Table 3.

LASAGNA motif binding search of GRE in the EDE region and the proximal promoter region spanning 5kb upstream of the TSS

Name of TF model	Sequence	Strand	Position	Score	P-value	E-value
GR-alpha (T00337)	CAGAGCAAAATGTCA	+	20940 (EDE, GRE2)	130.9	0.000675	0.56
GR-alpha (T00337)	TGTACACAGTGTCTC	-	21268 (EDE, GRE1)	148.72	0.0001	0.082
GR-alpha (T00337)	GCATCACATTGACCC	+	-2846 (promoter)	129.49	0.00075	3.7

Sequences indicated are either in the +/- strand and positions are relative to the TSS set as the zero position. Scores are obtained for the GR-alpha transcription factor model from the TRANSFAC database (T00337) based on position-specific scoring matrices. The P-value is empirically computed from the position-specific scoring matrices scores of individual nucleotides in the sequence relative to the TF model (62) and is indicative of the probability of observing a score equal to or higher than the score by chance (63). The E-value considers the length of the genomic region being tested and gives the number of expected times a hit of the same or higher score is found in the genomic region by chance (63).

Abbreviation: TF, transcription factor.