|
|
|
|
|
|
|
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 |
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 |
YCL055W |
KAR4 |
127 |
Low |
Dubious |
Evidence for sequence specific DNA binding seems weak, hence low confidence |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
YOR298C-A |
MBF1 |
0 |
|
Dubious |
This is a coactivator. I found no evidence that it is a sequence-specific TF. |
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 |
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 |
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 |
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 |
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 |
YFL031W |
HAC1 |
94 |
Medium |
|
1788 is the overall winner. But, literature motif 94 also scores well in ChIP-chip, despite being somewhat different. Possible difference in heterodimerazation partners, or proteolytic fragment? Retain both. |
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 |
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 |
YER169W |
RPH1 |
547 |
High |
|
About half of the motifs look similar to each other, with GGGG core typical of many yeast C2H2 proteins. PBM motif 547 has meaningful scores on both ChIP-chip and mutant expression data. I'm somewhat concerned that motif 279 lacks two A residues captured by both PBM experiments. |
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. |