Table 1 Prediction accuracy of BrainGENIE (40-PC model) computed via fivefold cross-validation of the GTEx Project (v.8) release across the 12 brain tissues.

		All predicted genes					Significantly predicted genes
Brain tissue	n donors (paired blood–brain transcriptomes)	# of measured genes	% of genes measured in tissue compared to all annotated genes (GRCh38)	Mean training R²	Mean CV R²	Max CV R²	# of genes	% of measured genes	% of genes measured in tissue compared to all annotated genes (GRCh38)	Mean training R²	Mean CV R²	Mean CV Pearson’s r
Amygdala	88	18,957	34	0.65	0.05	0.39	4265	22	8	0.70	0.13	0.36
Anterior cingulate cortex BA24	99	19,236	34	0.56	0.05	0.43	6799	35	12	0.59	0.11	0.33
Caudate basal ganglia	137	20,524	37	0.46	0.06	0.38	10,772	52	19	0.50	0.09	0.30
Cerebellum (Fresh frozen)	131	20,540	37	0.48	0.06	0.5	9573	47	17	0.53	0.11	0.33
Cerebellum (PAXgene preserved)	154	21,494	38	0.42	0.05	0.39	10,098	47	18	0.47	0.09	0.30
Frontal cortex (PAXgene preserved)	141	20,340	36	0.42	0.06	0.5	10,186	50	18	0.46	0.10	0.32
Frontal Cortex (Fresh frozen)	125	19,983	36	0.49	0.07	0.5	11,816	59	21	0.53	0.11	0.33
Hippocampus	122	20,189	36	0.47	0.03	0.46	4008	20	7	0.53	0.10	0.32
Hypothalamus	114	20,839	37	0.50	0.04	0.56	5749	28	10	0.56	0.11	0.33
Nucleus accumbens basal ganglia	148	20,884	37	0.43	0.05	0.46	11,252	54	20	0.47	0.09	0.30
Putamen basal ganglia	125	19,330	34	0.49	0.06	0.54	10,350	54	18	0.53	0.11	0.33
Substantia nigra	86	18,882	34	0.62	0.04	0.51	2947	16	5	0.69	0.14	0.37

The proportion of genes expressed in the whole blood accounts for 31% of all genes annotated in the GRCh38 genome assembly. The criteria for declaring genes “significantly predicted” is as follows: cross-validation [CV] R² ≥ 0.01, CV FDRp ≤ 0.05. The total number of genes detected in each brain tissue for which BrainGENIE models were trained appears in the third column (“# of genes”). The proportion of genes that were significantly predicted by BrainGENIE from the total number of detected genes per brain tissue is presented in the ninth column (“% of genes”).

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