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Systematic Name Gene Name Motif ID Expert Confidence Dubious? Notes
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 YDR485C VPS72 0   Dubious Unlikely to be true TF.
V YNL079C TPM1 0   Dubious Unlikely to be true TF.
V YER063W THO1 0   Dubious Unlikely to be true TF.
V YDR362C TFC6 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 YJL176C SWI3 0   Dubious Unlikely to be true TF.
V YPL016W SWI1 0   Dubious Unlikely to be true TF.
V YGR002C SWC4 0   Dubious Unlikely to be true TF.
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 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 YOR308C SNU66 0   Dubious Unlikely to be true TF.
V YCR033W SNT1 0   Dubious Unlikely to be true TF.
V YOR290C SNF2 0   Dubious Unlikely to be true TF.
V YDR409W SIZ1 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 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 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 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 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 YBL052C SAS3 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 YFR037C RSC8 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 YCR066W RAD18 0   Dubious Unlikely to be true TF.
V YIL122W POG1 0   Dubious Unlikely to be true TF.
V YOR363C PIP2 0     See Oaf1-Pip2-dimer
V YDR323C PEP7 0   Dubious Unlikely to be true TF.
V YBR060C ORC2 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 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 YGR089W NNF2 0   Dubious I did not find any evidence that this is a sequence-specific DNA-binding protein.
V YOR156C NFI1 0   Dubious Unlikely to be true TF.
V YLR254C NDL1 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 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 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 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 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 MBP1-SWI6-dimer MBP1-SWI6-dimer 0     Redundant with MBP1
V YOR298C-A MBF1 0   Dubious This is a coactivator. I found no evidence that it is a sequence-specific 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 YGR288W MAL13 0     None of the ChIP-chip motifs correspond wekk to the data they come from and/or resemble a GAL4 motif.
V YGR040W KSS1 0   Dubious There is no evidence that Kss1 is a sequence-specific 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 YNL227C JJJ1 0   Dubious Unlikely to be true TF.
V YKL032C IXR1 0   Dubious Binds cisplatin-modified DNA. HMG domains. ChIP-chip motifs not significant. Dubious and no credible motif.
V YGL133W ITC1 0   Dubious Unlikely to be true TF.
V YOR304W ISW2 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 YLR223C IFH1 0   Dubious Cofactor of Fhl1p. No evidence for sequence-specific DNA-binding.
V YBL003C HTA2 0   Dubious Unlikely to be true TF.
V YDR225W HTA1 0   Dubious Unlikely to be true TF.
V YMR172W HOT1 0   Dubious Unlikely to be true TF.
V YLR113W HOG1 0   Dubious This is a signalling molecule that associates with many TFs (see SGD)
V YJR140C HIR3 0   Dubious Hir1,2,3 are a nucleosome assembly complex, not TFs
V YOR038C HIR2 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 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 YNL023C FAP1 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 YMR176W ECM5 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 YER164W CHD1 0   Dubious Unlikely to be true TF.
V YMR213W CEF1 0   Dubious Unlikely to be true TF.
V YGR140W CBF2 0   Dubious Unlikely to be true TF.
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 YER159C BUR6 0   Dubious Unlikely to be true TF.
V YDL074C BRE1 0   Dubious Unlikely to be true TF.
V YNL039W BDP1 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 YDR448W ADA2 0   Dubious Unlikely to be true TF.
V YPL216W   0   Dubious Unlikely to be true TF.
V YLR211C   0   Dubious Unlikely to be true TF.
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 YGR071C   0   Dubious Unlikely to be true TF.
V YFL052W   0   Dubious Putative zinc-cluster protein.
V YDR049W   0   Dubious No evidence this is a TF, aside from a poorly-scoring C2H2 zinc finger
V MATA1   0     Need to study literature more carefully and consult experts.but at first glance none of these motifs seems right
V YJL056C ZAP1 2097 High   Most motifs are similar but do not exceed confidence thresholds on any data type. PBM motif 2097 has highest score for ChIP and expression, and is not circular
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 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 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 YDR451C YHP1 716 High   ChIP-chip, EMSA, and one-hybrid all arrive at a classic homeodomain TAATTG motif. Microarray enrichment motif (716) scores higher on OE data from another study than ChIP motifs do, and does nearly as well on ChIP data.
V YOL028C YAP7 1414 High   8-base bZIP core. Obtained by Mitomi, so this is a homodimer. Higher correspondence to unstressed ChIP-chip data. Little literature on this protein. 1414 chosen for higher ChIP-chip overall scores; plus, it is a palindrome as expected for a bZIP protein.
V YOL028C YAP7 1737 High   7-base bZIP core. Obtained in ChIP-chip studies and higher correspondence to stressed ChIP-chip data. Possible heterodimer? Little literature on this protein. 1737 chosen because it is largely symmetric and has highest score for both stressed and unstressed Harbison data, also, higher GO score
V YDR259C YAP6 599 High   PBM and ChIP-chip can derive basically the same motif, which is a classical YAP motif. They score similarly on all criteria. The ChIP-chip motif (599) has fewer low-information flanking bases.
V YIR018W YAP5 777 High   ChIP-chip yields a classic 7-mer Yap motif that scores well on ChIP and significantly on expression.
V YHL009C YAP3 672 High   ChIP-chip yields a classic 7-mer Yap motif that scores well on ChIP and significantly on expression. Could be a heterodimer. Chose 672 over 1463 because it has a higher score on expression data, which is independent.
V YHL009C YAP3 1411 High   Mitomi yields a nearly palindromic 8-mer motif with strong similarity to that of Yap6. PBM motif is similar but appears to be partial.
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 YIL101C XBP1 2039 High   PBM and in vitro selection-derived motifs have highest scores across the board. 842 is higher on GO, but only slightly in AUC, and it has a very large number of empty flanking bases. 2039 (in vitro selection) seems a reasonable compromise - it's highest on ChIP and almost the highest on expression.
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 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.
V YDR213W UPC2 544 High   The SRE is bound by UPC2 and the "canonical" sequence is TCGTATA. However, the more degenerate version obtained by PBM (motif 544) scores better in both expression analysis and OE experiments. Newer motif 2109 scores better on ChIP-chip, but lower on expression, and the SRE is well-characterized....I think this one deserves further experimental analysis.
V YDR207C UME6 2239 High   All motifs are similar to each other. BEEML-PBM motif 2239 scores highest across the board.
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