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Systematic Name Gene Name Motif ID Expert Confidence Dubious? Notes
V MATA1   0     Need to study literature more carefully and consult experts.but at first glance none of these motifs seems right
V MBP1-SWI6-dimer MBP1-SWI6-dimer 0     Redundant with MBP1
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 YGR288W MAL13 0     None of the ChIP-chip motifs correspond wekk to the data they come from and/or resemble a GAL4 motif.
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 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 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 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 YOR363C PIP2 0     See Oaf1-Pip2-dimer
V YBL003C HTA2 0   Dubious Unlikely to be true TF.
V YBL008W HIR1 0   Dubious Hir1,2,3 are a nucleosome assembly complex, not TFs
V YBL052C SAS3 0   Dubious Unlikely to be true TF.
V YBR060C ORC2 0   Dubious Unlikely to be true TF.
V YCR033W SNT1 0   Dubious Unlikely to be true TF.
V YCR066W RAD18 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 YDL074C BRE1 0   Dubious Unlikely to be true TF.
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 YDR009W GAL3 0   Dubious Gal3 is not a sequence-specific DNA-binding protein
V YDR049W   0   Dubious No evidence this is a TF, aside from a poorly-scoring C2H2 zinc finger
V YDR225W HTA1 0   Dubious Unlikely to be true TF.
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 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 YDR323C PEP7 0   Dubious Unlikely to be true TF.
V YDR362C TFC6 0   Dubious Unlikely to be true TF.
V YDR409W SIZ1 0   Dubious Unlikely to be true TF.
V YDR448W ADA2 0   Dubious Unlikely to be true TF.
V YDR485C VPS72 0   Dubious Unlikely to be true TF.
V YER063W THO1 0   Dubious Unlikely to be true TF.
V YER159C BUR6 0   Dubious Unlikely to be true TF.
V YER164W CHD1 0   Dubious Unlikely to be true TF.
V YFL052W   0   Dubious Putative zinc-cluster protein.
V YFR037C RSC8 0   Dubious Unlikely to be true TF.
V YGL133W ITC1 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 YGR002C SWC4 0   Dubious Unlikely to be true TF.
V YGR040W KSS1 0   Dubious There is no evidence that Kss1 is a sequence-specific TF.
V YGR071C   0   Dubious Unlikely to be true TF.
V YGR089W NNF2 0   Dubious I did not find any evidence that this is a sequence-specific DNA-binding protein.
V YGR097W ASK10 0   Dubious I did not find any evidence that this is a sequence-specific DNA-binding protein.
V YGR140W CBF2 0   Dubious Unlikely to be true TF.
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 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 YIL122W POG1 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 YJL176C SWI3 0   Dubious Unlikely to be true TF.
V YJR094C IME1 0   Dubious Interacts with UME6. The only significant motif shares 5/6 bases with the UME6 motif core (GCCGCC)
V YJR140C HIR3 0   Dubious Hir1,2,3 are a nucleosome assembly complex, not TFs
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 YKL032C IXR1 0   Dubious Binds cisplatin-modified DNA. HMG domains. ChIP-chip motifs not significant. Dubious and no credible motif.
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 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 YLR113W HOG1 0   Dubious This is a signalling molecule that associates with many TFs (see SGD)
V YLR182W SWI6 0   Dubious Swi6 is a cofactor, not a DNA-binding protein. These motifs are for Mbp1 or Swi4.
V YLR211C   0   Dubious Unlikely to be true TF.
V YLR223C IFH1 0   Dubious Cofactor of Fhl1p. No evidence for sequence-specific DNA-binding.
V YLR254C NDL1 0   Dubious Unlikely to be true TF.
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 YML051W GAL80 0   Dubious Gal80 is not a sequence-specific DNA-binding protein
V YMR172W HOT1 0   Dubious Unlikely to be true TF.
V YMR176W ECM5 0   Dubious Unlikely to be true TF.
V YMR213W CEF1 0   Dubious Unlikely to be true TF.
V YNL023C FAP1 0   Dubious Unlikely to be true TF.
V YNL039W BDP1 0   Dubious Unlikely to be true TF.
V YNL079C TPM1 0   Dubious Unlikely to be true TF.
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 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 YNL227C JJJ1 0   Dubious Unlikely to be true TF.
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 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 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 YOR038C HIR2 0   Dubious Hir1,2,3 are a nucleosome assembly complex, not TFs
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 YOR156C NFI1 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 YOR290C SNF2 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 YOR304W ISW2 0   Dubious Unlikely to be true TF.
V YOR308C SNU66 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 YPL016W SWI1 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 YPL216W   0   Dubious Unlikely to be true TF.
V YBL021C HAP3 695 High   Subunit of the heme-activated, glucose-repressed Hap2/3/4/5 CCAAT-binding complex - there should be a single motif for all four proteins, containing CCAAT. ChIP-chip motif 695 resembles CCAATCA, and scores highly on ChIP-chip, OE, and deletion expression 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 YBR033W EDS1 2093 High   PBM and ChIP-chip motifs are very similar. PBM motif 2093 scores most significantly on ChIP data. Classic GAL4 class motif.
V YBR049C REB1 907 High   All motifs are similar. ChIP-chip motif 907 has highest correspondence to both ChIP-chip and expression data, and strongly resembles MITOMI and PBM motifs.
V YBR066C NRG2 1383 High   MITOMI motif 1383 looks like a classic yeast C2H2 binding site (row of G's). Also resembles motifs obtained by both ChIP and PBMs for related protein Nrg1.
V YBR083W TEC1 815 High   All motifs agree, and are significant by several criteria. PBM motif 815 has the second-highest scores overall, and it is non-circular for in vivo binding. Also has highest GO score.
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 YBR240C THI2 1449 High   This is a GAL4-class protein. All motifs are ChIP-chip derived, none resembles each other. 1449 is the only one with respectable scores on ChIP and expression,and it also has the appearance of a GAL4 class motif..although, the structural prior presumably forces it to have this property.
V YBR267W REI1 489 High   PBM motif looks like a yeast C2H2 motif (row of C's); highly significant relationship to ChIP-chip data
V YCR039C MATALPHA2 1364 High   According to PMID: 9858582, "A comparison of the 2 binding sites in both asg and hsg operators yields the same consensus sequence, 5'-CATGTA-3"; results in Figure 2 of the same paper support a consensus of CATGTAA. MITOMI yields ACATG, which is the reverse complement of most of the literature consensus. Motif 1364 has highest information content; use this.
V YCR065W HCM1 570 High   PBM and SAAB/EMSA motifs both look similar to standard FH motif. PBM motif 570 has stronger correspondence to expression data.
V YCR106W RDS1 506 High   All motifs look similar. PBM motif 506 has a higher score on ChIP-chip than any of the ChIP-chip derived motifs.
V YDL020C RPN4 1700 High   In vitro motifs do not contain the TTT sequence on the end. But they were derived from the DBD only. The rest of the protein may contribute to binding the TTT segment. Motif 1700 has the highest correspondence to ChIP-chip and expression and GO.
V YDL056W MBP1 2138 High   Almost all motifs look similar to literature binding site. PBM motif 2138 scores at the top on ChIP-chip and expression. And is non-circular.
V YDL106C PHO2 2154 High   Motifs are largely all different from each other. PBM motif 2154 scores highly on ChIP data and resembles classic TAAT homeobox core. Note that PBM motif 794 even more strongly resembles homeobox (TAATTA) but scores slightly less highly.
V YDL170W UGA3 651 High   Appears to be a dimeric GAL4-class motif. Scores highest in ChIP-chip data, but is derived from the same data. GO seems to match known function!
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