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Systematic Name Gene Name Motif ID Expert Confidence Dubious? Notes
V YIL056W VHR1 2091 Medium   PBM motif has high score on GO because it looks a lot like Gcn4
V 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.
V 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.
V TBP-TFIIB TBP-TFIIB 1329 Medium   The TIRF-PBM data used to generate the motif included only 96 sequences; hence, medium confidence.
V TBP-TFIIA-TFIIB TBP-TFIIA-TFIIB 1330 Medium   The TIRF-PBM data used to generate the motif included only 96 sequences; hence, medium confidence.
V 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.
V 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.
V 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.
V 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.
V 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.
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 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.
V 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
V 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.
V 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.
V 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.
V 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.
V 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.
V 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.
V 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.
V 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.
V 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.
V 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.
V 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.
V 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.
V 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.
V 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.
V 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.
V 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.
V 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.
V 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.
V 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.
V 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
V 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.
V 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".
V 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.
V 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.
V 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.
V 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.
V YOR032C HMS1 1498 Medium   Motif 1498 scores reasonably on ChIP. Other corroborating data are not that convincing - medium confidence.
V YCR096C HMRA2 558 Medium   Should be similar to MATALPHA2. The one PBM motif is indeed related to the MITOMI motif for MATALPHA2.
V 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.
V 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.
V 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.
V YPR008W HAA1 1425 Medium   Literature motif is not completely determined, but scores highly on ChIP-chip data. Regardless, medium confidence.
V 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.
V 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.
V 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.
V 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).
V 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
V 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?
V 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.
V 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.
V 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.
V 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.
V YPR199C ARR1 603 Medium   Only motif 603 has significant scores with ChIP-chip and expression data; looks somewhat like a YAP motif
V YMR042W ARG80 1483 Medium   Motif 1482 is an Arg81 site. 1483, however, is similar to Mcm1. Choose this, give Medium confidence.
V YER069W ARG5,6 1426 Medium   Not clear that motif is optimal.
V MATALPHA1-MCM1-dimer alpha1-MCM1-dimer 1442 Medium   Not clear that motif is optimal.
V 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.
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 MATA1-MATALPHA2-dimer a1-alpha2-dimer 1436 Medium   Not clear that motif is optimal.
V 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.
V 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.
V 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.
V 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.
V 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.
V YER064C   2094 Medium   PBM motif has high score on GO because it looks a lot like Gcn4
V MAL63   136 Medium   This is an unconventional dimeric GAL4-class motif
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 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)
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 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 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.
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 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 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 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 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.
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 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 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.
V 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.
V 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.
V 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.
V 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.
V 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.
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 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.
V 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.
V 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.
V 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.
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 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 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.
V YCL055W KAR4 127 Low Dubious Evidence for sequence specific DNA binding seems weak, hence low confidence
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 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 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.
V 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.

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