richiardi et al., 2015) we reannotated all microarray probe sequences with gene names using Re-Annotator (Arloth et al., 2015). We excluded probes that sampled more than one gene (N = 1512), were mapped to intergenic regions (N = 5013) or could not be mapped to any genomic region (N = 1569), leaving 50 598 probes covering 19 980 unique genes. Furthermore, we removed probes that were marked as expressed in <300 of the 1248 cortical samples (N = 13 941). Thus, the analysis was carried out using 36 657 microarray probes covering 16 772 distinct genes.