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|
|
|
|
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
YCL055W |
KAR4 |
127 |
Low |
Dubious |
Evidence for sequence specific DNA binding seems weak, hence low confidence |
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 |
YKL032C |
IXR1 |
0 |
|
Dubious |
Binds cisplatin-modified DNA. HMG domains. ChIP-chip motifs not significant. Dubious and no credible motif. |
V |
YLR223C |
IFH1 |
0 |
|
Dubious |
Cofactor of Fhl1p. No evidence for sequence-specific DNA-binding. |
V |
YDR009W |
GAL3 |
0 |
|
Dubious |
Gal3 is not a sequence-specific DNA-binding protein |
V |
YML051W |
GAL80 |
0 |
|
Dubious |
Gal80 is not a sequence-specific DNA-binding protein |
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 |
YBL008W |
HIR1 |
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 |
YOR038C |
HIR2 |
0 |
|
Dubious |
Hir1,2,3 are a nucleosome assembly complex, not TFs |
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 |
YGR089W |
NNF2 |
0 |
|
Dubious |
I did not find any evidence that this is a sequence-specific DNA-binding protein. |
V |
YGR097W |
ASK10 |
0 |
|
Dubious |
I did not find any evidence that this is a sequence-specific DNA-binding protein. |
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 |
YJR094C |
IME1 |
0 |
|
Dubious |
Interacts with UME6. The only significant motif shares 5/6 bases with the UME6 motif core (GCCGCC) |
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 |
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 |
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 |
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 |
YDR049W |
|
0 |
|
Dubious |
No evidence this is a TF, aside from a poorly-scoring C2H2 zinc finger |
V |
YPL049C |
DIG1 |
0 |
|
Dubious |
Not a TF - it binds Ste12; all the motifs are Ste12 motifs. |
V |
YFL052W |
|
0 |
|
Dubious |
Putative zinc-cluster protein. |
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 |
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 |
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 |
YLR182W |
SWI6 |
0 |
|
Dubious |
Swi6 is a cofactor, not a DNA-binding protein. These motifs are for Mbp1 or Swi4. |
V |
YGR040W |
KSS1 |
0 |
|
Dubious |
There is no evidence that Kss1 is a sequence-specific TF. |
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 |
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 |
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 |
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 |
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 |
YOR298C-A |
MBF1 |
0 |
|
Dubious |
This is a coactivator. I found no evidence that it is a sequence-specific TF. |
V |
YLR113W |
HOG1 |
0 |
|
Dubious |
This is a signalling molecule that associates with many TFs (see SGD) |
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 |
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 |
YBL003C |
HTA2 |
0 |
|
Dubious |
Unlikely to be true TF. |
V |
YBL052C |
SAS3 |
0 |
|
Dubious |
Unlikely to be true TF. |
V |
YBR060C |
ORC2 |
0 |
|
Dubious |
Unlikely to be true TF. |
V |
YCR033W |
SNT1 |
0 |
|
Dubious |
Unlikely to be true TF. |
V |
YCR066W |
RAD18 |
0 |
|
Dubious |
Unlikely to be true TF. |
V |
YDL074C |
BRE1 |
0 |
|
Dubious |
Unlikely to be true TF. |
V |
YDR225W |
HTA1 |
0 |
|
Dubious |
Unlikely to be true TF. |
V |
YDR323C |
PEP7 |
0 |
|
Dubious |
Unlikely to be true TF. |
V |
YDR362C |
TFC6 |
0 |
|
Dubious |
Unlikely to be true TF. |
V |
YDR409W |
SIZ1 |
0 |
|
Dubious |
Unlikely to be true TF. |
V |
YDR448W |
ADA2 |
0 |
|
Dubious |
Unlikely to be true TF. |
V |
YDR485C |
VPS72 |
0 |
|
Dubious |
Unlikely to be true TF. |
V |
YER063W |
THO1 |
0 |
|
Dubious |
Unlikely to be true TF. |
V |
YER159C |
BUR6 |
0 |
|
Dubious |
Unlikely to be true TF. |
V |
YER164W |
CHD1 |
0 |
|
Dubious |
Unlikely to be true TF. |
V |
YFR037C |
RSC8 |
0 |
|
Dubious |
Unlikely to be true TF. |
V |
YGL133W |
ITC1 |
0 |
|
Dubious |
Unlikely to be true TF. |
V |
YGR002C |
SWC4 |
0 |
|
Dubious |
Unlikely to be true TF. |
V |
YGR071C |
|
0 |
|
Dubious |
Unlikely to be true TF. |
V |
YGR140W |
CBF2 |
0 |
|
Dubious |
Unlikely to be true TF. |
V |
YIL122W |
POG1 |
0 |
|
Dubious |
Unlikely to be true TF. |
V |
YJL176C |
SWI3 |
0 |
|
Dubious |
Unlikely to be true TF. |
V |
YLR211C |
|
0 |
|
Dubious |
Unlikely to be true TF. |
V |
YLR254C |
NDL1 |
0 |
|
Dubious |
Unlikely to be true TF. |
V |
YMR172W |
HOT1 |
0 |
|
Dubious |
Unlikely to be true TF. |
V |
YMR176W |
ECM5 |
0 |
|
Dubious |
Unlikely to be true TF. |
V |
YMR213W |
CEF1 |
0 |
|
Dubious |
Unlikely to be true TF. |
V |
YNL023C |
FAP1 |
0 |
|
Dubious |
Unlikely to be true TF. |
V |
YNL039W |
BDP1 |
0 |
|
Dubious |
Unlikely to be true TF. |
V |
YNL079C |
TPM1 |
0 |
|
Dubious |
Unlikely to be true TF. |
V |
YNL227C |
JJJ1 |
0 |
|
Dubious |
Unlikely to be true TF. |
V |
YOR156C |
NFI1 |
0 |
|
Dubious |
Unlikely to be true TF. |
V |
YOR290C |
SNF2 |
0 |
|
Dubious |
Unlikely to be true TF. |
V |
YOR304W |
ISW2 |
0 |
|
Dubious |
Unlikely to be true TF. |
V |
YOR308C |
SNU66 |
0 |
|
Dubious |
Unlikely to be true TF. |
V |
YPL016W |
SWI1 |
0 |
|
Dubious |
Unlikely to be true TF. |
V |
YPL216W |
|
0 |
|
Dubious |
Unlikely to be true TF. |
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. |