|
|
|
|
|
|
|
V |
YDR174W |
HMO1 |
2249 |
Low |
|
This motif is uncharacteristic for a Sox protein and HMG proteins typically do not bind DNA in a sequence specific manner. Since it is from ChIP data it could be a cofactor motif. Low confidence. |
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 |
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 |
YDR207C |
UME6 |
2239 |
High |
|
All motifs are similar to each other. BEEML-PBM motif 2239 scores highest across the board. |
V |
YPR009W |
SUT2 |
2236 |
High |
|
Highest-scoring motif (PBM) is a classical GAL4-type monomeric motif and is very significant in ChIP-chip |
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 |
YCR018C |
SRD1 |
2232 |
Medium |
|
PBM studies yield nearly identical motifs. 2232 closely resembles motif from related GATA factors and scores highest overall. This is an unusual motif for the GATA class; hence medium confidence level. |
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 |
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 |
YKL015W |
PUT3 |
2223 |
Medium |
|
Motifs vary considerably. ChIP motif 2065 is a dimeric/(trimeric?) GAL4-like site, and has the highest correspondence to ChIP-chip data (from which it is derived) and some correspondence to expression data (although it is not strong). PBM motif 2223 is a monomeric GAL4-like motif and has higher correspondence to expression data, albeit weaker (but still good) correspondence to ChIP-chip data. It is possible that the actual sequence preference is some other arrangement of monomeric sites that were not picked up in either assay - score as medium confidence. |
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 |
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 |
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 |
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 |
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 |
YKL222C |
|
2192 |
High |
|
Two motifs from PBMs resemble monomeric GAL4-like motif. 2192 agrees best with ChIP-chip data and 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 |
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 |
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 |
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 |
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 |
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 |
YHR056C |
RSC30 |
2164 |
Medium |
|
Arbitrary choice - all PBM motifs look similar (and resemble motif from homolog Rsc3). I have downgraded this one from high to medium because the best scoring motif actually looks the least like the Rsc3 motif. |
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 |
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 |
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 |
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 |
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 |
YGR249W |
MGA1 |
2141 |
Medium |
|
PBM motif 2141 is similar to Hsf1 motif 476 (TTCCA). Has TTC "core" which is shared by most Hsf1 motifs. Scores reasonably on ChIP data but no other supporting information; hence "medium". |
V |
YDR253C |
MET32 |
2140 |
High |
|
Most motifs look similar. PBM motif 2140 has highest correspondence to both ChIP and expression. |
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 |
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 |
YOL089C |
HAL9 |
2134 |
High |
|
PBM motifs 799 and 2134 score highest on ChIP-chip data; classic dimeric and monomeric GAL4 sites, respectively. |
V |
YJL110C |
GZF3 |
2133 |
High |
|
Classic GATA motif 2133 from PBM scores highest on 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 |
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 |
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 |
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 |
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 |
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 |
YLR278C |
|
2112 |
High |
|
Only 2112 (from PBMs) stands out; dimeric GAL4 motif with high score on ChIP-chip. |
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 |
YCL067C |
HMLALPHA2 |
2102 |
Medium |
|
Protein is similar to PBX/MEIS/TGIF; both PBM motifs have some similarity (central ACA/TGT), so do sites in crystal and in vivo (e.g. PMID: 1682054) but no clear winner between the two. Keep both PBM motifs in curated set (2102 and 2079) but give medium confidence - no supporting ChIP or 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 |
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 |
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 |
YER064C |
|
2094 |
Medium |
|
PBM motif has high score on GO because it looks a lot like Gcn4 |
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 |
YIL056W |
VHR1 |
2091 |
Medium |
|
PBM motif has high score on GO because it looks a lot like Gcn4 |
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 |
YCL067C |
HMLALPHA2 |
2079 |
Medium |
|
Protein is similar to PBX/MEIS/TGIF; both PBM motifs have some similarity (central ACA/TGT), so do sites in crystal and in vivo (e.g. PMID: 1682054) but no clear winner between the two. Keep both PBM motifs in curated set (2102 and 2079) but give medium confidence - no supporting ChIP or expression data. |
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 |
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 |
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 |
YHR178W |
STB5 |
2068 |
Medium |
|
All motifs have CGG core and most have CGGnG. Most ChIP-derived motifs have no relationship to expression data. Motif 2068 scores highest overall; looks a bit unusual for a Gal4 class motif but also does well on expression data. Retain as potential dimer motif, although it may also incorporate extrinsic information. |
V |
YJL089W |
SIP4 |
2067 |
Medium |
|
PBM motif 573 is a monomeric GAL4-type motif (others appear dimeric) but it has good correspondence to ChIP-chip data. Only a few of the dimeric sites are more significant - the motif from in vivo analysis (PMID: 14685767) does not score as highly as 2067 from ChIP-chip data, but they look very similar. This is 2067, the presumed dimeric site. |
V |
YKL015W |
PUT3 |
2065 |
Medium |
|
Motifs vary considerably. ChIP motif 2065 is a dimeric/(trimeric?) GAL4-like site, and has the highest correspondence to ChIP-chip data (from which it is derived) and some correspondence to expression data (although it is not strong). PBM motif 2223 is a monomeric GAL4-like motif and has higher correspondence to expression data, albeit weaker (but still good) correspondence to ChIP-chip data. It is possible that the actual sequence preference is some other arrangement of monomeric sites that were not picked up in either assay - score as medium confidence. |
V |
YLR014C |
PPR1 |
2064 |
Low |
|
ChIP-chip motif 2064 almost matches the literature site, which has been confirmed by directed experimentation, and scores highest on most measures. But, give it low confidence - it is not at all clear that this is an optimal binding site, and none of the scores for any of the motifs are all that high. |
V |
YBL005W |
PDR3 |
2062 |
Medium |
|
MITOMI yields a simple GAL4 monomeric site that scores well in ChIP-chip data. ChIP-chip yields a dimeric site that resembles the literature site. In vivo, PDR1 and PDR3 may form heterodimers. Retain both. This is the dimeric ChIP-chip motif. |
V |
YAL051W |
OAF1 |
2060 |
Medium |
|
Motif 2060 has a strong resemblance to the literature motifs for the Oaf1-Pip2 dimer, and scores highly on both ChIP and expression data. No in vitro support and it's kind of weak looking so Medium confidence. |
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 |
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 |
YJL127C |
SPT10 |
1880 |
Low |
|
This is the protein that binds histone promoters. The sequence specificity is derived from the histone promoters only so the literature motif may be inaccurate. Motif 1880 has higher scores overall but does not resemble the literature motif. Uncertain what to do here - use 1880, but give low confidence. Motif learned in vivo could contain extrinsic information. |
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 |
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 |
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 |
YLR403W |
SFP1 |
1710 |
Incorrect |
|
Likely represents Rap1 binding site. |
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 |
YDL106C |
PHO2 |
1680 |
Incorrect |
|
Likely represents Abf1 binding site. |
V |
YPR104C |
FHL1 |
1618 |
Incorrect |
|
Likely represents Rap1 binding site. |
V |
YLR098C |
CHA4 |
1607 |
Incorrect |
|
Likely represents Rap1 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 |
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 |
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 |
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 |
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 |
YPR104C |
FHL1 |
1504 |
Incorrect |
|
Likely represents Rap1 binding site. |
V |
YOR032C |
HMS1 |
1498 |
Medium |
|
Motif 1498 scores reasonably on ChIP. Other corroborating data are not that convincing - medium 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 |
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 |
YMR042W |
ARG80 |
1483 |
Medium |
|
Motif 1482 is an Arg81 site. 1483, however, is similar to Mcm1. Choose this, give Medium confidence. |
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 |
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 |
YGL073W |
HSF1 |
1461 |
Medium |
|
Four types of motifs contain TTC monomeric core and all score highly on both ChIP and expression. Appear to represent different monomeric/multimeric binding configurations. This is the dimeric head-to-tail site. From ChIP and prior. |
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 |
YBL103C |
RTG3 |
1446 |
Low |
|
Only the PBM motif is a classic HLH motif. Three different ChIP-chip-derived motifs are all diverse, but all score highly on ChIP-chip data! Are they motifs of other TFs? Check. 602: GCN4; 1095, TEC1; 1096: resembles 602, but is a closer match to CUP9/TOS8. Also hits GCN4. According to the literature (PMID: 9032238) the core binding site for the Rtg1p-Rtg3p heterodimer is 5'-GGTCAC-3'; the only motif that resembles this is 1446. Vague resemblance to 602 and 1096. I am going to retain 1446, which represents the literature site; PBM motif 870, which resembles an E-box, and ChIP-chip motif 1445, which scores highest on ChIP-chip data. But give all low confidence. |
V |
YBL103C |
RTG3 |
1445 |
Low |
|
Only the PBM motif is a classic HLH motif. Three different ChIP-chip-derived motifs are all diverse, but all score highly on ChIP-chip data! Are they motifs of other TFs? Check. 602: GCN4; 1095, TEC1; 1096: resembles 602, but is a closer match to CUP9/TOS8. Also hits GCN4. According to the literature (PMID: 9032238) the core binding site for the Rtg1p-Rtg3p heterodimer is 5'-GGTCAC-3'; the only motif that resembles this is 1446. Vague resemblance to 602 and 1096. I am going to retain 1446, which represents the literature site; PBM motif 870, which resembles an E-box, and ChIP-chip motif 1445, which scores highest on ChIP-chip data. But give all low confidence. |
V |
MATALPHA1-MCM1-dimer |
alpha1-MCM1-dimer |
1442 |
Medium |
|
Not clear that motif is optimal. |
V |
MATA1-MATALPHA2-dimer |
a1-alpha2-dimer |
1436 |
Medium |
|
Not clear that motif is optimal. |
V |
YER069W |
ARG5,6 |
1426 |
Medium |
|
Not clear that motif is optimal. |
V |
YPR008W |
HAA1 |
1425 |
Medium |
|
Literature motif is not completely determined, but scores highly on ChIP-chip data. Regardless, medium confidence. |
V |
YCR040W |
MATALPHA1 |
1418 |
Low |
|
According to PMID: 15118075, binds the "Q site" which has "consensus" ACAATGACAG. Seems all that is in common is the CAAT. I believe further study is required. |
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 |
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 |
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 |
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. |