Table 2.

Presence of consensus transcription factor binding sites in the − 300 to + 100 promoter sequence of differentially expressed genes in different clusters

	Rank	Binding site	FDR	No. genesa
Cluster 1	1	NF-kappaB	0.000094	6
	2	c-Rel	0.001353	5
Cluster 6	1	E2F	0.005309	5
Cluster 7	1	E2F	0.000527	6
Cluster 13	1	E2F	<  0.000001	99
	2	GABP	<  0.000001	49
	3	NRF1	<  0.000001	40
	4	CREBP1CJUN/ATF2:c-Jun	<  0.000001	35
	5	AHRHIF/AhR,	<  0.000001	35
	6	STAT1	<  0.000001	34
	7	CREBATF	<  0.000001	33
Cluster 14	1	E2F	<  0.000001	42
	2	CREBP1CJUN/ATF2:c-Jun	<  0.000001	26
	3	NRF1/NRF-1	<  0.000001	24
	4	CREB	<  0.000001	24
	5	ATF3	<  0.000001	22
	6	CREBATF	<  0.000001	22
	7	CREBP1/ATF2	<  0.000001	20
	8	ATF1	<  0.000001	20
Cluster 15	1	CREB	0.000004	15
	2	HIF1	0.000007	14
	3	ATF3	0.000007	14
	4	CREBATF	0.000007	14
	5	E2F	0.000037	25
	6	CREBP1/ATF2	0.000159	12
	7	STAT1	0.000559	11
	8	ATF1	0.000559	11
Cluster 17	1	CREBP1/ATF2	0.000257	16
	2	CREB	0.007176	13
	3	CREBATF/CREB,	0.007176	13
	4	SP1	0.013579	12
	5	TFII-I	0.013579	12
	6	AHRHIF/AhR,	0.013579	12
	7	CREBP1CJUN/ATF2:c-Jun	0.02189	11
	8	EGR1/Egr-1	0.02189	11
Cluster 18	1	MZF1	0.00585	8
	2	AP-2	0.021453	7
Cluster 19	1	SP1	<  0.000001	33
	2	GABP	<  0.000001	28
	3	STRA13	0.000023	25
	4	NF-Y	0.000053	24
	5	NRF-1	0.000053	24
	6	E2F	0.000132	31
	7	USF	0.000334	34
	8	CREBATF/CREB,	0.000334	22
	9	NFY	0.000845	21
	10	Egr-1	0.002093	20
Cluster 20	1	Stra13	<  0.000001	23
	2	USF	0.000007	19
	3	c-Myc:Max	0.000024	18
	4	CREBP1CJUN/ATF2:c-Jun	0.000304	16
	5	CREBATF/CREB,	0.000304	16
	6	GABP	0.00081	15
	7	ATF6	0.00081	15
	8	ATF4	0.00081	15
	9	ATF1	0.00273	14

^aThe number of genes contain the consensus TR binding site