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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	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	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	YCL055W	KAR4	127	Low	Dubious	Evidence for sequence specific DNA binding seems weak, hence low confidence
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	YDL002C	NHP10	502	Low	Dubious	NHP10 is an HMGB-type protein. Known to prefer DNA ends. There is no independent support for the single PBM motif.
V	YMR072W	ABF2	541	Medium	Dubious	Protein is not expected to be sequence specific. But motif is obtained in vitro. May need further investigation. Give medium confidence, but label as dubious.
V	YGL131C	SNT2	612	Low	Dubious	All three motifs are derived from the same ChIP-chip data. However, there is no corroborating data, and not all SANT domains are DNA-binding - or are non-specific, in chromatin proteins. So it could be a cofactor motif; in fact it is similar to motifs of Stp3 and Stp4. The protein has other chromatin-related domains (BAH, PHD/RING). Hence the "Low" assessment.
V	YER051W	JHD1	662	Low	Dubious	This is a histone demethylase. No evidence for direct DNA binding. Motif 662 is significant. Include, but give low confidence - could be a cofactor.
V	YKL020C	SPT23	670	Low	Dubious	I could not find any evidence that this protein binds directly to DNA. It has an IPT domain but no REL domain. None of the ChIP-derived motifs scores highly on ChIP data or anything else. Motif 670 bears some relationship to expression data.
V	YMR053C	STB2	710	Low	Dubious	No direct evidence that this is a DNA-binding protein. Three ChIP-derived motifs but none scores highly by any measure. Motif 710 is an arbitrary choice - looks tidy.
V	YNL139C	THO2	786	Low	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.
V	YGL192W	IME4	1000	Low	Dubious	I could not find evidence that IME4 is a sequence-specific DNA-binding protein. C3H1 is more typically an RNA-binding domain or something besides nucleic acid binding. There is one significant ChIP-chip motif but perhaps it binds through a cofactor. No other supporting data.
V	YMR075W	RCO1	1066	Low	Dubious	There is no evidence that this is a sequence-specific DNA-binding protein rather than a chromatin factor. The higher-scoring ChIP-chip motif appears to have low information content and does not display strong correspondence to the data it was generated from or to expression data.
V	YDR477W	SNF1	1110	Medium	Dubious	Motif 1110 has a quite strong correspondence to ChIP-chip data (from which it is derived). However, there seems to be no evidence that this is a sequence-specific DNA-binding protein. Aside from a weak relationship to expression data there is no corroborating evidence here (and no DNA-binding domain).
V	YER161C	SPT2	1114	Low	Dubious	I could not find any evidence that this protein binds directly to DNA. None of the motifs is significant. All are from ChIP-chip. Motif 1114 chosen simploy because it has the highest numbers overall.
V	YPL139C	UME1	1143	Low	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. But, it has a high P-value, and the motif has low similarity to other motifs, with the possible exception of Yox1. But the function of the protein is very different from that of Yox1. Tough call - leave as Dubious, but give Low confidence to motif 1143.
V	YOR230W	WTM1	1148	Low	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 motifs come only from ChIP-chip so scoring on ChIP-chip is circular.
V	YPR086W	SUA7	1327	Low	Dubious	This protein is not expected to bind DNA; it is supposed to bind DNA-bound TBP. The TIRF-PBM data used to generate the motif included only 96 sequences.
V	YPR054W	SMK1	1875	Low	Dubious	I could not find any evidence that this protein binds directly to DNA. There is only one motif derived from ChIP-chip but it bears little relationship to the data from which it was derived.
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

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