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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 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 1504 Incorrect   Likely represents Rap1 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 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 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 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 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 YPL216W   0   Dubious Unlikely to be true TF.
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 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 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 YPL049C DIG1 0   Dubious Not a TF - it binds Ste12; all the motifs are Ste12 motifs.
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 YPL016W SWI1 0   Dubious Unlikely to be true TF.
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 YOR372C NDD1 0   Dubious There is no evidence that this is a sequence-specific DNA-binding protein, either in vitro or in vivo or in its sequence. The ChIP-chip motif that scores most highly is actually an MCM1 motif, which is consistent with the role of NDD1 as a "transcriptional activator essential for nuclear division".
V 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 YOR308C SNU66 0   Dubious Unlikely to be true TF.
V YOR304W ISW2 0   Dubious Unlikely to be true TF.
V YOR298C-A MBF1 0   Dubious This is a coactivator. I found no evidence that it is a sequence-specific TF.
V YOR290C SNF2 0   Dubious Unlikely to be true TF.
V 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 YOR229W WTM2 0   Dubious It is not clear that this is a sequence-specific DNA-binding protein; it contains no DNA-binding domain and has no known in vitro sequence specificity. The motif comes only from ChIP-chip so scoring on ChIP-chip is circular.
V 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 YOR156C NFI1 0   Dubious Unlikely to be true TF.
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 YOR077W RTS2 0   Dubious Homolog of Kin17; not a typical C2H2 zinc finger. Believed to be "chromatin-associated proteins involved in UV response and DNA replication". No evidence for sequence-specific DNA-binding. Single ChIP-chip motif does not have strong correspondence to the data from which it is derived.
V YOR038C HIR2 0   Dubious Hir1,2,3 are a nucleosome assembly complex, not TFs
V 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 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 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 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 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 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 YNR054C ESF2 0   Dubious This is supposed to be a ribosome biogenesis factor. I found no evidence that it is a sequence-specific DNA-binding protein.
V 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 YNL309W STB1 0   Dubious No direct evidence that this is a DNA-binding protein. It binds Swi6 and the ChIP motifs all resemble Swi4 binding sites.
V YNL257C SIP3 0   Dubious Sip3 is a protein that "transcription through interaction with DNA-bound Snf1p" (SGD); no DNA-binding domain and no evidence for direct interaction with DNA or intrinsic sequence specificity.
V YNL227C JJJ1 0   Dubious Unlikely to be true TF.
V YNL216W RAP1 254 High   Most motifs look similar. ChIP-chip motif 254 has highest correspondence to expression data.
V YNL199C GCR2 0   Dubious Gcr2 is not a DNA-binding protein. SGD: "Gcr1p is a DNA-binding protein interacting with the consensus sequence CTTCC, whereas Gcr2p interacts with Gcr1p". But, ChIP-chip motif 606 is probably the best Gcr1 motif available (even though it came from Gcr2 ChIP).
V 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 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 YNL132W KRE33 0   Dubious This is supposed to be a ribosome biogenesis factor. I found no evidence that it is a sequence-specific DNA-binding protein.
V 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 YNL079C TPM1 0   Dubious Unlikely to be true TF.
V YNL068C FKH2 830 High   Most motifs are classic Forkhead. PBM motif 830 is one of the highest scoring and is not circular.
V YNL039W BDP1 0   Dubious Unlikely to be true TF.
V YNL027W CRZ1 516 High   PBM motif 516 scores highest on ChIP and expression; resembles classic literature motifs
V YNL023C FAP1 0   Dubious Unlikely to be true TF.
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 YMR213W CEF1 0   Dubious Unlikely to be true TF.
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 YMR176W ECM5 0   Dubious Unlikely to be true TF.
V YMR172W HOT1 0   Dubious Unlikely to be true TF.
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 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 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 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 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 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 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.

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