ends, precentral gyrus near postcentral gyrus, and so on. To provide a quantitative measure of this result we then applied the MDS method in 3D. As the positions of the samples were mapped back into MRI coordinate space, the correlation between ‘genetic distance’ and physical distance can be calculated after projecting the original cortical samples to a sphere and applying suitable rotation and scaling operations (Supplementary Methods 3). MDS-based sample correlations vary nearly linearly with 3D physical distance (Fig. 6e, inset), with a goodness of fit between native and MDS coordinates of 28.36% (P < 10−4, Supplementary Fig. 9). This effect is strongest when limited to genes that are differential between gyri as above, but can also be seen using the entire ~30,000 gene set, achieving a fit of 12.48% between native and MDS coordinates (P < 10−4, Supplementary Fig. 10). Therefore, gene expression profiles substantially determine position on the cortical sheet.
