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Systematic Name Gene Name Motif ID Expert Confidence Dubious? Notes
V YPL216W   0   Dubious Unlikely to be true TF.
V YPL016W SWI1 0   Dubious Unlikely to be true TF.
V YOR308C SNU66 0   Dubious Unlikely to be true TF.
V YOR304W ISW2 0   Dubious Unlikely to be true TF.
V YOR290C SNF2 0   Dubious Unlikely to be true TF.
V YOR156C NFI1 0   Dubious Unlikely to be true TF.
V YNL227C JJJ1 0   Dubious Unlikely to be true TF.
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 YLR254C NDL1 0   Dubious Unlikely to be true TF.
V YLR211C   0   Dubious Unlikely to be true TF.
V YJL176C SWI3 0   Dubious Unlikely to be true TF.
V YIL122W POG1 0   Dubious Unlikely to be true TF.
V YGR140W CBF2 0   Dubious Unlikely to be true TF.
V YGR071C   0   Dubious Unlikely to be true TF.
V YGR002C SWC4 0   Dubious Unlikely to be true TF.
V YGL133W ITC1 0   Dubious Unlikely to be true TF.
V YFR037C RSC8 0   Dubious Unlikely to be true TF.
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 YDR225W HTA1 0   Dubious Unlikely to be true TF.
V YDL074C BRE1 0   Dubious Unlikely to be true TF.
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 YBL003C HTA2 0   Dubious Unlikely to be true TF.
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 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 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 YLR113W HOG1 0   Dubious This is a signalling molecule that associates with many TFs (see SGD)
V YOR298C-A MBF1 0   Dubious This is a coactivator. I found no evidence that it is a sequence-specific 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 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 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 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 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 YGR040W KSS1 0   Dubious There is no evidence that Kss1 is a sequence-specific TF.
V YLR182W SWI6 0   Dubious Swi6 is a cofactor, not a DNA-binding protein. These motifs are for Mbp1 or Swi4.
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 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 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 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 YOR363C PIP2 0     See Oaf1-Pip2-dimer
V MBP1-SWI6-dimer MBP1-SWI6-dimer 0     Redundant with MBP1
V YFL052W   0   Dubious Putative zinc-cluster protein.
V YPL049C DIG1 0   Dubious Not a TF - it binds Ste12; all the motifs are Ste12 motifs.
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 YDR049W   0   Dubious No evidence this is a TF, aside from a poorly-scoring C2H2 zinc finger
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 MATA1   0     Need to study literature more carefully and consult experts.but at first glance none of these motifs seems right
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 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 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 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 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 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 YJR094C IME1 0   Dubious Interacts with UME6. The only significant motif shares 5/6 bases with the UME6 motif core (GCCGCC)
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 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 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 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 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 YJR140C HIR3 0   Dubious Hir1,2,3 are a nucleosome assembly complex, not TFs
V YBL008W HIR1 0   Dubious Hir1,2,3 are a nucleosome assembly complex, not TFs
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 YML051W GAL80 0   Dubious Gal80 is not a sequence-specific DNA-binding protein
V YDR009W GAL3 0   Dubious Gal3 is not a sequence-specific DNA-binding protein
V YLR223C IFH1 0   Dubious Cofactor of Fhl1p. No evidence for sequence-specific DNA-binding.
V YKL032C IXR1 0   Dubious Binds cisplatin-modified DNA. HMG domains. ChIP-chip motifs not significant. Dubious and no credible motif.
V YEL009C GCN4 1363 High   Virtually all motifs look the same. MITOMI motif 1363 is as good as any of the ChIP-chip motifs but not circular; scores high across the board.
V YKR099W BAS1 402 High   Virtually all motifs are similar, with GAGTCA core. ChIP motif 402 has highest correspondence to both ChIP-chip and expression data.
V YOR172W YRM1 813 High   Two PBM studies largely agree on classic GAL4-class monomeric motif. Motif 813 has indications of spacing and orientation of dimeric protein.
V YPL230W USV1 509 High   Two PBM studies essentially agree on classical C2H2 GGGG-containing motif. Chose 509 because it scores much higher on both ChIP and expression data.
V YML027W YOX1 498 High   Two PBM studies and Pramila et al. (PMID 12464633) agree on classic homeodomain TAATTA motif. All three correlate with expression change and OE. Motif 453 is not a direct measurement so choose PBM motif that is the same length as the typical homeodomain footprint - 498 also correlates best with OE data; expression scores are skewed low by the large number of cell-cycle measurements.
V YIR013C GAT4 565 High   Two PBM motifs look similar, also similar to a subset of other GATAs. 565 scores higher on expression and OE data.
V YBL054W TOD6 852 High   Two PBM motifs largely agree; 852 has higher correspondence to expression data while 495 has higher correspondence to ChIP-chip. Use 852; score is way higher. Also for GO.
V YMR168C CEP3 524 High   Two PBM motifs agree. Went with 524 because it appears neater. No other supporting data for any of them.
V YLR098C CHA4 2120 High   Two PBM motifs agree, and PBM motif 2120 has highest correspondence to ChIP-chip data, even highter than the best ChIP-chip motif. Has a GAL4-like appearance, albeit a variant. Monomeric. (Highest scoring motif - 1607 - is actually a Rap1 motif).
V YKL222C   2192 High   Two motifs from PBMs resemble monomeric GAL4-like motif. 2192 agrees best with ChIP-chip data and expression data.
V YBR150C TBS1 552 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 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 YDR026C   696 High   Three ChIP-chip motifs are virtually identical in appearance; resemble Reb1 motifs; high correspondence to ChIP-chip data
V YDR310C SUM1 478 High   This is the motif for the SUM1 AT_hook; scores highest in deletion expression data
V YDR310C SUM1 383 High   This is the motif for the FL SUM1; scores highest on ChIP-chip and resembles the canonical literature motif; also has some relationship to deletion expression data
V YER148W SPT15 798 High   This is TATA-binding protein. PBM motif 798 chosen because 1326 was derived from the 96-sequence TIRF-PBM array instead of a full 40K PBM
V YDR520C URC2 553 High   This is a monomeric GAL4-class motif. Two PBM studies essentially agree, and have some relationship to ChIP-chip data. No other informative data.
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