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Systematic Name Gene Name Motif ID Expert Confidence Dubious? Notes
V MATA1   0     Need to study literature more carefully and consult experts.but at first glance none of these motifs seems right
V MBP1-SWI6-dimer MBP1-SWI6-dimer 0     Redundant with MBP1
V YBR297W MAL33 0     None of the ChIP-chip motifs correspond wekk to the data they come from and/or resemble a GAL4 motif.
V YGR288W MAL13 0     None of the ChIP-chip motifs correspond wekk to the data they come from and/or resemble a GAL4 motif.
V 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.
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 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.
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 YOR363C PIP2 0     See Oaf1-Pip2-dimer
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 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.
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 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.
V 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.
V 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.
V 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.
V 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.
V 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.
V YBR267W REI1 489 High   PBM motif looks like a yeast C2H2 motif (row of C's); highly significant relationship to ChIP-chip data
V 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.
V 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.
V 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.
V 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.
V 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.
V 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.
V 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!
V YDR026C   696 High   Three ChIP-chip motifs are virtually identical in appearance; resemble Reb1 motifs; high correspondence to ChIP-chip data
V 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.
V 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.
V 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.
V YDR096W GIS1 562 High   All motifs similar; PBM motif 562 has highest correspondence to deletion expression data and overexpression data
V 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.
V 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.
V 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.
V YDR207C UME6 2239 High   All motifs are similar to each other. BEEML-PBM motif 2239 scores highest across the board.
V 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.
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 YDR253C MET32 2140 High   Most motifs look similar. PBM motif 2140 has highest correspondence to both ChIP and expression.
V 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.
V 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.
V YDR310C SUM1 478 High   This is the motif for the SUM1 AT_hook; scores highest in deletion expression data
V 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
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 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 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 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.
V 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.
V 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.
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 YER028C MIG3 2144 High   PBM motif 2144 has highest correspondence to ChIP-chip data
V YER040W GLN3 539 High   Most motifs are classic GATA or GATAAG. PBM motif 539 scores highest on ChIP.
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 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.
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 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
V 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.
V YFL021W GAT1 962 High   ChIP-chip motif 962 scores higher on both ChIP-chip and expression data
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 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.
V 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.
V 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.
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 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.
V YGL209W MIG2 2143 High   PBM motif 2143 has highest correspondence to ChIP-chip data
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 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 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.
V 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.
V 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.
V 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.
V 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.
V 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.
V 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
V 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.
V 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.
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 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.
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 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 YIR018W YAP5 777 High   ChIP-chip yields a classic 7-mer Yap motif that scores well on ChIP and significantly on expression.
V 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
V YJL110C GZF3 2133 High   Classic GATA motif 2133 from PBM scores highest on ChIP-chip and expression data
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 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).
V 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.
V 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).
V 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.
V 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.
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.
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 YKL222C   2192 High   Two motifs from PBMs resemble monomeric GAL4-like motif. 2192 agrees best with ChIP-chip data and expression data.
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 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 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 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 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 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.

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