Markup | Genome Research

Table 1.

cis/TF's Matches to Documented TF Binding Sites

TF	Rank	Correlation (rvalue)[i]	Significance level	Program prediction	Documented site[ii]
Knockout lines
STE12	4	0.89	0.001	`?TGAAAC[iii]`	`ATGAAA`
BAS1	7	0.52	0.01	`?GAGTCA`	`GAGTCA`
PDR3	5	0.65	0.05	`CGCGG?T`	`TCCG(C,T)GGA`
MET28	4	0.87	0.001	`?GTCACG`	`TCACGTG`
GCR1[iv]	2	0.99	0.001	`ACCA?CC`	`C(A,T)TCC`
GCN4[iv]	38	0.50	0.01	`TGACTC?`	`TGANTN [v]`
Total evaluated: 11
Cell cycle (high density arrays)
MET32	2	0.99	0.001	`CT?TGGC`	`AACTGTGG`
GCN4	2	0.95	0.001	`CTGAC?C`	`TGANTN [v]`
Total evaluated: 6
Cell cycle (cDNA arrays)
PHO4	1	0.95	0.002	`CACG?G`	`CACGT(T,G)`
Total evaluated: 9

[i] Probability that the correlation is different from zero.

[ii] Taken from SCPD.

[iii] “?” denotes a position where the program allowed any base.

[iv] These two did not meet criteria for successful hits.

[v] Approximately one-half of the 20 documented GCN4 binding sites in SCPD contained the sequence TGACTC.