Cross-platform comparisons of our hiPSC microarray and the AllenBrain Atlas microarrays were done by (1) ranking absolute gene expression for each microarray using Partek, (2) assigning a rank difference value for each gene using a MATLAB script, and (3) calculating Spearman Rank Correlation Coefficients for each microarray comparison in Microsoft Excel. Wilcoxon's rank-sum test was assessed if a category of interest (spatial, temporal or combined) had significantly higher Spearman correlations than the background of all pairwise correlations. No hard cutoffs of ‘best matches' were used. Methods for using weighted gene co-expression network analysis (WGCNA) to identify modules composed of highly co-expressed genes were previously published.12
