Table 2.

Integration of TCF4 binding profile with functional and SCZ data sets

Gene-based enrichment via permutation analysis
TCF4 knockdown experiments	Set size	Overlap	Odds ratio	Fisher P value	Permutation P value
SH-SY5Y siRNA knockdown (all)	921	267	1.30	0.0003	0.0005
Upregulated	396	100	1.06	0.3159	n/a
Downregulated	525	167	1.48	3.28E-05	0.0001
Cortical precursor siRNA knockdown (all)	502	138	1.20	0.0434	0.0438
Upregulated	240	47	0.76	0.9603	n/a
Downregulated	262	91	1.68	6.78E-05	<4.11E-05a
SCZ gene expression
Fromer et. al (2016) (all)	623	190	1.38	0.0002	0.0001
Upregulated	296	37	0.45	1	n/a
Downregulated	326	153	2.77	2.20E-16	<4.11E-05a
Genomic locus enrichment tests using LOLA
UCSC annotations	Bed file	Overlap	Odds ratio	P value
Evo CpG islands	evoCpg.bed	3706	7.08	∼0
CpG islands	cpgIslandExt.bed	960	2.76	2.30E-151
Switch DB TSSs	switchDbTss.bed	584	3.19	2.46E-118
LaminBq	laminB1.bed	4404	1.49	1.46E-94
Simple repeats	simpleRepeat.bed	836	1.99	3.46E-68
Top 15 overlapping DNA binding protein profiles from ENCODE
Experiment	Antibody	Overlap	Odds ratio	P value
ChIP SK-N-SH	NRSF	587	5.75	2.90E-231
ChIP GM12878	Pol2	637	2.26	5.54E-71
ChIP MCF-7	CTCF	561	2.26	3.53E-63
ChIP H1-hESC	CTCF	437	2.40	3.38E-56
ChIP K562	Max	580	2.09	3.11E-54
ChIP HEK293	ZNF263	508	2.18	4.30E-53
ChIP HepG2	Pol2	425	2.36	8.00E-53
ChIP PFSK-1	FOXP2	305	2.73	2.83E-50
ChIP K562	ZBTB7A	357	2.48	2.88E-49
ChIP GM12891	CTCF	422	2.26	5.42E-48
ChIP A549	CTCF	505	2.02	3.23E-44
ChIP SK-N-SH	p300	494	2.03	6.72E-44
ChIP K562	Egr-1	403	2.18	7.15E-43
ChIP K562	MAZ	450	2.04	8.06E-41
ChIP SH-SY5Y	GATA-2	413	2.09	9.19E-40
Psychiatric Genomics Consortium risk loci overlap
Data file	Background	Overlap	Odds ratio	Fisher P value	Permutation P value
scz2.anneal.108	ActiveDHSb	158	1.38	8.88E-05	0.0816
	SK-N-SH DHSb	55	1.56	0.0017	0.035

^a4.11E-05 is the minimum P value obtainable when permuting over 24, 358 genes (includes non-coding RNAs and provisional IDs).

^bDNaseI Hypersensitivity Sites.