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Systematic Name Gene Name Motif ID Expert Confidence Dubious? Notes
V 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.
V 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.
V YNR063W   804 High   Motifs from PBMs are virtually identical. This is a monomeric GAL4-like motif. 804 agrees more with ChIP-chip data.
V MATA1   0     Need to study literature more carefully and consult experts.but at first glance none of these motifs seems right
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 YLR278C   2112 High   Only 2112 (from PBMs) stands out; dimeric GAL4 motif with high score on ChIP-chip.
V YPR022C   588 High   Only one motif available, from PBMs; classical yeast C2H2 motif, and has some relationship to ChIP-chip data.
V 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.
V YER064C   2094 Medium   PBM motif has high score on GO because it looks a lot like Gcn4
V 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.
V 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.
V YJL206C   0     Seven motifs from ChIP-chip, but none of them corresponds well to ChIP-chip data, and none of them resembles a GAL4 motif. 1169 has a CGG in the middle, but too much flanking information to be credible without further independent support.
V MAL63   136 Medium   This is an unconventional dimeric GAL4-class motif
V YDR026C   696 High   Three ChIP-chip motifs are virtually identical in appearance; resemble Reb1 motifs; high correspondence to ChIP-chip data
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 YKL222C   2192 High   Two motifs from PBMs resemble monomeric GAL4-like motif. 2192 agrees best with ChIP-chip data and expression data.
V MATA1-MATALPHA2-dimer a1-alpha2-dimer 1436 Medium   Not clear that motif is optimal.
V 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
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 YLR131C ACE2 1332 High   Highest-scoring ChIP-chip motif is Rap1 site. MITOMI motif 1332 is next, and resembles the classic Swi5/Ace2 motif.
V YLR131C ACE2 918 Incorrect   Likely represents Rap1 binding site.
V 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.
V 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.
V YPL202C AFT2 389 High   All motifs look similar. ChIP-chip motif 389 scores high on ChIP-chip data and also best on expression data.
V MATALPHA1-MCM1-dimer alpha1-MCM1-dimer 1442 Medium   Not clear that motif is optimal.
V YER069W ARG5,6 1426 Medium   Not clear that motif is optimal.
V YMR042W ARG80 1483 Medium   Motif 1482 is an Arg81 site. 1483, however, is similar to Mcm1. Choose this, give Medium confidence.
V YML099C ARG81 1506 High   ChIP motif 1506 correlates well with ChIP and also with expression data. Resembles dimeric GAL4 class motif.
V YML099C ARG81 1507 Incorrect   Likely represents Mcm1 binding site.
V 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.
V 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.
V 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.
V YPR199C ARR1 603 Medium   Only motif 603 has significant scores with ChIP-chip and expression data; looks somewhat like a YAP motif
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 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 YKL185W ASH1 932 Incorrect   Likely represents Mcm1 binding site.
V YKL185W ASH1 648 Incorrect   Likely represents Mcm1 binding site.
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 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.
V 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.
V 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.
V 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.
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 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
V YMR168C CEP3 524 High   Two PBM motifs agree. Went with 524 because it appears neater. No other supporting data for any of them.
V YLR098C CHA4 1607 Incorrect   Likely represents Rap1 binding site.
V 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).
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 YOR028C CIN5 409 High   Most motifs match the classic YAP motif. This is the best in vivo motif (highest match to ChIP-chip).
V 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.
V 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.
V YNL027W CRZ1 516 High   PBM motif 516 scores highest on ChIP and expression; resembles classic literature motifs
V 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.
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 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.
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 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.
V 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.
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 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.
V 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.
V 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.
V YPL021W ECM23 578 High   PBM motif 578 strongly resembles that from other yeast GATA-class TFs
V YBR033W EDS1 2093 High   PBM and ChIP-chip motifs are very similar. PBM motif 2093 scores most significantly on ChIP data. Classic GAL4 class motif.
V 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 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.
V YPR104C FHL1 406 Incorrect   Likely represents Rap1 binding site.
V YPR104C FHL1 893 Incorrect   Likely represents Rap1 binding site.
V YPR104C FHL1 1618 Incorrect   Likely represents Rap1 binding site.
V YPR104C FHL1 629 Incorrect   Likely represents Rap1 binding site.
V YPR104C FHL1 1196 Incorrect   Likely represents Rap1 binding site.
V YPR104C FHL1 1504 Incorrect   Likely represents Rap1 binding site.
V 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).
V YNL068C FKH2 830 High   Most motifs are classic Forkhead. PBM motif 830 is one of the highest scoring and is not circular.
V 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.
V 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.
V 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.
V 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.
V YFL021W GAT1 962 High   ChIP-chip motif 962 scores higher on both ChIP-chip and expression data
V 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.
V 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.
V 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.
V 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).
V YDR096W GIS1 562 High   All motifs similar; PBM motif 562 has highest correspondence to deletion expression data and overexpression data
V YER040W GLN3 539 High   Most motifs are classic GATA or GATAAG. PBM motif 539 scores highest on ChIP.
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 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.
V YJL110C GZF3 2133 High   Classic GATA motif 2133 from PBM scores highest on ChIP-chip and expression data
V YPR008W HAA1 1425 Medium   Literature motif is not completely determined, but scores highly on ChIP-chip data. Regardless, medium confidence.
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 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.
V YOL089C HAL9 799 High   PBM motifs 799 and 2134 score highest on ChIP-chip data; classic dimeric and monomeric GAL4 sites, respectively.
V YOL089C HAL9 2134 High   PBM motifs 799 and 2134 score highest on ChIP-chip data; classic dimeric and monomeric GAL4 sites, respectively.
V 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.
V 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.
V YBL021C HAP3 695 High   Subunit of the heme-activated, glucose-repressed Hap2/3/4/5 CCAAT-binding complex - there should be a single motif for all four proteins, containing CCAAT. ChIP-chip motif 695 resembles CCAATCA, and scores highly on ChIP-chip, OE, and deletion expression data.
V 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.
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