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Systematic Name Gene Name Motif ID Expert Confidence Dubious? Notes
V YOR363C PIP2 0     See Oaf1-Pip2-dimer
V YNL103W MET4 0     My understanding is that Met4 is a modifier of the specificity of other proteins. SGD states that it "requires different combinations of the auxiliary factors Cbf1p, Met28p, Met31p and Met32p". ChIP-chip motifs 1023 and 1024 I believe are cofactor motifs; they are E-boxes. ChIP-chip motif 689 is different and matches Met28 and Met32 motifs. (CTGTGG core). Met28 is a bZIP protein, and Met32 is a C2H2. MITOMI motif for Met32 is TGTGG. So this is the Met32 motif. I do not believe that any of the Met4 motifs is correct. Need to obtain motifs for complexes.
V YKR064W OAF3 0     I do not see how either of these motifs could possibly be a Gal4-class binding motif. And, there is no correspondence to any of the data, even the ChIP-chip data from which it is derived.
V YJL206C   0     Seven motifs from ChIP-chip, but none of them corresponds well to ChIP-chip data, and none of them resembles a GAL4 motif. 1169 has a CGG in the middle, but too much flanking information to be credible without further independent support.
V YIR017C MET28 0     Like MET4, component of a complex. SGD: "Basic leucine zipper (bZIP) transcriptional activator in the Cbf1p-Met4p-Met28p complex".."Both Met4p and Met28p bind to DNA only in the presence of Cbf1p, and the presence of Cbf1p and Met4p stimulates the binding of Met28p to DNA (1, 2).". ChIP-chip motif 703 (CTGTGG) is clearly the Met31/32 motif. The other ChIP-chip motif is essentially poly-A, and scores poorly. Hence, neither of these motifs represents the intrinsic sequence specificity of MET28. Need in vitro data for complexes.
V YGR288W MAL13 0     None of the ChIP-chip motifs correspond wekk to the data they come from and/or resemble a GAL4 motif.
V YBR297W MAL33 0     None of the ChIP-chip motifs correspond wekk to the data they come from and/or resemble a GAL4 motif.
V MBP1-SWI6-dimer MBP1-SWI6-dimer 0     Redundant with MBP1
V MATA1   0     Need to study literature more carefully and consult experts.but at first glance none of these motifs seems right
V YPL216W   0   Dubious Unlikely to be true TF.
V YPL049C DIG1 0   Dubious Not a TF - it binds Ste12; all the motifs are Ste12 motifs.
V YPL016W SWI1 0   Dubious Unlikely to be true TF.
V YOR372C NDD1 0   Dubious There is no evidence that this is a sequence-specific DNA-binding protein, either in vitro or in vivo or in its sequence. The ChIP-chip motif that scores most highly is actually an MCM1 motif, which is consistent with the role of NDD1 as a "transcriptional activator essential for nuclear division".
V YOR308C SNU66 0   Dubious Unlikely to be true TF.
V YOR304W ISW2 0   Dubious Unlikely to be true TF.
V YOR298C-A MBF1 0   Dubious This is a coactivator. I found no evidence that it is a sequence-specific TF.
V YOR290C SNF2 0   Dubious Unlikely to be true TF.
V YOR229W WTM2 0   Dubious It is not clear that this is a sequence-specific DNA-binding protein; it contains no DNA-binding domain and has no known in vitro sequence specificity. The motif comes only from ChIP-chip so scoring on ChIP-chip is circular.
V YOR156C NFI1 0   Dubious Unlikely to be true TF.
V YOR077W RTS2 0   Dubious Homolog of Kin17; not a typical C2H2 zinc finger. Believed to be "chromatin-associated proteins involved in UV response and DNA replication". No evidence for sequence-specific DNA-binding. Single ChIP-chip motif does not have strong correspondence to the data from which it is derived.
V YOR038C HIR2 0   Dubious Hir1,2,3 are a nucleosome assembly complex, not TFs
V YNR054C ESF2 0   Dubious This is supposed to be a ribosome biogenesis factor. I found no evidence that it is a sequence-specific DNA-binding protein.
V YNL309W STB1 0   Dubious No direct evidence that this is a DNA-binding protein. It binds Swi6 and the ChIP motifs all resemble Swi4 binding sites.
V YNL257C SIP3 0   Dubious Sip3 is a protein that "transcription through interaction with DNA-bound Snf1p" (SGD); no DNA-binding domain and no evidence for direct interaction with DNA or intrinsic sequence specificity.
V YNL227C JJJ1 0   Dubious Unlikely to be true TF.
V YNL199C GCR2 0   Dubious Gcr2 is not a DNA-binding protein. SGD: "Gcr1p is a DNA-binding protein interacting with the consensus sequence CTTCC, whereas Gcr2p interacts with Gcr1p". But, ChIP-chip motif 606 is probably the best Gcr1 motif available (even though it came from Gcr2 ChIP).
V YNL132W KRE33 0   Dubious This is supposed to be a ribosome biogenesis factor. I found no evidence that it is a sequence-specific DNA-binding protein.
V YNL079C TPM1 0   Dubious Unlikely to be true TF.
V YNL039W BDP1 0   Dubious Unlikely to be true TF.
V YNL023C FAP1 0   Dubious Unlikely to be true TF.
V YMR213W CEF1 0   Dubious Unlikely to be true TF.
V YMR176W ECM5 0   Dubious Unlikely to be true TF.
V YMR172W HOT1 0   Dubious Unlikely to be true TF.
V YML051W GAL80 0   Dubious Gal80 is not a sequence-specific DNA-binding protein
V YLR442C SIR3 0   Dubious There is no evidence that the SIR proteins are sequence-specific DNA-binding proteins. Most of the motifs for them are Rap1 sites.
V YLR254C NDL1 0   Dubious Unlikely to be true TF.
V YLR223C IFH1 0   Dubious Cofactor of Fhl1p. No evidence for sequence-specific DNA-binding.
V YLR211C   0   Dubious Unlikely to be true TF.
V YLR182W SWI6 0   Dubious Swi6 is a cofactor, not a DNA-binding protein. These motifs are for Mbp1 or Swi4.
V YLR113W HOG1 0   Dubious This is a signalling molecule that associates with many TFs (see SGD)
V YKR101W SIR1 0   Dubious There is no evidence that the SIR proteins are sequence-specific DNA-binding proteins. Most of the motifs for them are Rap1 sites.
V YKL072W STB6 0   Dubious It is not clear that this is a sequence-specific DNA-binding protein; it contains no DNA-binding domain and has no known in vitro sequence specificity. The motif comes only from ChIP-chip so scoring on ChIP-chip is circular. The ChIP-chip motif looks a little like a Rap1 motif.
V YKL032C IXR1 0   Dubious Binds cisplatin-modified DNA. HMG domains. ChIP-chip motifs not significant. Dubious and no credible motif.
V YKL005C BYE1 0   Dubious SGD: "Negative regulator of transcription elongation, contains a TFIIS-like domain and a PHD finger, multicopy suppressor of temperature-sensitive ess1 mutations, probably binds RNA polymerase II large subunit". No evidence this is a sequence-specific TF.
V YJR140C HIR3 0   Dubious Hir1,2,3 are a nucleosome assembly complex, not TFs
V YJR094C IME1 0   Dubious Interacts with UME6. The only significant motif shares 5/6 bases with the UME6 motif core (GCCGCC)
V YJL176C SWI3 0   Dubious Unlikely to be true TF.
V YIL128W MET18 0   Dubious I found no evidence that this is a sequence-specific DNA-binding protein. ChIP-chip motif does not correlate with ChIP-chip data, or anything else.
V YIL122W POG1 0   Dubious Unlikely to be true TF.
V YIL119C RPI1 0   Dubious It is not clear that this is a sequence-specific DNA-binding protein; it contains no DNA-binding domain and has no known in vitro sequence specificity. The motif comes only from ChIP-chip so scoring on ChIP-chip is circular.
V YHL020C OPI1 0   Dubious Motifs do not match and do not explain the ChIP-chip data from which they are derived. Motif 1049 resembles the expected UAS-INO (Ino2/4) binding site (CATGTGAAAT) - Opi1 acts as a repressor by binding Ino2. I believe this protein is a corepressor, and Ino2/4 are the DNA-binding factors. Dubious as sequence-specific TF.
V YGR140W CBF2 0   Dubious Unlikely to be true TF.
V YGR097W ASK10 0   Dubious I did not find any evidence that this is a sequence-specific DNA-binding protein.
V YGR089W NNF2 0   Dubious I did not find any evidence that this is a sequence-specific DNA-binding protein.
V YGR071C   0   Dubious Unlikely to be true TF.
V YGR040W KSS1 0   Dubious There is no evidence that Kss1 is a sequence-specific TF.
V YGR002C SWC4 0   Dubious Unlikely to be true TF.
V YGL197W MDS3 0   Dubious I found no evidence that this is a sequence-specific DNA-binding protein. ChIP-chip motif does not correlate with ChIP-chip data, or anything else.
V YGL133W ITC1 0   Dubious Unlikely to be true TF.
V YFR037C RSC8 0   Dubious Unlikely to be true TF.
V YFL052W   0   Dubious Putative zinc-cluster protein.
V YER164W CHD1 0   Dubious Unlikely to be true TF.
V YER159C BUR6 0   Dubious Unlikely to be true TF.
V YER063W THO1 0   Dubious Unlikely to be true TF.
V YDR485C VPS72 0   Dubious Unlikely to be true TF.
V YDR448W ADA2 0   Dubious Unlikely to be true TF.
V YDR409W SIZ1 0   Dubious Unlikely to be true TF.
V YDR362C TFC6 0   Dubious Unlikely to be true TF.
V YDR323C PEP7 0   Dubious Unlikely to be true TF.
V YDR277C MTH1 0   Dubious SGD: "interacts with Rgt1p and the Snf3p and Rgt2p glucose sensors". There is no evidence that this is a sequence-specific transcription factor.
V YDR227W SIR4 0   Dubious There is no evidence that the SIR proteins are sequence-specific DNA-binding proteins. Most of the motifs for them are Rap1 sites.
V YDR225W HTA1 0   Dubious Unlikely to be true TF.
V YDR049W   0   Dubious No evidence this is a TF, aside from a poorly-scoring C2H2 zinc finger
V YDR009W GAL3 0   Dubious Gal3 is not a sequence-specific DNA-binding protein
V YDL166C FAP7 0   Dubious This is supposed to be a ribosome biogenesis factor. I found no evidence that it is a sequence-specific DNA-binding protein.
V YDL074C BRE1 0   Dubious Unlikely to be true TF.
V YDL042C SIR2 0   Dubious There is no evidence that the SIR proteins are sequence-specific DNA-binding proteins. Most of the motifs for them are Rap1 sites.
V YCR066W RAD18 0   Dubious Unlikely to be true TF.
V YCR033W SNT1 0   Dubious Unlikely to be true TF.
V YBR060C ORC2 0   Dubious Unlikely to be true TF.
V YBL052C SAS3 0   Dubious Unlikely to be true TF.
V YBL008W HIR1 0   Dubious Hir1,2,3 are a nucleosome assembly complex, not TFs
V YBL003C HTA2 0   Dubious Unlikely to be true TF.
V YER045C ACA1 8 Medium   Literature motif 8 is supported by experimental investigation, and resembles a bZIP site, but has no other support; motif was not obtained objectively. Can bind as heterodimer. The highest-scoring motif (from ChIP, 1457) has low information content - I'm concerned it is learning other features of bound promoters.
V YKL185W ASH1 28 Medium   The literature motif may not represent the full binding activity of the protein. Also, it is not supported by ChIP-chip. ChIP-chip identifies Mcm1-like motifs. But, it does score highly in both ChIP-chip and expression. The only higher-scoring motif has almost no information content.
V YMR280C CAT8 33 Medium   Near-classic dimeric GAL4 motif. Literature-based. Not clear this is an optimal site but it does bind. Seems to hit the right GO category.
V YGL166W CUP2 48 Medium   Three motifs account for three possible spacings in the literature motif; it is not clear that this is the optimal site, however
V YIR023W DAL81 53 Low   None of the motifs agree with each other. The literature motif characterization was indirect; hence low confidence that this is the true motif. The ChIP-chip motifs score higher on ChIP data but that's circular.
V YER109C FLO8 67 Low Dubious I found no evidence that this is a sequence-specific DNA-binding protein, i.e. that it binds directly to DNA in vitro. The motif has a limited relationship to ChIP-chip data. The literature motif scores better than the motif derived from the ChIP-chip study. Also, the motif is identical to that for MSS11.
V YGL254W FZF1 69 Low   Literature motif is the only one that appears credible. PBM motif I believe is a known artifact. Literature motif gets low confidence however as it is based on a single known binding sequence.
V YFL031W HAC1 94 Medium   1788 is the overall winner. But, literature motif 94 also scores well in ChIP-chip, despite being somewhat different. Possible difference in heterodimerazation partners, or proteolytic fragment? Retain both.
V YCL055W KAR4 127 Low Dubious Evidence for sequence specific DNA binding seems weak, hence low confidence
V YDR034C LYS14 133 High   PBM motifs are virtually identical and appear monomeric; literature motif is dimeric. Include both. Choose PBM motif 865 as it appears to have more robust CGG.
V MAL63   136 Medium   This is an unconventional dimeric GAL4-class motif
V YMR164C MSS11 204 Low Dubious There is no evidence that this is a sequence-specific DNA-binding protein, rather than a cofactor. The motif has a limited relationship to ChIP-chip data. The literature motif scores better than the motif derived from the ChIP-chip study. Also, the motif is identical to that for FLO8.
V YLR266C PDR8 244 Medium   Both motifs are equally credible but have very limited support. Literature motif is related to that of YRR1 literature motif. PBM motif, however, is a classic GAL4 monomer. This is the literature motif.
V YNL216W RAP1 254 High   Most motifs look similar. ChIP-chip motif 254 has highest correspondence to expression data.
V YGR044C RME1 273 Low   Motif 273 shows similarity to RME response elements (RREs), GTACC(T/A)ACAAAA (in fact it is derived from them). The fact that RME has three C2H2 zinc fingers and also requires an additional C-terminal region for binding in vitro, together with its relatively large footprint, are consistent with such a large binding site. However, I gave this motif a "low" score as there is no systematic analysis in vivo or in vitro indicating that these are really the most preferred sites. It would be valuable to redo the in vitro and in vivo experiments under appropriate conditions.
V YML076C WAR1 325 Low   None of the motifs are convincing, but at least sequences with the literature motif have been experimentally confirmed to bind the protein (even if it is not shown that this is the optimal binding site)
V YLR403W SFP1 357 Incorrect   Likely represents Rap1 binding site.
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