Genomic Promoter Analysis Predicts Functional Transcription Factor Binding

Table 8

Prediction of in vivo occupancy by HNF1 and HNF4 by BAM MEI analysis using human-mouse genomic alignments instead of local pairwise BLAST alignments restricted to regions of positive regulatory potential and a window size of 25 bp.

Predicted
Observed	HNF1 both	HNF1 hep	HNF1 panc	HNF4 both	HNF4 hep	HNF4 panc	Unbound	Total (obs)	Sensitivity
HNF1 both	3	0	0	0	0	0	1	4	75%
HNF1 hep	0	0	0	0	0	0	16	16	0%
HNF1 panc	0	0	1	0	0	0	3	4	25%
HNF4 both	0	0	0	20	0	0	30	50	40%
HNF4 hep	0	0	0	0	18	0	71	89	20%
HNF4 panc	0	0	0	0	0	8	8	16	50%
Unbound	0	0	0	3	3	2	908	916	99%
Total (pred)	3	0	1	23	21	10	1037	1095
Specificity	100%	NA	100%	87%	86%	80%	87%