Browse Motifs Help/About View Cart
Search for TF:
Selected Version: 1.02 - CHANGE

Browsing Expert Curation...

Need help?
Systematic Name Gene Name Motif ID Expert Confidence Dubious? Notes
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 YOR363C PIP2 0     See Oaf1-Pip2-dimer
V MBP1-SWI6-dimer MBP1-SWI6-dimer 0     Redundant with MBP1
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 YBR297W MAL33 0     None of the ChIP-chip motifs correspond wekk to the data they come from and/or resemble a GAL4 motif.
V MATA1   0     Need to study literature more carefully and consult experts.but at first glance none of these motifs seems right
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 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 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 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 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 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 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 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 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 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 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 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 YKL222C   2192 High   Two motifs from PBMs resemble monomeric GAL4-like motif. 2192 agrees best with ChIP-chip data and expression data.
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 YDR026C   696 High   Three ChIP-chip motifs are virtually identical in appearance; resemble Reb1 motifs; high correspondence to ChIP-chip data
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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 YBR267W REI1 489 High   PBM motif looks like a yeast C2H2 motif (row of C's); highly significant relationship to ChIP-chip 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 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 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 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 YPL021W ECM23 578 High   PBM motif 578 strongly resembles that from other yeast GATA-class TFs
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 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 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 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 YNL027W CRZ1 516 High   PBM motif 516 scores highest on ChIP and expression; resembles classic literature motifs
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 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 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 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 YER028C MIG3 2144 High   PBM motif 2144 has highest correspondence to ChIP-chip data
V YGL209W MIG2 2143 High   PBM motif 2143 has highest correspondence to ChIP-chip data
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 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 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 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 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 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 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 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 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 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 YPR022C   588 High   Only one motif available, from PBMs; classical yeast C2H2 motif, and has some relationship to ChIP-chip data.
V YLR278C   2112 High   Only 2112 (from PBMs) stands out; dimeric GAL4 motif with high score on ChIP-chip.
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 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 YNR063W   804 High   Motifs from PBMs are virtually identical. This is a monomeric GAL4-like motif. 804 agrees more with ChIP-chip data.
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 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 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 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 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 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 YOR028C CIN5 409 High   Most motifs match the classic YAP motif. This is the best in vivo motif (highest match to ChIP-chip).
V YDR253C MET32 2140 High   Most motifs look similar. PBM motif 2140 has highest correspondence to both ChIP and expression.
V YPL038W MET31 1370 High   Most motifs look similar. MITOMI motif 1370 has highest overall correlation to ChIP-chip, OE, and deletion data.
V YNL216W RAP1 254 High   Most motifs look similar. ChIP-chip motif 254 has highest correspondence to expression data.
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 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 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 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 YER040W GLN3 539 High   Most motifs are classic GATA or GATAAG. PBM motif 539 scores highest on ChIP.
V YNL068C FKH2 830 High   Most motifs are classic Forkhead. PBM motif 830 is one of the highest scoring and is not circular.
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 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 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.
 Download displayed records: text csv html excel word Page: 1 of 4  Records: 354