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Systematic Name Gene Name Motif ID Expert Confidence Dubious? Notes
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 YOR363C PIP2 0     See Oaf1-Pip2-dimer
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 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 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 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 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 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 YJL176C SWI3 0   Dubious Unlikely to be true TF.
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 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 YGR288W MAL13 0     None of the ChIP-chip motifs correspond wekk to the data they come from and/or resemble a GAL4 motif.
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 YBR297W MAL33 0     None of the ChIP-chip motifs correspond wekk to the data they come from and/or resemble a GAL4 motif.
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 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 YOR162C YRR1 2245 High   Classic monomeric GAL4-class motif. PBM studies agree and score significantly on Harbison data. No other motifs have spacing/orientation except 11909958, but even the authors of this study note that "Only half a dyad seems to be conserved in this consensus sequence". 2245 scores highest in Harbison data.
V YDR207C UME6 2239 High   All motifs are similar to each other. BEEML-PBM motif 2239 scores highest across the board.
V YPR009W SUT2 2236 High   Highest-scoring motif (PBM) is a classical GAL4-type monomeric motif and is very significant in ChIP-chip
V YDR169C STB3 2233 High   STB3 binds RRPE element (AAAAATTT) both in vivo and in vitro (PMID 17616518). PBM motifs 810 and 2233 strongly resembles the RRPE element, scores significantly in deletion expression data, and nail the GO categories "nucleolus" and "ribosome biogenesis". 2233 gets slightly higher scores.
V YKL038W RGT1 2227 High   PBM motif 2227 is very similar to "traditional" motif and to monomeric GAL4 motifs, and scores highest on ChIP-chip data. All PBM motifs are similar.
V YFR034C PHO4 2222 High   Almost all motifs match classic HLH E-box. PBM motif 2222 has highest match to both ChIP-chip and expression data, without being circular.
V YER088C DOT6 2221 High   PBM motif 812 most closely resembles that of homolog TOD6, which is well-supported; has highest correlation to both ChIP and expression data.
V YPL248C GAL4 2206 High   ChIP-chip motif 1510 resembles literature motif, and PBM motif 875, but scores highly on ChIP and expression data, across the board. Note, however, that the high ChIP-chip scores stem from an experiment with high negative correlation. PBM motif 2206 appears to be a monomeric version, socres even higher on ChIP-chip and expression.
V YPR104C FHL1 2203 High   ChIP-chip motifs are all Rap1. PBMs identify a different motif which also corresponds to ChIP-chip data. Selected 2203 as it scores highest on ChIP-chip and expression data.
V YML081W   2194 High   PBM motifs are a classical C2H2 motif that match each other and have some correspondence to ChIP-chip data. 2194 has highest correspondence to ChIP chip.
V YKL222C   2192 High   Two motifs from PBMs resemble monomeric GAL4-like motif. 2192 agrees best with ChIP-chip data and expression data.
V YGR067C   2191 High   PBM motif is a classical C2H2 motif that has good correspondence to ChIP-chip data. 2191 corresponds best and has fewer empty columns in the PWM.
V YML007W YAP1 2186 High   PBM motif 2186 looks like a monomeric bZIP site but it has the highest scores on both ChIP and expression
V YBR150C TBS1 2179 High   Two motifs from PBMs are nearly identical GAL4-class motifs with defined spacing and orientation. Motif 552 has slightly higher scores. Two motifs from BEEML analysis of PBM data give monomeric motif - also give this high confidence.
V YPL128C TBF1 2178 High   All motifs, obtained by three different means, are all very similar, although there is no ChIP or expression support for any of them. Went with 2178, which is the BEEML output.
V YHR006W STP2 2174 High   STP1 and 2 have very similar DNA-binding domains. However, they are not similar to those of STP3 and 4. PBM motif for STP2 (2174) correlates highest with ChIP-chip and expression data. ChIP-chip motif for STP1 (660) most strongly resembles motif 800, and scores highly on ChIP-chip data. In addition, these motifs resemble halfmers of literature-derived binding sites.
V YOR380W RDR1 2158 High   All motifs are related except 1851. PBM motif 2158 is monomeric and has highest correspondence to ChIP-chip data. The literature motif 756 consists of two back-to-back and slightly overlapping versions of the monomeric PBM motif. There is no evidence for direct binding in this specific spacing and orientation; however, the results of mutations in reporters indicate that both copies are necessary for induction in the mutant. Retain both motifs.
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