Scoring functions for transcription factor binding site prediction

BMC Bioinformatics

Table 3 Data sets of promoter sequences of genes regulated by different transcription factors. By 'molecular biology approaches' we mean methods like DNAse footprinting and methylation interference. 'AlignACE' stands for functional group data from the AlignACE web server. '#seqs' stands for number of promoter sequences in the data set.

TF	TFBS consensus motif	#seqs	source and type of evidence
abf1	CGTNNNNNNTGA	20	molecular biology approaches [20]
gal4	CGGNNNNNNNNNNNCCG	10	molecular biology approaches [20] and AlignACE [6]
mac1	TTTGCTCA	6	microarray [21]
mcm1	TTTCCCAAANNGGAAA	24	molecular biology approaches [20]
mig1	AAAAATCTGGGG	11	molecular biology approaches [22]
pdr	TCCGCGGA	11	AlignACE [6]
rap1	TACACCCATACATT	44	molecular biology approaches [23] [24]
reb1	TTACCCG	13	molecular biology approaches [20]

ISSN: 1471-2105