CAGE-TSSchip: promoter-based expression profiling using the 5'-leading label of capped transcripts

Table 2 Over-represented TFBSs around the over-expressed promoter in Hepa1-6 compared with liver

TRANSFAC matrixID	\|Log₁₀(Hepa1-6/liver)\| > 0.5				P value^a	Binding factors
	Hepa1-6 > liver		Liver > Hepa1-6
	Number of probes	%	Number of probes	%
V$E2F1_Q3	87	74.4%	16	34.0%	2.31 × e^-06	E2f1
V$SP1_01	73	62.4%	11	23.4%	6.04 × e^-06	Sp1
V$ETF_Q6	62	53.0%	9	19.1%	9.96 × e^-05	ETF ^b
V$ZF5_01	77	65.8%	16	34.0%	2.50 × e^-04	Zfp161
V$CHCH_01	81	69.2%	18	38.3%	3.72 × e^-04	Churc1
Total	117		47

^aStatistical significance of the over-representation of each transcription-factor binding site (TFBS) around the over-expressed promoter in Hepa1-6 compared with liver, determined using Fisher's exact probability test. ^bAlthough TRANSFAC indicated that EGFR-specific transcription factor (ETF) binds to V$ETF_Q6 matrix, there was no report of this interaction in the mouse ortholog.

ISSN: 1474-760X