|
|
|
|
|
|
|
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 |
1196 |
Incorrect |
|
Likely represents Rap1 binding site. |
V |
YPR104C |
FHL1 |
1504 |
Incorrect |
|
Likely represents Rap1 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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
YOR028C |
CIN5 |
409 |
High |
|
Most motifs match the classic YAP motif. This is the best in vivo motif (highest match to ChIP-chip). |
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 |
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 |
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. |