|
|
|
|
|
|
|
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 |
MATA1 |
|
0 |
|
|
Need to study literature more carefully and consult experts.but at first glance none of these motifs seems right |
V |
YPL216W |
|
0 |
|
Dubious |
Unlikely to be true TF. |
V |
YLR211C |
|
0 |
|
Dubious |
Unlikely to be true TF. |
V |
YGR071C |
|
0 |
|
Dubious |
Unlikely to be true TF. |
V |
YFL052W |
|
0 |
|
Dubious |
Putative zinc-cluster protein. |
V |
YDR049W |
|
0 |
|
Dubious |
No evidence this is a TF, aside from a poorly-scoring C2H2 zinc finger |
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 |
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 |
YNR063W |
|
804 |
High |
|
Motifs from PBMs are virtually identical. This is a monomeric GAL4-like motif. 804 agrees more with ChIP-chip 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 |
YLR278C |
|
2112 |
High |
|
Only 2112 (from PBMs) stands out; dimeric GAL4 motif with high score on 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 |
YDR026C |
|
696 |
High |
|
Three ChIP-chip motifs are virtually identical in appearance; resemble Reb1 motifs; high correspondence to ChIP-chip data |
V |
YDR266C |
|
1161 |
Low |
|
Motifs from ChIP-chip do not correspond to ChIP-chip, and there is no other supporting data. Chose 1161 only because it looks more reasonable. Low confidence. |
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 |
YLL054C |
|
816 |
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 |
YLL054C |
|
526 |
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 |
YER184C |
|
512 |
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 |
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 |
MAL63 |
|
136 |
Medium |
|
This is an unconventional dimeric GAL4-class motif |
V |
MATA1-MATALPHA2-dimer |
a1-alpha2-dimer |
1436 |
Medium |
|
Not clear that motif is optimal. |
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 |
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 |
YER045C |
ACA1 |
8 |
Medium |
|
Literature motif 8 is supported by experimental investigation, and resembles a bZIP site, but has no other support; motif was not obtained objectively. Can bind as heterodimer. The highest-scoring motif (from ChIP, 1457) has low information content - I'm concerned it is learning other features of bound promoters. |
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 |
YDR448W |
ADA2 |
0 |
|
Dubious |
Unlikely to be true TF. |
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 |
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 |
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 |
MATALPHA1-MCM1-dimer |
alpha1-MCM1-dimer |
1442 |
Medium |
|
Not clear that motif is optimal. |
V |
YER069W |
ARG5,6 |
1426 |
Medium |
|
Not clear that motif is optimal. |
V |
YMR042W |
ARG80 |
1483 |
Medium |
|
Motif 1482 is an Arg81 site. 1483, however, is similar to Mcm1. Choose this, give Medium confidence. |
V |
YML099C |
ARG81 |
1506 |
High |
|
ChIP motif 1506 correlates well with ChIP and also with expression data. Resembles dimeric GAL4 class motif. |
V |
YML099C |
ARG81 |
1507 |
Incorrect |
|
Likely represents Mcm1 binding site. |
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 |
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 |
YPR199C |
ARR1 |
603 |
Medium |
|
Only motif 603 has significant scores with ChIP-chip and expression data; looks somewhat like a YAP motif |
V |
YIL130W |
ASG1 |
807 |
Medium |
|
Two PBM motifs appear to represent monomeric and dimeric versions of the same motif. This is the dimeric version. No other supporting data; hence medium confidence. |
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 |
YKL185W |
ASH1 |
648 |
Incorrect |
|
Likely represents Mcm1 binding site. |
V |
YKL185W |
ASH1 |
932 |
Incorrect |
|
Likely represents Mcm1 binding site. |
V |
YKL185W |
ASH1 |
28 |
Medium |
|
The literature motif may not represent the full binding activity of the protein. Also, it is not supported by ChIP-chip. ChIP-chip identifies Mcm1-like motifs. But, it does score highly in both ChIP-chip and expression. The only higher-scoring motif has almost no information content. |
V |
YGR097W |
ASK10 |
0 |
|
Dubious |
I did not find any evidence that this is a sequence-specific DNA-binding protein. |
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 |
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 |
YNL039W |
BDP1 |
0 |
|
Dubious |
Unlikely to be true TF. |
V |
YDL074C |
BRE1 |
0 |
|
Dubious |
Unlikely to be true TF. |
V |
YER159C |
BUR6 |
0 |
|
Dubious |
Unlikely to be true TF. |
V |
YKL005C |
BYE1 |
0 |
|
Dubious |
SGD: "Negative regulator of transcription elongation, contains a TFIIS-like domain and a PHD finger, multicopy suppressor of temperature-sensitive ess1 mutations, probably binds RNA polymerase II large subunit". No evidence this is a sequence-specific TF. |
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 |
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 |
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 |
YGR140W |
CBF2 |
0 |
|
Dubious |
Unlikely to be true TF. |
V |
YMR213W |
CEF1 |
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 |
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. |
V |
YER164W |
CHD1 |
0 |
|
Dubious |
Unlikely to be true TF. |
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 |
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 |
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 |
YNL027W |
CRZ1 |
516 |
High |
|
PBM motif 516 scores highest on ChIP and expression; resembles classic literature motifs |
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 |
YGL166W |
CUP2 |
48 |
Medium |
|
Three motifs account for three possible spacings in the literature motif; it is not clear that this is the optimal site, however |
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 |
YKR034W |
DAL80 |
1355 |
Medium |
|
MITOMI motif 1355 has highest correspondence to ChIP-chip. But it's not striking..none of them are, despite the fact that this is a classic GATA site (GATAAG). |
V |
YIR023W |
DAL81 |
53 |
Low |
|
None of the motifs agree with each other. The literature motif characterization was indirect; hence low confidence that this is the true motif. The ChIP-chip motifs score higher on ChIP data but that's circular. |
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 |
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 |
YPL049C |
DIG1 |
0 |
|
Dubious |
Not a TF - it binds Ste12; all the motifs are Ste12 motifs. |
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 |
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 |
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 |
YPL021W |
ECM23 |
578 |
High |
|
PBM motif 578 strongly resembles that from other yeast GATA-class TFs |
V |
YMR176W |
ECM5 |
0 |
|
Dubious |
Unlikely to be true TF. |
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 |
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 |
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 |
YNL023C |
FAP1 |
0 |
|
Dubious |
Unlikely to be true TF. |
V |
YDL166C |
FAP7 |
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 |
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 |
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 |
406 |
Incorrect |
|
Likely represents Rap1 binding site. |
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 |
YNL068C |
FKH2 |
830 |
High |
|
Most motifs are classic Forkhead. PBM motif 830 is one of the highest scoring and is not circular. |
V |
YER109C |
FLO8 |
67 |
Low |
Dubious |
I found no evidence that this is a sequence-specific DNA-binding protein, i.e. that it binds directly to DNA in vitro. 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 MSS11. |
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 |
YGL254W |
FZF1 |
69 |
Low |
|
Literature motif is the only one that appears credible. PBM motif I believe is a known artifact. Literature motif gets low confidence however as it is based on a single known binding sequence. |