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Systematic Name Gene Name Motif ID Expert Confidence Dubious? Notes
V YPR199C ARR1 603 Medium   Only motif 603 has significant scores with ChIP-chip and expression data; looks somewhat like a YAP motif
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 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 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 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 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.
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 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 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 YPR009W SUT2 2236 High   Highest-scoring motif (PBM) is a classical GAL4-type monomeric motif and is very significant in ChIP-chip
V YPR008W HAA1 1425 Medium   Literature motif is not completely determined, but scores highly on ChIP-chip data. Regardless, medium confidence.
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 YPL230W USV1 509 High   Two PBM studies essentially agree on classical C2H2 GGGG-containing motif. Chose 509 because it scores much higher on both ChIP and expression data.
V 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 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 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 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.
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 YPL089C RLM1 1079 Incorrect   Likely represents Mcm1 binding site.
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 YPL038W MET31 1370 High   Most motifs look similar. MITOMI motif 1370 has highest overall correlation to ChIP-chip, OE, and deletion data.
V YPL021W ECM23 578 High   PBM motif 578 strongly resembles that from other yeast GATA-class TFs
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 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.
V YOR372C NDD1 366 Incorrect   Likely represents Mcm1 binding site.
V YOR363C PIP2 0     See Oaf1-Pip2-dimer
V 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.
V 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.
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 YOR172W YRM1 813 High   Two PBM studies largely agree on classic GAL4-class monomeric motif. Motif 813 has indications of spacing and orientation of dimeric protein.
V YOR162C YRR1 2245 High   Classic monomeric GAL4-class motif. PBM studies agree and score significantly on Harbison data. No other motifs have spacing/orientation except 11909958, but even the authors of this study note that "Only half a dyad seems to be conserved in this consensus sequence". 2245 scores highest in Harbison data.
V 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 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 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 YOR032C HMS1 1498 Medium   Motif 1498 scores reasonably on ChIP. Other corroborating data are not that convincing - medium confidence.
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 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 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.
V 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.
V 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.
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 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 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 YOL028C YAP7 1737 High   7-base bZIP core. Obtained in ChIP-chip studies and higher correspondence to stressed ChIP-chip data. Possible heterodimer? Little literature on this protein. 1737 chosen because it is largely symmetric and has highest score for both stressed and unstressed Harbison data, also, higher GO score
V YOL028C YAP7 1414 High   8-base bZIP core. Obtained by Mitomi, so this is a homodimer. Higher correspondence to unstressed ChIP-chip data. Little literature on this protein. 1414 chosen for higher ChIP-chip overall scores; plus, it is a palindrome as expected for a bZIP protein.
V YNR063W   804 High   Motifs from PBMs are virtually identical. This is a monomeric GAL4-like motif. 804 agrees more with ChIP-chip data.
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 YNL216W RAP1 254 High   Most motifs look similar. ChIP-chip motif 254 has highest correspondence to expression data.
V 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.
V YNL103W MET4 0     My understanding is that Met4 is a modifier of the specificity of other proteins. SGD states that it "requires different combinations of the auxiliary factors Cbf1p, Met28p, Met31p and Met32p". ChIP-chip motifs 1023 and 1024 I believe are cofactor motifs; they are E-boxes. ChIP-chip motif 689 is different and matches Met28 and Met32 motifs. (CTGTGG core). Met28 is a bZIP protein, and Met32 is a C2H2. MITOMI motif for Met32 is TGTGG. So this is the Met32 motif. I do not believe that any of the Met4 motifs is correct. Need to obtain motifs for complexes.
V YNL068C FKH2 830 High   Most motifs are classic Forkhead. PBM motif 830 is one of the highest scoring and is not circular.
V YNL027W CRZ1 516 High   PBM motif 516 scores highest on ChIP and expression; resembles classic literature motifs
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 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.
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 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 YMR053C STB2 710 Incorrect   Likely represents Reb1 binding site.
V 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.
V YMR042W ARG80 1483 Medium   Motif 1482 is an Arg81 site. 1483, however, is similar to Mcm1. Choose this, give Medium confidence.
V YMR037C MSN2 1380 High   MITOMI motif 1380 has the highest overall correspondence to ChIP-chip, overexpression, and deletion data. Resembles classic Msn2/4 motif.
V 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.
V 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.
V YMR016C SOK2 404 High   ChIP-chip motif 404 has highest correspondence to both ChIP-chip and expression data - and strongly resembles PBM motif
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 YML099C ARG81 1507 Incorrect   Likely represents Mcm1 binding site.
V YML099C ARG81 1506 High   ChIP motif 1506 correlates well with ChIP and also with expression data. Resembles dimeric GAL4 class motif.
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 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 YML065W ORC1 1549 High   Looks like ORC1 motif. Which is not really a TF, but it is a sequence-specific DNA-binding protein.
V YML027W YOX1 498 High   Two PBM studies and Pramila et al. (PMID 12464633) agree on classic homeodomain TAATTA motif. All three correlate with expression change and OE. Motif 453 is not a direct measurement so choose PBM motif that is the same length as the typical homeodomain footprint - 498 also correlates best with OE data; expression scores are skewed low by the large number of cell-cycle measurements.
V YML007W YAP1 2186 High   PBM motif 2186 looks like a monomeric bZIP site but it has the highest scores on both ChIP and expression
V 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.
V 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.
V 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.
V YLR403W SFP1 621 Incorrect   Likely represents Rap1 binding site.
V YLR403W SFP1 1710 Incorrect   Likely represents Rap1 binding site.
V YLR403W SFP1 1100 Incorrect   Likely represents Rap1 binding site.
V YLR403W SFP1 357 Incorrect   Likely represents Rap1 binding site.
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 YLR278C   2112 High   Only 2112 (from PBMs) stands out; dimeric GAL4 motif with high score on ChIP-chip.
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 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 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 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 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 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 YLR098C CHA4 1607 Incorrect   Likely represents Rap1 binding site.

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