A FreeSurfer view of the cortical transcriptome generated from the Allen Human Brain Atlas

The Allen Human Brain Atlas provides an anatomically detailed view of gene expression in the brain. This full transcriptomic dataset contains over 200 million expression values. To facilitate use of this resource, we distilled the data into a matrix of 20,737 genes by 68 cortical regions that represent the automatically segmented FreeSurfer regions (Desikan-Killiany parcellation). In this data report, we describe the Allen-FreeSurfer mapping, sampling information and provide regional values of gene expression. The resulting cortical transcriptome facilitates interpretation of human neuroimaging findings by providing a molecular context. AllenHBA_to_DKRegion_Map.xls - Excel file containing the mapping from Allen Brain Atlas samples to the FreeSurfer cortical regions. Each sample is referenced with a unique identifier by combining the donor ID with the x, y and z MNI152 coordinates (“10021_5.1_27.1_28.6“ for example). DKRegionStatistics.tsv - Tab separated file characterizing the FreeSurfer cortical regions. This file lists how many donors contribute to each region, Allen Brain Atlas samples per region and alternative identifiers. AllenHBA_DK_ExpessionMatrix.tsv - tab separated file containing correlation to the median values across the donors (left hemisphere only, column named ”Average donor correlation to median”) and gene expression values across the 68 FreeSurfer cortical regions (columns). This file can be opened with read.table in R or as a tab separated file in a spreadsheet program. ConsistentGOGroups.tsv – Gene Ontology enrichment analyses results for the consistency measure. InconsistentGOGroups.tsv – Gene Ontology enrichment analyses results for the consistency measure (with high ranked groups showing more inconsistency). CreateExpressionLUT.r - This R script provides the method to load and convert expression values for a specific gene into a color lookup table that can be used to visualize the averaged expression values in FreeSurfer.