|
|
|
|
|
|
|
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 |
YDR448W |
ADA2 |
0 |
|
Dubious |
Unlikely to be true TF. |
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 |
YGR140W |
CBF2 |
0 |
|
Dubious |
Unlikely to be true TF. |
V |
YMR213W |
CEF1 |
0 |
|
Dubious |
Unlikely to be true TF. |
V |
YER164W |
CHD1 |
0 |
|
Dubious |
Unlikely to be true TF. |
V |
YMR176W |
ECM5 |
0 |
|
Dubious |
Unlikely to be true TF. |
V |
YNL023C |
FAP1 |
0 |
|
Dubious |
Unlikely to be true TF. |
V |
YMR172W |
HOT1 |
0 |
|
Dubious |
Unlikely to be true TF. |
V |
YDR225W |
HTA1 |
0 |
|
Dubious |
Unlikely to be true TF. |
V |
YBL003C |
HTA2 |
0 |
|
Dubious |
Unlikely to be true TF. |
V |
YOR304W |
ISW2 |
0 |
|
Dubious |
Unlikely to be true TF. |
V |
YGL133W |
ITC1 |
0 |
|
Dubious |
Unlikely to be true TF. |
V |
YNL227C |
JJJ1 |
0 |
|
Dubious |
Unlikely to be true TF. |
V |
YLR254C |
NDL1 |
0 |
|
Dubious |
Unlikely to be true TF. |
V |
YOR156C |
NFI1 |
0 |
|
Dubious |
Unlikely to be true TF. |
V |
YBR060C |
ORC2 |
0 |
|
Dubious |
Unlikely to be true TF. |
V |
YDR323C |
PEP7 |
0 |
|
Dubious |
Unlikely to be true TF. |
V |
YIL122W |
POG1 |
0 |
|
Dubious |
Unlikely to be true TF. |
V |
YCR066W |
RAD18 |
0 |
|
Dubious |
Unlikely to be true TF. |
V |
YFR037C |
RSC8 |
0 |
|
Dubious |
Unlikely to be true TF. |
V |
YBL052C |
SAS3 |
0 |
|
Dubious |
Unlikely to be true TF. |
V |
YDR409W |
SIZ1 |
0 |
|
Dubious |
Unlikely to be true TF. |
V |
YOR290C |
SNF2 |
0 |
|
Dubious |
Unlikely to be true TF. |
V |
YCR033W |
SNT1 |
0 |
|
Dubious |
Unlikely to be true TF. |
V |
YOR308C |
SNU66 |
0 |
|
Dubious |
Unlikely to be true TF. |
V |
YGR002C |
SWC4 |
0 |
|
Dubious |
Unlikely to be true TF. |
V |
YPL016W |
SWI1 |
0 |
|
Dubious |
Unlikely to be true TF. |
V |
YJL176C |
SWI3 |
0 |
|
Dubious |
Unlikely to be true TF. |
V |
YDR362C |
TFC6 |
0 |
|
Dubious |
Unlikely to be true TF. |
V |
YER063W |
THO1 |
0 |
|
Dubious |
Unlikely to be true TF. |
V |
YNL079C |
TPM1 |
0 |
|
Dubious |
Unlikely to be true TF. |
V |
YDR485C |
VPS72 |
0 |
|
Dubious |
Unlikely to be true TF. |
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 |
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 |
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 |
YLR113W |
HOG1 |
0 |
|
Dubious |
This is a signalling molecule that associates with many TFs (see SGD) |
V |
YOR298C-A |
MBF1 |
0 |
|
Dubious |
This is a coactivator. I found no evidence that it is a sequence-specific TF. |
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 |
YKR101W |
SIR1 |
0 |
|
Dubious |
There is no evidence that the SIR proteins are sequence-specific DNA-binding proteins. Most of the motifs for them are Rap1 sites. |
V |
YDL042C |
SIR2 |
0 |
|
Dubious |
There is no evidence that the SIR proteins are sequence-specific DNA-binding proteins. Most of the motifs for them are Rap1 sites. |
V |
YLR442C |
SIR3 |
0 |
|
Dubious |
There is no evidence that the SIR proteins are sequence-specific DNA-binding proteins. Most of the motifs for them are Rap1 sites. |
V |
YDR227W |
SIR4 |
0 |
|
Dubious |
There is no evidence that the SIR proteins are sequence-specific DNA-binding proteins. Most of the motifs for them are Rap1 sites. |
V |
YGR040W |
KSS1 |
0 |
|
Dubious |
There is no evidence that Kss1 is a sequence-specific TF. |
V |
YLR182W |
SWI6 |
0 |
|
Dubious |
Swi6 is a cofactor, not a DNA-binding protein. These motifs are for Mbp1 or Swi4. |
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 |
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 |
YDR277C |
MTH1 |
0 |
|
Dubious |
SGD: "interacts with Rgt1p and the Snf3p and Rgt2p glucose sensors". There is no evidence that this is a sequence-specific transcription factor. |
V |
YFL052W |
|
0 |
|
Dubious |
Putative zinc-cluster protein. |
V |
YPL049C |
DIG1 |
0 |
|
Dubious |
Not a TF - it binds Ste12; all the motifs are Ste12 motifs. |
V |
YDR049W |
|
0 |
|
Dubious |
No evidence this is a TF, aside from a poorly-scoring C2H2 zinc finger |
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 |
YHL020C |
OPI1 |
0 |
|
Dubious |
Motifs do not match and do not explain the ChIP-chip data from which they are derived. Motif 1049 resembles the expected UAS-INO (Ino2/4) binding site (CATGTGAAAT) - Opi1 acts as a repressor by binding Ino2. I believe this protein is a corepressor, and Ino2/4 are the DNA-binding factors. Dubious as sequence-specific TF. |
V |
YKL072W |
STB6 |
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. The ChIP-chip motif looks a little like a Rap1 motif. |
V |
YIL119C |
RPI1 |
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 |
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 |
YJR094C |
IME1 |
0 |
|
Dubious |
Interacts with UME6. The only significant motif shares 5/6 bases with the UME6 motif core (GCCGCC) |
V |
YGL197W |
MDS3 |
0 |
|
Dubious |
I found no evidence that this is a sequence-specific DNA-binding protein. ChIP-chip motif does not correlate with ChIP-chip data, or anything else. |
V |
YIL128W |
MET18 |
0 |
|
Dubious |
I found no evidence that this is a sequence-specific DNA-binding protein. ChIP-chip motif does not correlate with ChIP-chip data, or anything else. |
V |
YGR097W |
ASK10 |
0 |
|
Dubious |
I did not find any evidence that this is a sequence-specific DNA-binding protein. |
V |
YGR089W |
NNF2 |
0 |
|
Dubious |
I did not find any evidence that this is a sequence-specific DNA-binding protein. |
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 |
YBL008W |
HIR1 |
0 |
|
Dubious |
Hir1,2,3 are a nucleosome assembly complex, not TFs |
V |
YOR038C |
HIR2 |
0 |
|
Dubious |
Hir1,2,3 are a nucleosome assembly complex, not TFs |
V |
YJR140C |
HIR3 |
0 |
|
Dubious |
Hir1,2,3 are a nucleosome assembly complex, not TFs |
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 |
YML051W |
GAL80 |
0 |
|
Dubious |
Gal80 is not a sequence-specific DNA-binding protein |
V |
YDR009W |
GAL3 |
0 |
|
Dubious |
Gal3 is not a sequence-specific DNA-binding protein |
V |
YLR223C |
IFH1 |
0 |
|
Dubious |
Cofactor of Fhl1p. No evidence for sequence-specific DNA-binding. |
V |
YKL032C |
IXR1 |
0 |
|
Dubious |
Binds cisplatin-modified DNA. HMG domains. ChIP-chip motifs not significant. Dubious and no credible motif. |
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 |
YCL055W |
KAR4 |
127 |
Low |
Dubious |
Evidence for sequence specific DNA binding seems weak, hence low confidence |
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 |
YDL002C |
NHP10 |
502 |
Low |
Dubious |
NHP10 is an HMGB-type protein. Known to prefer DNA ends. There is no independent support for the single PBM motif. |
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 |
YGL131C |
SNT2 |
612 |
Low |
Dubious |
All three motifs are derived from the same ChIP-chip data. However, there is no corroborating data, and not all SANT domains are DNA-binding - or are non-specific, in chromatin proteins. So it could be a cofactor motif; in fact it is similar to motifs of Stp3 and Stp4. The protein has other chromatin-related domains (BAH, PHD/RING). Hence the "Low" assessment. |
V |
YER051W |
JHD1 |
662 |
Low |
Dubious |
This is a histone demethylase. No evidence for direct DNA binding. Motif 662 is significant. Include, but give low confidence - could be a cofactor. |
V |
YKL020C |
SPT23 |
670 |
Low |
Dubious |
I could not find any evidence that this protein binds directly to DNA. It has an IPT domain but no REL domain. None of the ChIP-derived motifs scores highly on ChIP data or anything else. Motif 670 bears some relationship to expression data. |
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 |
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 |
YGL192W |
IME4 |
1000 |
Low |
Dubious |
I could not find evidence that IME4 is a sequence-specific DNA-binding protein. C3H1 is more typically an RNA-binding domain or something besides nucleic acid binding. There is one significant ChIP-chip motif but perhaps it binds through a cofactor. No other supporting data. |
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 |
YDR477W |
SNF1 |
1110 |
Medium |
Dubious |
Motif 1110 has a quite strong correspondence to ChIP-chip data (from which it is derived). However, there seems to be no evidence that this is a sequence-specific DNA-binding protein. Aside from a weak relationship to expression data there is no corroborating evidence here (and no DNA-binding domain). |
V |
YER161C |
SPT2 |
1114 |
Low |
Dubious |
I could not find any evidence that this protein binds directly to DNA. None of the motifs is significant. All are from ChIP-chip. Motif 1114 chosen simploy because it has the highest numbers overall. |
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 |
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 |
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 |
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 |
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. |