Table 1.

Summary of array datasets and network parameters.

Brain Bank	Study dataset	Conditions	Species	Array platform	Nominal brain region	Control samples	Disease samples	Samples used in network	Network nodes	Optimal Pearson threshold	Mean Clustering coefficient (CC)	Mean non- zero CC	Scale-free?	Assortativity
Columbia	Sibille et al. (2004)	Depression	Human	Affy U133a + 2	BA 9	15	15	30	22277	0.82	0.14	0.38	Yes	0.49
Columbia	Sibille et al. (2004)	Depression	Human	Affy U133a + 2	BA 47	15	15	30	22277	0.82	0.15	0.42	Yes	0.53
Pittsburgh	Sibille et al. (2009)	Depression	Human	Affy U133a + 2	Amygdala	14	14	28	26199	0.85	0.20	0.48	Yes	0.26
Pittsburgh	Sibille et al. (2009)	Depression	Human	Affy U133a + 2	BA 25	14	14	28	26199	0.85	0.16	0.51	Yes	0.47
Pittsburgh	Tripp et al. (submitted)	Depression	Human	Affy U133a + 2	BA 9	29	29	58	29211	0.8	0.16	0.55	Yes	0.46
Pittsburgh	Tripp et al. (submitted)	Depression	Human	Affy U133a + 2	BA 25	28	28	56	29211	0.8	0.14	0.53	Yes	0.35
Stanley	Feinberg et al.	Depression	Human	Affy U95av2	Cerebellum	14	13	50	12453	0.8	0.15	0.50	Yes	0.47
Stanley		Bipolar	Human	Affy U95av2	Cerebellum		12
Stanley		Schizophrenia	Human	Affy U95av2	Cerebellum		11
Stanley	Altar (B) et al.	Depression	Human	Agilent	BA 46/10	10	20	39	12235	0.82	0.14	0.38	Yes	0.61
Stanley		Schizophrenia	Human	Agilent	BA 46/10		9
Stanley	Altar (C) et al.	Depression	Human	Affy U133a	BA 46	10	11	44	22383	0.85	0.19	0.50	Yes	0.28
Stanley		Bipolar	Human	Affy U133a	BA 46		12
Stanley		Schizophrenia	Human	Affy U133a	BA 46		11
Stanley	Skyler (A) et al.	Depression	Human	Affy U95av2	BA 8/9	12	11	47	12453	0.79	0.44	0.65	Yes	0.09
Stanley		Bipolar	Human	Affy U95av2	BA 8/9		11
Stanley		Schizophrenia	Human	Affy U95av2	BA 8/9		13
Stanley	Skylar (B) et al.	Depression	Human	Affy U95av2	Cerebellum	10	13	46	12453	0.84	0.31	0.50	Yes	0.20
Stanley		Bipolar	Human	Affy U95av2	Cerebellum		11
Stanley		Schizophrenia	Human	Affy U95av2	Cerebellum		12
Stanley	Iwamoto et al. (2004)	Depression	Human	Affy U95av2	BA 10	15	11	50	12453	0.82	0.18	0.53	Yes	0.38
Stanley		Bipolar	Human	Affy U95av2	BA 10		11
Stanley		Schizophrenia	Human	Affy U95av2	BA 10		13
Stanley	Aston et al. (2005)	Depression	Human	Affy U95av2	BA 21	19	13	59	12453	0.79	0.26	0.56	Yes	0.10
Stanley		Bipolar	Human	Affy U95av2	BA 21		12
Stanley		Schizophrenia	Human	Affy U95av2	BA 21		15
na	Surget et al. (2009)	UCMS	Mouse	MOE 430_2	Amygdala	6	6	24	25859	0.83	0.17	0.35	Yes	0.50
na		UCMS + FLX	Mouse	MOE 430_2	Amygdala		6
na		UCMS + CRF1A	Mouse	MOE 430_2	Amygdala		6
na	Surget et al. (2009)	UCMS	Mouse	MOE 430_2	Cingulate cortex	6	6	24	25859	0.78	0.24	0.32	Yes	0.48
na		UCMS + FLX	Mouse	MOE 430_2	Cingulate cortex		6
na		UCMS + CRF1A	Mouse	MOE 430_2	Cingulate cortex		6
na	Surget et al. (2009)	UCMS	Mouse	MOE 430_2	Dentate gyrus	6	6	24	25859	0.87	0.09	0.43	Yes	0.65
na		UCMS + FLX	Mouse	MOE 430_2	Dentate gyrus		6
na		UCMS + CRF1A	Mouse	MOE 430_2	Dentate gyrus		6

Array datasets from different cohorts, brain regions, and species were used to create a set of coexpression networks, in which we tested several connectivity-to-expression relationships. Figures showing meta-analysis (Figures 4D and 5D) combine equally-weighted results from every study listed. The amygdala dataset (Sibille et al., 2009) was used to illustrate specific results in Figures 1-5. Two of the datasets are under review (Guilloux et al., submitted; Tripp et al., submitted), and results from all other datasets have been published previously. Several datasets were downloaded from the Stanley Medical Research Institute (Higgs et al., 2006) and when a specific publication is not associated with those datasets, they are referenced as listed on www.stanleyfoundation.org