Table 1.
Representative results of predicted motif pairs
| Input TF pair | Known binding motifs | Predicted top motif pair | Known TF–TF interaction | −log(p) |
|---|---|---|---|---|
| Mbp1:Swi4 | ACGCGTnA:TTTTCGCG | ACGCG:CGCGa | 1 | 25.6 |
| Fkh1:Fkh2 | TTGTTTACST:TTGTTTACST | TTGTTTA:TGTTTA | 1 | 17.0 |
| Msn4:Swi5 | CCCCT:KGCTGR | CCCTg:caGCcGc | 16.7 | |
| Fkh2:Swi6 | TTGTTTACST:ACGCGT | TGTTTAC:ACGCG | 16.2 | |
| Fkh2:Mbp1 | TTGTTTACST:ACGCGTnA | TTGTTTA:gACGCG | 16.1 | |
| Ste12:Swi6 | RTGAAACA:ACGCGT | cAcGAAA:ACGCG | 14.2 | |
| Pdr1:Rap1 | CCGCGG:ACACCCATACATTT | GCGG:ACCCA | 14.0 | |
| Cup9:Yap6 | N.A.:N.A. | GGCAC:TGCAGG | 13.7 | |
| Rlm1:Swi6 | CTAWWWWTAG:ACGCGT | AAACTA:aACGCG | 13.6 | |
| Fkh1:Swi6 | TTGTTTACST:ACGCGT | TTGTTTA:ACGCG | 13.5 | |
| Mcm1:Swi6 | TTWCCCnWWWRGGAAA:ACGCGT | ATCGGGA:ACGCG | 12.9 | |
| Fkh2:Mcm1 | TTGTTTACST:TTWCCCnWWWRGGAAA | TGTTTAC:TAGGA | 1 | 11.3 |
| Ace2:Fkh1 | GCTGGT:TTGTTTACST | GCTGGTt:TcTTTAg | 11.2 | |
| Ino2:Ino4 | CATGTGAAAT:CATGTGAAAT | CATGTGA:caCATGC | 1 | 10.4 |
| Msn4:Rap1 | CCCCT:ACACCCATACATTT | CACCCA:CCCCCA | 9.4 | |
| Mcm1:Ste12 | TTWCCCnWWWRGGAAA:RTGAAACA | GGAAAtt:TGAAACA | 1 | 9.2 |