Table 2. Intrastrand and interstrand G-quadruplex forming sequences associated with functional sites in the human genome.

		Intrastrand PQS			DS-PQS				Any PQS			DS/SS
Site	# in genome	with G4	Enr.	%sites	with G4	Enr.	%sites	significance	with G4	Enr.	%sites	ratio
XPD peaks	14,570	3,288	1.99	22.6%	6,052	2.49	41.5%	< 1e-308	6,995	1.91	48.0%	1.84
XPB peaks	21,555	4,466	2.05	20.7%	8,363	2.61	38.8%	< 1e-308	9,769	2.02	45.3%	1.87
ORI MCF7	94,195	24,117	5.05	25.6%	34,425	4.90	36.6%	< 1e-308	42,108	3.97	44.7%	1.43
ORI K562	62,971	12,583	5.08	20.0%	16,724	4.59	26.6%	< 1e-308	22,331	4.05	35.5%	1.33
1kb upstream	39,927	17,975	3.96	45.0%	20,976	3.15	52.5%	< 1e-308	25,199	2.50	63.1%	1.17
Hf2 bind (1+)	9,149	1,095	1.34	12.0%	754	0.63	8.2%	not enriched	1,582	0.87	17.3%	0.69
Hf2 bind (2+)	771	177	1.43	23.0%	128	0.70	16.6%	not enriched	256	0.93	33.2%	0.72
G4seq Pds&K+	490,269	177,119	39.8	36.2%	108,229	16.6	22.1%	< 1e-308	226,496	22.4	46.2%	0.61
Unique G4s		374,834			550,977				832,540			1.47

For each type of functional site (transcriptional helicase binding, origin of replication, promoter, hf2 antibody binding), the number and percentage of sites with a G4 motif, and enrichment ratio of G4’s within the sites are listed. Data are provided for intrastrand PQS’s, inter-strand PQS’s, and for PQS of any type, with loops up to 7nt long. For enriched DS-PQS’s, a limit on binomial significance is listed. Rightmost column: ratio of number of sites with DS-PQS to number of sites with intrastrand PQS; for XPD and XPB binding sites it exceeds the whole-genome ratio (bottom row).