Systematic Name	Gene Name	Motif ID	Expert Confidence	Dubious?	Notes
YDR266C		1161	Low		Motifs from ChIP-chip do not correspond to ChIP-chip, and there is no other supporting data. Chose 1161 only because it looks more reasonable. Low confidence.
YPR196W		861	High		Motifs from PBMs are very similar and are a variant monomeric GAL4-like motif. Chose 861 as it passes the significance threshold against ChIP-chip data.
YNR063W		804	High		Motifs from PBMs are virtually identical. This is a monomeric GAL4-like motif. 804 agrees more with ChIP-chip data.
MATA1		0			Need to study literature more carefully and consult experts.but at first glance none of these motifs seems right
YDR049W		0		Dubious	No evidence this is a TF, aside from a poorly-scoring C2H2 zinc finger
YER184C		2095	Medium		One motif from PBMs is a monomeric GAL4-like motif and the other is dimeric. Medium confidence because there is little independent support, and both contain the CCGG core that I believe may be an artifact. However, both score significantly on ChIP-chip data. Only 512 is significant on expression data.
YER184C		512	Medium		One motif from PBMs is a monomeric GAL4-like motif and the other is dimeric. Medium confidence because there is little independent support, and both contain the CCGG core that I believe may be an artifact. However, both score significantly on ChIP-chip data. Only 512 is significant on expression data.
YLR278C		2112	High		Only 2112 (from PBMs) stands out; dimeric GAL4 motif with high score on ChIP-chip.
YPR022C		588	High		Only one motif available, from PBMs; classical yeast C2H2 motif, and has some relationship to ChIP-chip data.
YPR015C		871	High		Only one motif available, from PBMs; resembles motof from CMR3 which is a paralogous gene (and nearly adjacent on the chromosome). And, scores significantly against expression data.
YER064C		2094	Medium		PBM motif has high score on GO because it looks a lot like Gcn4
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.
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.
YFL052W		0		Dubious	Putative zinc-cluster protein.
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.
MAL63		136	Medium		This is an unconventional dimeric GAL4-class motif
YDR026C		696	High		Three ChIP-chip motifs are virtually identical in appearance; resemble Reb1 motifs; high correspondence to ChIP-chip data
YLL054C		526	Medium		Three motifs available, from PBMs; two dimeric GAL4-like motifs but with different spacings and one monomeric. No backup data but looks tidy. Keep all three.
YLL054C		816	Medium		Three motifs available, from PBMs; two dimeric GAL4-like motifs but with different spacings and one monomeric. No backup data but looks tidy. Keep all three.
YLL054C		2242	Medium		Three motifs available, from PBMs; two dimeric GAL4-like motifs but with different spacings and one monomeric. No backup data but looks tidy. Keep all three.
YKL222C		2192	High		Two motifs from PBMs resemble monomeric GAL4-like motif. 2192 agrees best with ChIP-chip data and expression data.
YGR071C		0		Dubious	Unlikely to be true TF.
YLR211C		0		Dubious	Unlikely to be true TF.
YPL216W		0		Dubious	Unlikely to be true TF.
MATA1-MATALPHA2-dimer	a1-alpha2-dimer	1436	Medium		Not clear that motif is optimal.
YKL112W	ABF1	1993	High		Most motifs are similar, and five have pegged the ChIP P-value. Choose 791- it's the highest scoring overall, and is from PBMs
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.
YER045C	ACA1	8	Medium		Literature motif 8 is supported by experimental investigation, and resembles a bZIP site, but has no other support; motif was not obtained objectively. Can bind as heterodimer. The highest-scoring motif (from ChIP, 1457) has low information content - I'm concerned it is learning other features of bound promoters.
YLR131C	ACE2	1332	High		Highest-scoring ChIP-chip motif is Rap1 site. MITOMI motif 1332 is next, and resembles the classic Swi5/Ace2 motif.
YLR131C	ACE2	918	Incorrect		Likely represents Rap1 binding site.
YDR448W	ADA2	0		Dubious	Unlikely to be true TF.
YDR216W	ADR1	576	High		PBM motif 576 has significant correspondence to both ChIP-chip and highest to expression data. And has a classic yeast C2H2 look.
YGL071W	AFT1	658	High		Most motifs are similar. Also very similar to AFT2 motifs. ChIP-chip motif 658 scores highest on both ChIP-chip and expression data.
YPL202C	AFT2	389	High		All motifs look similar. ChIP-chip motif 389 scores high on ChIP-chip data and also best on expression data.
MATALPHA1-MCM1-dimer	alpha1-MCM1-dimer	1442	Medium		Not clear that motif is optimal.
YER069W	ARG5,6	1426	Medium		Not clear that motif is optimal.
YMR042W	ARG80	1483	Medium		Motif 1482 is an Arg81 site. 1483, however, is similar to Mcm1. Choose this, give Medium confidence.
YML099C	ARG81	1506	High		ChIP motif 1506 correlates well with ChIP and also with expression data. Resembles dimeric GAL4 class motif.
YML099C	ARG81	1507	Incorrect		Likely represents Mcm1 binding site.
YDR421W	ARO80	725	High		PBM motif 2115 appears monomeric and has highest correspondence to ChIP-chip data. ChIP motif 1509 appears dimeric and correlates with ChIP data. Literature motif 725 appears trimeric and has experimental support. Retain all three.
YDR421W	ARO80	1509	High		PBM motif 2115 appears monomeric and has highest correspondence to ChIP-chip data. ChIP motif 1509 appears dimeric and correlates with ChIP data. Literature motif 725 appears trimeric and has experimental support. Retain all three.
YDR421W	ARO80	2115	High		PBM motif 2115 appears monomeric and has highest correspondence to ChIP-chip data. ChIP motif 1509 appears dimeric and correlates with ChIP data. Literature motif 725 appears trimeric and has experimental support. Retain all three.
YPR199C	ARR1	603	Medium		Only motif 603 has significant scores with ChIP-chip and expression data; looks somewhat like a YAP motif
YIL130W	ASG1	807	Medium		Two PBM motifs appear to represent monomeric and dimeric versions of the same motif. This is the dimeric version. No other supporting data; hence medium confidence.
YIL130W	ASG1	2116	Medium		Two PBM motifs appear to represent monomeric and dimeric versions of the same motif. This is the monomeric version. No other supporting data; hence medium confidence. Picked 2116 because it has a higher GO score and expression score.
YKL185W	ASH1	932	Incorrect		Likely represents Mcm1 binding site.
YKL185W	ASH1	648	Incorrect		Likely represents Mcm1 binding site.
YKL185W	ASH1	28	Medium		The literature motif may not represent the full binding activity of the protein. Also, it is not supported by ChIP-chip. ChIP-chip identifies Mcm1-like motifs. But, it does score highly in both ChIP-chip and expression. The only higher-scoring motif has almost no information content.
YGR097W	ASK10	0		Dubious	I did not find any evidence that this is a sequence-specific DNA-binding protein.
YOR113W	AZF1	499	High		PBM motif 499 scores as well as the ChIP-chip motifs, but without the circularity. No significant data except ChIP-chip, however.
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.
YNL039W	BDP1	0		Dubious	Unlikely to be true TF.
YDL074C	BRE1	0		Dubious	Unlikely to be true TF.
YER159C	BUR6	0		Dubious	Unlikely to be true TF.
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.
YDR423C	CAD1	2098	High		Classic YAP motif in most cases. Include examples of both overlapping and adjacent monomeric sites - there are examples of both in PBM data and they both score highly on ChIP data. This one is adjacent.
YDR423C	CAD1	2073	High		Classic YAP motif in most cases. Include examples of both overlapping and adjacent monomeric sites - there are examples of both in PBM data and they both score highly on ChIP data. This one is overlapping.
YMR280C	CAT8	33	Medium		Near-classic dimeric GAL4 motif. Literature-based. Not clear this is an optimal site but it does bind. Seems to hit the right GO category.
YJR060W	CBF1	1346	High		Classic E-box. MITOMI motif 1346 nearly has highest correspondence to ChIP-chip data and is non-circular; no other supporting data
YGR140W	CBF2	0		Dubious	Unlikely to be true TF.
YMR213W	CEF1	0		Dubious	Unlikely to be true TF.
YMR168C	CEP3	524	High		Two PBM motifs agree. Went with 524 because it appears neater. No other supporting data for any of them.
YLR098C	CHA4	1607	Incorrect		Likely represents Rap1 binding site.
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).
YER164W	CHD1	0		Dubious	Unlikely to be true TF.
YOR028C	CIN5	1349	Medium		Most motifs match the classic YAP motif. This is the best in vitro motif (highest match to ChIP-chip) and it is different from the ChIP-based motifs - might reflect homo vs. heterodimer?
YOR028C	CIN5	409	High		Most motifs match the classic YAP motif. This is the best in vivo motif (highest match to ChIP-chip).
YPR013C	CMR3	859	High		PBM motifs are very similar. No other supporting data, but it's a clean motif. Chose 859 because it most closely resembles motif from paralog YPR015c.
YER130C	COM2	534	High		PBM motif 534 has the highest correspondence to expression data. Not much else supporting any of the motifs, although the two PBM motifs look about the same. Also look like typical yeast C2H2 motifs.
YNL027W	CRZ1	516	High		PBM motif 516 scores highest on ChIP and expression; resembles classic literature motifs
YIL036W	CST6	585	High		PBM motif 585 correlates with expression data (deletion and overexpression). ChIP motif 1466 has higher ChIP score but is lower on expression.
YGL166W	CUP2	48	Medium		Three motifs account for three possible spacings in the literature motif; it is not clear that this is the optimal site, however
YPL177C	CUP9	2121	High		MITOMI and PBM motifs are similar. PBM motif 2121 has slightly lower correspondence to ChIP data, but more significant correspondence to expression data.
YKR034W	DAL80	1355	Medium		MITOMI motif 1355 has highest correspondence to ChIP-chip. But it's not striking..none of them are, despite the fact that this is a classic GATA site (GATAAG).
YIR023W	DAL81	53	Low		None of the motifs agree with each other. The literature motif characterization was indirect; hence low confidence that this is the true motif. The ChIP-chip motifs score higher on ChIP data but that's circular.
YNL314W	DAL82	690	High		PBM and ChIP-chip motifs agree; select ChIP-chip as it scores higher on ChIP-chip although the extra A's on the side could be either due to the FL protein or some other in vivo factor.
YML113W	DAT1	1416	Medium		The literature (e.g. PMID: 8532535) suggests that the sequence specificity may be more promiscuous than the name suggests. To my knowledge there has not been any SELEX or PBM demonstrating that any motif is correct. But, it does bear some relationship to ChIP-chip and expression data.
YPL049C	DIG1	0		Dubious	Not a TF - it binds Ste12; all the motifs are Ste12 motifs.
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.
YLR228C	ECM22	849	High		PBM motif 2122 is a monomeric GAL4 class motif, and scores highest on both ChIP and expression ata. 849 is a classic dimeric GAL4 motif with lower but still reasonable scores and is moderately predictive across the board.
YLR228C	ECM22	2122	High		PBM motif 2122 is a monomeric GAL4 class motif, and scores highest on both ChIP and expression ata. 849 is a classic dimeric GAL4 motif with lower but still reasonable scores and is moderately predictive across the board.
YPL021W	ECM23	578	High		PBM motif 578 strongly resembles that from other yeast GATA-class TFs
YMR176W	ECM5	0		Dubious	Unlikely to be true TF.
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.
YBR239C	ERT1	2188	Medium		Three PBM motifs are all classic monomeric GAL4 motifs. Chose 2188 because it has fewer noninformative flanking positions, and higher significance on expression data. Also, 826 has the CCGG core that I suspect may be an artefact of PBMs or the DBD clones used in these studies. The highest-scoring ChIP motif is circular and does not resemble a GAL4 class binding site.
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.
YNL023C	FAP1	0		Dubious	Unlikely to be true TF.
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.
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.
YPR104C	FHL1	1504	Incorrect		Likely represents Rap1 binding site.
YPR104C	FHL1	1196	Incorrect		Likely represents Rap1 binding site.
YPR104C	FHL1	893	Incorrect		Likely represents Rap1 binding site.
YPR104C	FHL1	1618	Incorrect		Likely represents Rap1 binding site.
YPR104C	FHL1	629	Incorrect		Likely represents Rap1 binding site.
YPR104C	FHL1	406	Incorrect		Likely represents Rap1 binding site.
YIL131C	FKH1	2002	High		Classic Forkhead motif for most of them. 2002 strongly resembles PBM motif but scores higher on both ChIP (which is circular) and expression (which is not).
YNL068C	FKH2	830	High		Most motifs are classic Forkhead. PBM motif 830 is one of the highest scoring and is not circular.
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.
YCL058C	FYV5	1417	Low		Literature motif is derived from a single promoter and while the protein seems to have some DNA-binding activity, perhaps in conjunction with other TFs, I find the evidence supporting this precise binding site incomplete, since it is derived from a single site. Hence, low confidence in the motif.
YGL254W	FZF1	69	Low		Literature motif is the only one that appears credible. PBM motif I believe is a known artifact. Literature motif gets low confidence however as it is based on a single known binding sequence.
YDR009W	GAL3	0		Dubious	Gal3 is not a sequence-specific DNA-binding protein
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.
YPL248C	GAL4	1510	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.
YML051W	GAL80	0		Dubious	Gal80 is not a sequence-specific DNA-binding protein
YFL021W	GAT1	962	High		ChIP-chip motif 962 scores higher on both ChIP-chip and expression data
YLR013W	GAT3	2128	High		All PBM motifs look similar, also similar to a subset of other GATAs. 2128 scores quite highly on ChIP-chip (albeit with negative correlation!), and also higher on expression and OE data.
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.
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.
YPL075W	GCR1	2071	High		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).
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).
YDR096W	GIS1	562	High		All motifs similar; PBM motif 562 has highest correspondence to deletion expression data and overexpression data
YER040W	GLN3	539	High		Most motifs are classic GATA or GATAAG. PBM motif 539 scores highest on ChIP.
YJL103C	GSM1	856	Medium		Only PBM motif 856 reaches significance, on expression. Classic GAL4-type monomeric site. No other data, relation to expression not strong. Medium confidence.
YGL181W	GTS1	694	Low		None of the three motifs resembles an AT-hook binding site. Only one correlates with the ChIP-chip data, but that's circular. Low confidence.
YJL110C	GZF3	2133	High		Classic GATA motif 2133 from PBM scores highest on ChIP-chip and expression data
YPR008W	HAA1	1425	Medium		Literature motif is not completely determined, but scores highly on ChIP-chip data. Regardless, medium confidence.
YFL031W	HAC1	94	Medium		1788 is the overall winner. But, literature motif 94 also scores well in ChIP-chip, despite being somewhat different. Possible difference in heterodimerazation partners, or proteolytic fragment? Retain both.
YFL031W	HAC1	1788	High		1788 is the overall winner. But, literature motif 94 also scores well in ChIP-chip, despite being somewhat different. Possible difference in heterodimerization partners, or proteolytic fragment? Retain both, score 94 as medium.
YOL089C	HAL9	2134	High		PBM motifs 799 and 2134 score highest on ChIP-chip data; classic dimeric and monomeric GAL4 sites, respectively.
YOL089C	HAL9	799	High		PBM motifs 799 and 2134 score highest on ChIP-chip data; classic dimeric and monomeric GAL4 sites, respectively.
YLR256W	HAP1	2078	High		Literature binding site is direct CGG repeats with a 6bp spacer (PMID: 7958882). PBM motif 2078 gets this; it scores highest overall, including significant scores on both ChIP-chip and expression.
YGL237C	HAP2	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.
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.
YKL109W	HAP4	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.
YOR358W	HAP5	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.
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.
YBL008W	HIR1	0		Dubious	Hir1,2,3 are a nucleosome assembly complex, not TFs
YOR038C	HIR2	0		Dubious	Hir1,2,3 are a nucleosome assembly complex, not TFs
YJR140C	HIR3	0		Dubious	Hir1,2,3 are a nucleosome assembly complex, not TFs
YCL067C	HMLALPHA2	2079	Medium		Protein is similar to PBX/MEIS/TGIF; both PBM motifs have some similarity (central ACA/TGT), so do sites in crystal and in vivo (e.g. PMID: 1682054) but no clear winner between the two. Keep both PBM motifs in curated set (2102 and 2079) but give medium confidence - no supporting ChIP or expression data.
YCL067C	HMLALPHA2	2102	Medium		Protein is similar to PBX/MEIS/TGIF; both PBM motifs have some similarity (central ACA/TGT), so do sites in crystal and in vivo (e.g. PMID: 1682054) but no clear winner between the two. Keep both PBM motifs in curated set (2102 and 2079) but give medium confidence - no supporting ChIP or expression data.
YDR174W	HMO1	2249	Low		This motif is uncharacteristic for a Sox protein and HMG proteins typically do not bind DNA in a sequence specific manner. Since it is from ChIP data it could be a cofactor motif. Low confidence.
YCR096C	HMRA2	558	Medium		Should be similar to MATALPHA2. The one PBM motif is indeed related to the MITOMI motif for MATALPHA2.
YOR032C	HMS1	1498	Medium		Motif 1498 scores reasonably on ChIP. Other corroborating data are not that convincing - medium confidence.
YJR147W	HMS2	992	Low		The one ChIP-chip motif bears little relationship to the ChIP data.it kind of looks like an HNF-like site, but still, low confidence.
YLR113W	HOG1	0		Dubious	This is a signalling molecule that associates with many TFs (see SGD)
YMR172W	HOT1	0		Dubious	Unlikely to be true TF.
YGL073W	HSF1	1461	Medium		Four types of motifs contain TTC monomeric core and all score highly on both ChIP and expression. Appear to represent different monomeric/multimeric binding configurations. This is the dimeric head-to-tail site. From ChIP and prior.
YGL073W	HSF1	476	Medium		Four types of motifs contain TTC monomeric core and all score highly on both ChIP and expression. Appear to represent different monomeric/multimeric binding configurations. This is the monomeric site. From PBM.
YGL073W	HSF1	411	Medium		Four types of motifs contain TTC monomeric core and all score highly on both ChIP and expression. Appear to represent different monomeric/multimeric binding configurations. This is the spaced direct repeat dimeric site. From ChIP.
YGL073W	HSF1	615	Medium		Four types of motifs contain TTC monomeric core and all score highly on both ChIP and expression. Appear to represent different monomeric/multimeric binding configurations. This is the trimeric site. From ChIP.
YDR225W	HTA1	0		Dubious	Unlikely to be true TF.
YBL003C	HTA2	0		Dubious	Unlikely to be true TF.
YLR223C	IFH1	0		Dubious	Cofactor of Fhl1p. No evidence for sequence-specific DNA-binding.
YJR094C	IME1	0		Dubious	Interacts with UME6. The only significant motif shares 5/6 bases with the UME6 motif core (GCCGCC)
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.
YDR123C	INO2	713	High		Ino2/4 binds as a heterodimer, so there should just be one motif for the two proteins. All motifs appear similar but none of them is derived from in vitro data. Nonetheless most motifs match a classic E-box with some preference for flanking bases. Motif 713 is derived from ChIP-chip; it is not the highest-scoring ChIP-chip motif but it is highest for OE and deletion expression.
YOL108C	INO4	713	High		Ino2/4 binds as a heterodimer, so there should just be one motif for the two proteins. All motifs appear similar but none of them is derived from in vitro data. Nonetheless most motifs match a classic E-box with some preference for flanking bases. Motif 713 is derived from ChIP-chip; it is not the highest-scoring ChIP-chip motif but it is highest for OE and deletion expression.
YOR304W	ISW2	0		Dubious	Unlikely to be true TF.
YGL133W	ITC1	0		Dubious	Unlikely to be true TF.
YKL032C	IXR1	0		Dubious	Binds cisplatin-modified DNA. HMG domains. ChIP-chip motifs not significant. Dubious and no credible motif.
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.
YNL227C	JJJ1	0		Dubious	Unlikely to be true TF.
YCL055W	KAR4	127	Low	Dubious	Evidence for sequence specific DNA binding seems weak, hence low confidence
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.
YGR040W	KSS1	0		Dubious	There is no evidence that Kss1 is a sequence-specific TF.
YLR451W	LEU3	2135	High		Most motifs look similar - dimeric GAL4 motif. Literature motif (781) has high correspondence to ChIP-chip and expression data and is not circular. But, PBM motif 2135, which is a monomeric GAL4 motif, scores highest on both ChIP-chip and expression data.
YLR451W	LEU3	781	High		Most motifs look similar - dimeric GAL4 motif. Literature motif (781) has high correspondence to ChIP-chip and expression data and is not circular. But, PBM motif 2135, which is a monomeric GAL4 motif, scores highest on both ChIP-chip and expression data.
YDR034C	LYS14	865	High		PBM motifs are virtually identical and appear monomeric; literature motif is dimeric. Include both. Choose PBM motif 865 as it appears to have more robust CGG.
YDR034C	LYS14	133	High		PBM motifs are virtually identical and appear monomeric; literature motif is dimeric. Include both. Choose PBM motif 865 as it appears to have more robust CGG.
YMR021C	MAC1	1540	High		Literature motif 1540 most closely most closely corresponds to ChIP-chip data (albeit barely significant). Nothing else to gauge by, but no reason to doubt literature motif.
YGR288W	MAL13	0			None of the ChIP-chip motifs correspond wekk to the data they come from and/or resemble a GAL4 motif.
YBR297W	MAL33	0			None of the ChIP-chip motifs correspond wekk to the data they come from and/or resemble a GAL4 motif.
YCR040W	MATALPHA1	1418	Low		According to PMID: 15118075, binds the "Q site" which has "consensus" ACAATGACAG. Seems all that is in common is the CAAT. I believe further study is required.
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.
YOR298C-A	MBF1	0		Dubious	This is a coactivator. I found no evidence that it is a sequence-specific TF.
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.
MBP1-SWI6-dimer	MBP1-SWI6-dimer	0			Redundant with MBP1
YMR043W	MCM1	831	High		Most motifs resemble a classic SRF site. PBM motif 831 scores highly across the board, except for expression data where none does well, and its scores are non-circular.
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.
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.
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.
YPL038W	MET31	1370	High		Most motifs look similar. MITOMI motif 1370 has highest overall correlation to ChIP-chip, OE, and deletion data.
YDR253C	MET32	2140	High		Most motifs look similar. PBM motif 2140 has highest correspondence to both ChIP and expression.
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.
YGR249W	MGA1	2141	Medium		PBM motif 2141 is similar to Hsf1 motif 476 (TTCCA). Has TTC "core" which is shared by most Hsf1 motifs. Scores reasonably on ChIP data but no other supporting information; hence "medium".
YGL035C	MIG1	2142	High		PBM motif 2142 has highest correspondence to ChIP-chip AND AUC for GO category "generation of precursor metabolites and energy". The adjacent A/T stretch, which is also noted in the literature, is found in ChIP-chip motif 654 and others; however, that motif does not sort as well for GO category "generation of precursor metabolites and energy" and also scores lower for both ChIP and expression, so it seems unlikely to represent a key intrinsic activity of the protein itself.
YGL209W	MIG2	2143	High		PBM motif 2143 has highest correspondence to ChIP-chip data
YER028C	MIG3	2144	High		PBM motif 2144 has highest correspondence to ChIP-chip data
YER068W	MOT2	556	Medium		PBM motif 556 has high correspondence to ChIP-chip data. However, also resembles TATA element, and could also be a structural motif. RRMs normally bind single-stranded RNA or DNA. Give medium confidence.
YMR070W	MOT3	2080	Medium		PBM motif 2080 is very similar to the literature motif and scores highest on expression data. Moreover, this motif explains high-scoring ChIP-chip motifs for many other TFs, e.g. Nrg1, Yap6, Sok2
YOL116W	MSN1	1378	High		MITOMI motif 1376 has the highest correspondence to ChIP-chip. MITOMI motif 1378 is very close, however, and seems to be a circular permutation. Retain both motifs.
YOL116W	MSN1	1376	High		MITOMI motif 1376 has the highest correspondence to ChIP-chip. MITOMI motif 1378 is very close, however, and seems to be a circular permutation. Retain both motifs.
YMR037C	MSN2	1380	High		MITOMI motif 1380 has the highest overall correspondence to ChIP-chip, overexpression, and deletion data. Resembles classic Msn2/4 motif.
YKL062W	MSN4	518	High		PBM motif 518 resembles both the classical MSN motif and the PBM motif, and scores highest on both expression and ChIP-chip.
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.
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.
YOR372C	NDD1	366	Incorrect		Likely represents Mcm1 binding site.
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".
YLR254C	NDL1	0		Dubious	Unlikely to be true TF.
YHR124W	NDT80	1464	High		Motif 1464 matches literature motifs and PBM motif, and nails sporulation on GO. It also has the highest correspondence to ChIP-chip data.
YOR156C	NFI1	0		Dubious	Unlikely to be true TF.
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.
YPR052C	NHP6A	879	Medium		NHP6A and NHP6B are similar to the HMGB family, which is thought to lack sequence specificity. However, the proteins do bend the DNA when they bind, and so may have some level of sequence specificity. Essentially similar motifs were obtained for the two different proteins (in the same study) and the PBM motif for Nhp6A has a good correspondence to ChIP-chip data. Give both Medium confidence.
YBR089C-A	NHP6B	792	Medium		NHP6A and NHP6B are similar to the HMGB family, which is thought to lack sequence specificity. However, the proteins do bend the DNA when they bind, and so may have some level of sequence specificity. Essentially similar motifs were obtained for the two different proteins (in the same study) and the PBM motif for Nhp6A has a good correspondence to ChIP-chip data. Give both Medium confidence.
YGR089W	NNF2	0		Dubious	I did not find any evidence that this is a sequence-specific DNA-binding protein.
YDR043C	NRG1	2148	High		PBM, ChIP-chip, and literature motifs all appear very similar, and resemble motif for the related protein NRG2. Choose top PBM motif (2148). There is also a recurring ChIP-chip motif (TGTGCCT) which I believe is actually the MOT3 binding site.
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.
YAL051W	OAF1	2060	Medium		Motif 2060 has a strong resemblance to the literature motifs for the Oaf1-Pip2 dimer, and scores highly on both ChIP and expression data. No in vitro support and it's kind of weak looking so Medium confidence.
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.
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.
YML065W	ORC1	1549	High		Looks like ORC1 motif. Which is not really a TF, but it is a sequence-specific DNA-binding protein.
YBR060C	ORC2	0		Dubious	Unlikely to be true TF.
YFL044C	OTU1	1166	Low		ChIP-chip motif 1166 has a good relationship to ChIP-chip data, but it is unusual for C2H2 motifs to be A/T rich, and there is no other support for this motif, so it could be a cofactor, nucleosome-excluding, TATA element, etc. In addition, it only has a single C2H2 domain, and is known to function as a deubiquitylation enzyme. Low confidence.
YDR081C	PDC2	1050	Low		Motifs do not correlate with the ChIP-chip data from which it was derived. I found no other experimental evidence that this is a sequence-specific DNA-binding protein. However, it does have HTH and transposase motifs. Retain motif 1050 but give low confidence.
YGL013C	PDR1	899	Incorrect		Likely represents Rap1 binding site.
YGL013C	PDR1	485	High		PBM motif 485 looks like a traditional literature motif and has highest correspondence to ChIP and expression data. Dimeric GAL4 motif.
YBL005W	PDR3	2062	Medium		MITOMI yields a simple GAL4 monomeric site that scores well in ChIP-chip data. ChIP-chip yields a dimeric site that resembles the literature site. In vivo, PDR1 and PDR3 may form heterodimers. Retain both. This is the dimeric ChIP-chip motif.
YBL005W	PDR3	1387	Medium		MITOMI yields a simple GAL4 monomeric site that scores well in ChIP-chip data. ChIP-chip yields a dimeric site that resembles the literature site. In vivo, PDR1 and PDR3 may form heterodimers. Retain both. This is the monomeric motif.
YLR266C	PDR8	244	Medium		Both motifs are equally credible but have very limited support. Literature motif is related to that of YRR1 literature motif. PBM motif, however, is a classic GAL4 monomer. This is the literature motif.
YLR266C	PDR8	528	Medium		Both motifs are equally credible but have very limited support. Literature motif is related to that of YRR1 literature motif. PBM motif, however, is a classic GAL4 monomer. This is the PBM motif.
YDR323C	PEP7	0		Dubious	Unlikely to be true TF.
YKL043W	PHD1	393	High		High-scoring motifs are all similar, with characteristic APSES GC core and palindromic. PBM motifs score highest on ChIP-seq data, while ChIP-chip motif 393 (which contains flanking G/C residues) scores highest on expression data. Retain both - possibly, the rest of the protein contributes to binding flanking residues. This is the ChIP motif that scores highest on expression data.
YKL043W	PHD1	2153	High		High-scoring motifs are all similar, with characteristic APSES GC core and palindromic. PBM motifs score highest on ChIP-seq data, while ChIP-chip motif 393 (which contains flanking G/C residues) scores highest on expression data. Retain both - possibly, the rest of the protein contributes to binding flanking residues. This is the higher-scoring PBM motif (2153).
YDL106C	PHO2	1680	Incorrect		Likely represents Abf1 binding site.
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.
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.
YOR363C	PIP2	0			See Oaf1-Pip2-dimer
YIL122W	POG1	0		Dubious	Unlikely to be true TF.
YLR014C	PPR1	2064	Low		ChIP-chip motif 2064 almost matches the literature site, which has been confirmed by directed experimentation, and scores highest on most measures. But, give it low confidence - it is not at all clear that this is an optimal binding site, and none of the scores for any of the motifs are all that high.
YKL015W	PUT3	2065	Medium		Motifs vary considerably. ChIP motif 2065 is a dimeric/(trimeric?) GAL4-like site, and has the highest correspondence to ChIP-chip data (from which it is derived) and some correspondence to expression data (although it is not strong). PBM motif 2223 is a monomeric GAL4-like motif and has higher correspondence to expression data, albeit weaker (but still good) correspondence to ChIP-chip data. It is possible that the actual sequence preference is some other arrangement of monomeric sites that were not picked up in either assay - score as medium confidence.
YKL015W	PUT3	2223	Medium		Motifs vary considerably. ChIP motif 2065 is a dimeric/(trimeric?) GAL4-like site, and has the highest correspondence to ChIP-chip data (from which it is derived) and some correspondence to expression data (although it is not strong). PBM motif 2223 is a monomeric GAL4-like motif and has higher correspondence to expression data, albeit weaker (but still good) correspondence to ChIP-chip data. It is possible that the actual sequence preference is some other arrangement of monomeric sites that were not picked up in either assay - score as medium confidence.
YPR186C	PZF1	1321	Low		This is a single literature site. The protein almost certainly binds the site but it has not been demonstrated that this is an optimal binding site.
YCR066W	RAD18	0		Dubious	Unlikely to be true TF.
YNL216W	RAP1	254	High		Most motifs look similar. ChIP-chip motif 254 has highest correspondence to expression data.
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.
YOR380W	RDR1	756	Medium		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.
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.
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.
YPL133C	RDS2	2226	Medium		All motifs contain CGG. PBM motif 2226 appears to be a monomeric version of literature motif 757. However, the paper that produced motif 757 did not demonstrate that this is an optimal binding site. Retain both motifs and give them a "medium" confidence.
YPL133C	RDS2	757	Medium		All motifs contain CGG. PBM motif 2226 appears to be a monomeric version of literature motif 757. However, the paper that produced motif 757 did not demonstrate that this is an optimal binding site. Retain both motifs and give them a "medium" confidence.
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.
YBR267W	REI1	489	High		PBM motif looks like a yeast C2H2 motif (row of C's); highly significant relationship to ChIP-chip data
YLR176C	RFX1	1478	Medium		Curious case - virtually all motifs are similar in appearance, with a common TGGCAAC core. They range from what appear to be monomers to full dimers, with multiple partial forms. However, none of them scores highly on both ChIP-chip and expression data. Select two representatives: one that scores well on ChIP-chip, and one that scores well on expression. This is the one that scores most highly on ChIP-chip. It is a dimer motif. Give medium confidence, since it has little relationship to expression data.
YLR176C	RFX1	496	Medium		Curious case - virtually all motifs are similar in appearance, with a common TGGCAAC core. They range from what appear to be monomers to full dimers, with multiple partial forms. However, none of them scores highly on both ChIP-chip and expression data. Select two representatives: one that scores well on ChIP-chip, and one that scores well on expression. This is the one that scores most highly on expression (close 2nd on deletion and 1st on overexpression). It is the only purely monomeric motif. Give medium confidence, since according to the literature this protein should bind as a dimer.
YMR182C	RGM1	531	High		PBM motif 531 looks like a C2H2 motif (row of G's), and scores well on both ChIP-chip and deletion expression data.
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.
YHL027W	RIM101	600	High		ChIP-chip motif 600 is almost identical to PBM motif 513, but scores slightly higher on expression data. Three of six motifs are very similar.
YPL089C	RLM1	1079	Incorrect		Likely represents Mcm1 binding site.
YPL089C	RLM1	419	Medium		Motif 419 has a MADS-like appearance, and scores very highly in ChIP-chip data, despite being derived from the literature. Not much correspondence to expression however, hence Medium confidence. ChIP-chip motif 910 does slightly better on expression but to me is not a credible MADS box binding site.
YGR044C	RME1	273	Low		Motif 273 shows similarity to RME response elements (RREs), GTACC(T/A)ACAAAA (in fact it is derived from them). The fact that RME has three C2H2 zinc fingers and also requires an additional C-terminal region for binding in vitro, together with its relatively large footprint, are consistent with such a large binding site. However, I gave this motif a "low" score as there is no systematic analysis in vivo or in vitro indicating that these are really the most preferred sites. It would be valuable to redo the in vitro and in vivo experiments under appropriate conditions.
YPR065W	ROX1	1396	High		About half the motifs have a typical ACAAT Sox core. MITOMI motif 1396 has highest correspondence to both ChIP-chip and deletion expression data.
YER169W	RPH1	547	High		About half of the motifs look similar to each other, with GGGG core typical of many yeast C2H2 proteins. PBM motif 547 has meaningful scores on both ChIP-chip and mutant expression data. I'm somewhat concerned that motif 279 lacks two A residues captured by both PBM experiments.
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.
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.
YDL020C	RPN4	1090	Incorrect		Likely represents Reb1 binding site.
YDR303C	RSC3	580	High		PBM motif 580 has best correspondence to expression data - the only significant independent criterion - considering that the correlations are all in the same orientation (they are not for 2165). All motifs look similar. Propose that longer motifs could be due to multiple binding sites in the same sequence.
YHR056C	RSC30	2164	Medium		Arbitrary choice - all PBM motifs look similar (and resemble motif from homolog Rsc3). I have downgraded this one from high to medium because the best scoring motif actually looks the least like the Rsc3 motif.
YFR037C	RSC8	0		Dubious	Unlikely to be true TF.
YJR127C	RSF2	575	High		No supporting data, but the PBM motif 575 looks like a typical yeast C2H2 motif (Adr1, which has similar zinc fingers, Mig1, etc).
YOL067C	RTG1	1494	Low		1493 and 1494 are a toss-up and could represent different dimerization partners, conceivably. Similar to 1445 and 1446 above. Retain both but give low confidence.
YOL067C	RTG1	1493	Low		1493 and 1494 are a toss-up and could represent different dimerization partners, conceivably. Similar to 1445 and 1446 above. Retain both but give low confidence.
YBL103C	RTG3	1445	Low		Only the PBM motif is a classic HLH motif. Three different ChIP-chip-derived motifs are all diverse, but all score highly on ChIP-chip data! Are they motifs of other TFs? Check. 602: GCN4; 1095, TEC1; 1096: resembles 602, but is a closer match to CUP9/TOS8. Also hits GCN4. According to the literature (PMID: 9032238) the core binding site for the Rtg1p-Rtg3p heterodimer is 5'-GGTCAC-3'; the only motif that resembles this is 1446. Vague resemblance to 602 and 1096. I am going to retain 1446, which represents the literature site; PBM motif 870, which resembles an E-box, and ChIP-chip motif 1445, which scores highest on ChIP-chip data. But give all low confidence.
YBL103C	RTG3	870	Low		Only the PBM motif is a classic HLH motif. Three different ChIP-chip-derived motifs are all diverse, but all score highly on ChIP-chip data! Are they motifs of other TFs? Check. 602: GCN4; 1095, TEC1; 1096: resembles 602, but is a closer match to CUP9/TOS8. Also hits GCN4. According to the literature (PMID: 9032238) the core binding site for the Rtg1p-Rtg3p heterodimer is 5'-GGTCAC-3'; the only motif that resembles this is 1446. Vague resemblance to 602 and 1096. I am going to retain 1446, which represents the literature site; PBM motif 870, which resembles an E-box, and ChIP-chip motif 1445, which scores highest on ChIP-chip data. But give all low confidence.
YBL103C	RTG3	1446	Low		Only the PBM motif is a classic HLH motif. Three different ChIP-chip-derived motifs are all diverse, but all score highly on ChIP-chip data! Are they motifs of other TFs? Check. 602: GCN4; 1095, TEC1; 1096: resembles 602, but is a closer match to CUP9/TOS8. Also hits GCN4. According to the literature (PMID: 9032238) the core binding site for the Rtg1p-Rtg3p heterodimer is 5'-GGTCAC-3'; the only motif that resembles this is 1446. Vague resemblance to 602 and 1096. I am going to retain 1446, which represents the literature site; PBM motif 870, which resembles an E-box, and ChIP-chip motif 1445, which scores highest on ChIP-chip data. But give all low confidence.
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.
YBL052C	SAS3	0		Dubious	Unlikely to be true TF.
YOR140W	SFL1	605	Medium		None of the motifs are highly related to each other. But, most share a GAAG core and are otherwise A-rich. The PBM motif 839 in particular is compatible with the putative binding sites that are mutated in PMID 17594096, and it scores well on ChIP-chip. Other motifs may represent different multimerization configurations. ChIP-chip motif 605 also scores well on ChIP-chip data, which is circular, but I will retain it for completeness.
YOR140W	SFL1	839	Medium		None of the motifs are highly related to each other. But, most share a GAAG core and are otherwise A-rich. The PBM motif 839 in particular is compatible with the putative binding sites that are mutated in PMID 17594096, and it scores well on ChIP-chip. Other motifs may represent different multimerization configurations. ChIP-chip motif 605 also scores well on ChIP-chip data, which is circular, but I will retain it for completeness.
YLR403W	SFP1	1710	Incorrect		Likely represents Rap1 binding site.
YLR403W	SFP1	357	Incorrect		Likely represents Rap1 binding site.
YLR403W	SFP1	1100	Incorrect		Likely represents Rap1 binding site.
YLR403W	SFP1	621	Incorrect		Likely represents Rap1 binding site.
YLR403W	SFP1	797	High		Most ChIP-seq studies identified the Rap1 motif. PBM motif 797 is less significant by ChIP-seq (although still highly significant) but is the winner across the board for all types of expression data.
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.
YJL089W	SIP4	2067	Medium		PBM motif 573 is a monomeric GAL4-type motif (others appear dimeric) but it has good correspondence to ChIP-chip data. Only a few of the dimeric sites are more significant - the motif from in vivo analysis (PMID: 14685767) does not score as highly as 2067 from ChIP-chip data, but they look very similar. This is 2067, the presumed dimeric site.
YJL089W	SIP4	573	Medium		PBM motif 573 is a monomeric GAL4-type motif (others appear dimeric) but it has good correspondence to ChIP-chip data. Only a few of the dimeric sites are more significant - the motif from in vivo analysis (PMID: 14685767) does not score as highly as 2067 from ChIP-chip data, but they look very similar. This is 573, the presumed monomeric site
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.
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.
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.
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.
YDR409W	SIZ1	0		Dubious	Unlikely to be true TF.
YHR206W	SKN7	583	High		Motifs are remarkably discordant considering that they all resemble each other in being G+C rich and containing a GGCC core. Possibly reflecting different modes of multimerization? Include the two that score highest on independent data: PBM motif 583, which represents a monomer, and ChIP-chip motif 380, which appears to represent a dimer.
YHR206W	SKN7	380	High		Motifs are remarkably discordant considering that they all resemble each other in being G+C rich and containing a GGCC core. Possibly reflecting different modes of multimerization? Include the two that score highest on independent data: PBM motif 583, which represents a monomer, and ChIP-chip motif 380, which appears to represent a dimer.
YNL167C	SKO1	1401	High		The MITOMI motif 1401 is an offset and asymmetric version of the traditional consensus (TGACGTCA) but has a higher ChIP-chip and expression correspondence than the motifs that are more symmetric.
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.
YBR182C	SMP1	864	Medium		PBM motif 864 scores highest on ChIP-chip and expression data. I gave it a medium, however, because it has low information content at most positions, does not closely match the literature motif (although the literature motif does not mach ChIP-chip or expression data), and also does not resemble that of RLM1, which according to the literature should be related.
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).
YOR290C	SNF2	0		Dubious	Unlikely to be true TF.
YCR033W	SNT1	0		Dubious	Unlikely to be true TF.
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.
YOR308C	SNU66	0		Dubious	Unlikely to be true TF.
YMR016C	SOK2	404	High		ChIP-chip motif 404 has highest correspondence to both ChIP-chip and expression data - and strongly resembles PBM motif
YJL127C	SPT10	1880	Low		This is the protein that binds histone promoters. The sequence specificity is derived from the histone promoters only so the literature motif may be inaccurate. Motif 1880 has higher scores overall but does not resemble the literature motif. Uncertain what to do here - use 1880, but give low confidence. Motif learned in vivo could contain extrinsic information.
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
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.
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.
YCR018C	SRD1	2232	Medium		PBM studies yield nearly identical motifs. 2232 closely resembles motif from related GATA factors and scores highest overall. This is an unusual motif for the GATA class; hence medium confidence level.
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.
YMR053C	STB2	710	Incorrect		Likely represents Reb1 binding site.
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.
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.
YMR019W	STB4	2107	High		PBM motif 2107 is clearly a dimeric GAL4-class motif, and it blows all the other motifs out of the water.
YHR178W	STB5	1405	High		All motifs have CGG core and most have CGGnG. Most ChIP-derived motifs have no relationship to expression data. Mitomi motif 1405 and PBM motif 514 score decently on both ChIP-chip and expression data, and seem to nail the GO category (oxidative stress response), and look like classic Gal4 halfmers. MITOMI motif scores slighly higher overall. This is presumably the monomeric motif
YHR178W	STB5	2068	Medium		All motifs have CGG core and most have CGGnG. Most ChIP-derived motifs have no relationship to expression data. Motif 2068 scores highest overall; looks a bit unusual for a Gal4 class motif but also does well on expression data. Retain as potential dimer motif, although it may also incorporate extrinsic information.
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.
YHR084W	STE12	400	High		All motifs but one resemble the canonical literature site. Motif 400 is derived from ChIP-chip data (on which it scores highest) but also scores highest on expression data.
YDR463W	STP1	660	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 (800) correlates 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.
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.
YLR375W	STP3	568	Medium		STP3 and 4 have very similar DNA-binding domains. However, they are not similar to those of STP1 and 2; the next most closely related are SWI5 and ACE2, with major differences in the recognition alpha helices. All of the STP4 motifs are different from each other and none have any supporting data. There is only one motif for STP3 (568) from PBM and it matches the STP4 motif from the same study (559) which is the basis for choosing these two motifs.
YDL048C	STP4	559	Medium		STP3 and 4 have very similar DNA-binding domains. However, they are not similar to those of STP1 and 2; the next most closely related are SWI5 and ACE2, with major differences in the recognition alpha helices. All of the STP4 motifs are different from each other and none have any supporting data. There is only one motif for STP3 (568) from PBM and it matches the STP4 motif from the same study (559) which is the basis for choosing these two motifs.
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.
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
YDR310C	SUM1	478	High		This is the motif for the SUM1 AT_hook; scores highest in deletion expression data
YGL162W	SUT1	673	Medium		Four motifs, all derived from ChIP-chip, contain CGG, but are unusual, with degeneracy and a core of CGGGG. Correlate somewhat with both OE and deletion data, however.
YPR009W	SUT2	2236	High		Highest-scoring motif (PBM) is a classical GAL4-type monomeric motif and is very significant in ChIP-chip
YGR002C	SWC4	0		Dubious	Unlikely to be true TF.
YPL016W	SWI1	0		Dubious	Unlikely to be true TF.
YJL176C	SWI3	0		Dubious	Unlikely to be true TF.
YER111C	SWI4	584	High		Motif is well-characterized and most published motifs match the expected one. PBM motif (584) scores highly (although not highest) in Chip-chip data. It is, however, non-circular, and specifically captures "DNA metabolic process" in GO analysis.
YDR146C	SWI5	569	High		PBM, Chip-chip, and conservation all yield similar motifs. ChIP-chip scores highest in ChIP-chip but that is circular. Choose PBM motif 569 which is nearly identical.
YLR182W	SWI6	0		Dubious	Swi6 is a cofactor, not a DNA-binding protein. These motifs are for Mbp1 or Swi4.
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.
TBP-TFIIA	TBP-TFIIA	1328	Low		The TIRF-PBM data used to generate the motif included only 96 sequences. Also it is curious that there is no TATA sequence in the logo.
TBP-TFIIA-TFIIB	TBP-TFIIA-TFIIB	1330	Medium		The TIRF-PBM data used to generate the motif included only 96 sequences; hence, medium confidence.
TBP-TFIIB	TBP-TFIIB	1329	Medium		The TIRF-PBM data used to generate the motif included only 96 sequences; hence, medium confidence.
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.
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.
YOR337W	TEA1	817	Medium		Three motifs, all from PBMs. Choose 817 because it has a more robust GAL4 "CGG" core. But there is no convincing corroborating data for either motif and they do not match each other.
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.
YDR362C	TFC6	0		Dubious	Unlikely to be true TF.
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.
YER063W	THO1	0		Dubious	Unlikely to be true TF.
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.
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.
YGL096W	TOS8	494	High		No corroborating data on this TF, and only one PBM motif known and one ChIP motif. But, it resembles TGTCA, which was also obtained for paralog Cup9 by multiple approaches (GTGNCA), as well as PBM results for the Meis/Mrg/Pknox/Tgif family, which are the closest mammalian homologs. The ChIP motif (1902) does not resemble a homeodomain binding sequence, and scores lower on expression data.
YNL079C	TPM1	0		Dubious	Unlikely to be true TF.
YOR344C	TYE7	397	High		All studies except one get canonical HLH motif. 795 (PBM) is nearly tied for best ChIP-chip score with the best ChIP-chip motif. Still, ChIP motif 397 scores higher, and looks identical, but with fewer flanking empty positions.
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!
YDL170W	UGA3	486	Medium		Appears to be a monomeric GAL4-class motif. Derived from PBM data, scores highly in ChIP-chip data, but not as high as the dimeric site derived from the ChIP-chip data.
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.
YDR207C	UME6	2239	High		All motifs are similar to each other. BEEML-PBM motif 2239 scores highest across the board.
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.
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.
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.
YIL056W	VHR1	2091	Medium		PBM motif has high score on GO because it looks a lot like Gcn4
YDR485C	VPS72	0		Dubious	Unlikely to be true TF.
YML076C	WAR1	325	Low		None of the motifs are convincing, but at least sequences with the literature motif have been experimentally confirmed to bind the protein (even if it is not shown that this is the optimal binding site)
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.
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.
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.
YML007W	YAP1	2186	High		PBM motif 2186 looks like a monomeric bZIP site but it has the highest scores on both ChIP and expression
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.
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.
YIR018W	YAP5	777	High		ChIP-chip yields a classic 7-mer Yap motif that scores well on ChIP and significantly on expression.
YIR018W	YAP5	896	Incorrect		Likely represents Rap1 binding site.
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.
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
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.
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.
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.
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.
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.
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