|
|
|
|
|
|
|
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 |
YDR485C |
VPS72 |
0 |
|
Dubious |
Unlikely to be true TF. |
V |
YNL079C |
TPM1 |
0 |
|
Dubious |
Unlikely to be true TF. |
V |
YER063W |
THO1 |
0 |
|
Dubious |
Unlikely to be true TF. |
V |
YDR362C |
TFC6 |
0 |
|
Dubious |
Unlikely to be true TF. |
V |
YLR182W |
SWI6 |
0 |
|
Dubious |
Swi6 is a cofactor, not a DNA-binding protein. These motifs are for Mbp1 or Swi4. |
V |
YJL176C |
SWI3 |
0 |
|
Dubious |
Unlikely to be true TF. |
V |
YPL016W |
SWI1 |
0 |
|
Dubious |
Unlikely to be true TF. |
V |
YGR002C |
SWC4 |
0 |
|
Dubious |
Unlikely to be true 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 |
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 |
YOR308C |
SNU66 |
0 |
|
Dubious |
Unlikely to be true TF. |
V |
YCR033W |
SNT1 |
0 |
|
Dubious |
Unlikely to be true TF. |
V |
YOR290C |
SNF2 |
0 |
|
Dubious |
Unlikely to be true TF. |
V |
YDR409W |
SIZ1 |
0 |
|
Dubious |
Unlikely to be true TF. |
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 |
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 |
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 |
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 |
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 |
YBL052C |
SAS3 |
0 |
|
Dubious |
Unlikely to be true TF. |
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 |
YFR037C |
RSC8 |
0 |
|
Dubious |
Unlikely to be true TF. |
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 |
YCR066W |
RAD18 |
0 |
|
Dubious |
Unlikely to be true TF. |
V |
YIL122W |
POG1 |
0 |
|
Dubious |
Unlikely to be true TF. |
V |
YOR363C |
PIP2 |
0 |
|
|
See Oaf1-Pip2-dimer |
V |
YDR323C |
PEP7 |
0 |
|
Dubious |
Unlikely to be true TF. |
V |
YBR060C |
ORC2 |
0 |
|
Dubious |
Unlikely to be true TF. |
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 |
YKR064W |
OAF3 |
0 |
|
|
I do not see how either of these motifs could possibly be a Gal4-class binding motif. And, there is no correspondence to any of the data, even the ChIP-chip 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 |
YOR156C |
NFI1 |
0 |
|
Dubious |
Unlikely to be true TF. |
V |
YLR254C |
NDL1 |
0 |
|
Dubious |
Unlikely to be true 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 |
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 |
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. |
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 |
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 |
MBP1-SWI6-dimer |
MBP1-SWI6-dimer |
0 |
|
|
Redundant with MBP1 |
V |
YOR298C-A |
MBF1 |
0 |
|
Dubious |
This is a coactivator. I found no evidence that it is a sequence-specific TF. |
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 |
YGR288W |
MAL13 |
0 |
|
|
None of the ChIP-chip motifs correspond wekk to the data they come from and/or resemble a GAL4 motif. |
V |
YGR040W |
KSS1 |
0 |
|
Dubious |
There is no evidence that Kss1 is a sequence-specific TF. |
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 |
YNL227C |
JJJ1 |
0 |
|
Dubious |
Unlikely to be true TF. |
V |
YKL032C |
IXR1 |
0 |
|
Dubious |
Binds cisplatin-modified DNA. HMG domains. ChIP-chip motifs not significant. Dubious and no credible motif. |
V |
YGL133W |
ITC1 |
0 |
|
Dubious |
Unlikely to be true TF. |
V |
YOR304W |
ISW2 |
0 |
|
Dubious |
Unlikely to be true TF. |
V |
YJR094C |
IME1 |
0 |
|
Dubious |
Interacts with UME6. The only significant motif shares 5/6 bases with the UME6 motif core (GCCGCC) |
V |
YLR223C |
IFH1 |
0 |
|
Dubious |
Cofactor of Fhl1p. No evidence for sequence-specific DNA-binding. |
V |
YBL003C |
HTA2 |
0 |
|
Dubious |
Unlikely to be true TF. |
V |
YDR225W |
HTA1 |
0 |
|
Dubious |
Unlikely to be true TF. |
V |
YMR172W |
HOT1 |
0 |
|
Dubious |
Unlikely to be true TF. |
V |
YLR113W |
HOG1 |
0 |
|
Dubious |
This is a signalling molecule that associates with many TFs (see SGD) |
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 |
YBL008W |
HIR1 |
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 |
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 |
YNL023C |
FAP1 |
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 |
YMR176W |
ECM5 |
0 |
|
Dubious |
Unlikely to be true TF. |
V |
YPL049C |
DIG1 |
0 |
|
Dubious |
Not a TF - it binds Ste12; all the motifs are Ste12 motifs. |
V |
YER164W |
CHD1 |
0 |
|
Dubious |
Unlikely to be true TF. |
V |
YMR213W |
CEF1 |
0 |
|
Dubious |
Unlikely to be true TF. |
V |
YGR140W |
CBF2 |
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 |
YER159C |
BUR6 |
0 |
|
Dubious |
Unlikely to be true TF. |
V |
YDL074C |
BRE1 |
0 |
|
Dubious |
Unlikely to be true TF. |
V |
YNL039W |
BDP1 |
0 |
|
Dubious |
Unlikely to be true TF. |
V |
YGR097W |
ASK10 |
0 |
|
Dubious |
I did not find any evidence that this is a sequence-specific DNA-binding protein. |
V |
YDR448W |
ADA2 |
0 |
|
Dubious |
Unlikely to be true TF. |
V |
YGR071C |
|
0 |
|
Dubious |
Unlikely to be true TF. |
V |
YLR211C |
|
0 |
|
Dubious |
Unlikely to be true TF. |
V |
YPL216W |
|
0 |
|
Dubious |
Unlikely to be true TF. |
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 |
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 |
MATA1 |
|
0 |
|
|
Need to study literature more carefully and consult experts.but at first glance none of these motifs seems right |
V |
YJL056C |
ZAP1 |
2097 |
High |
|
Most motifs are similar but do not exceed confidence thresholds on any data type. PBM motif 2097 has highest score for ChIP and expression, and is not circular |
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 |
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 |
YML027W |
YOX1 |
498 |
High |
|
Two PBM studies and Pramila et al. (PMID 12464633) agree on classic homeodomain TAATTA motif. All three correlate with expression change and OE. Motif 453 is not a direct measurement so choose PBM motif that is the same length as the typical homeodomain footprint - 498 also correlates best with OE data; expression scores are skewed low by the large number of cell-cycle measurements. |
V |
YDR451C |
YHP1 |
716 |
High |
|
ChIP-chip, EMSA, and one-hybrid all arrive at a classic homeodomain TAATTG motif. Microarray enrichment motif (716) scores higher on OE data from another study than ChIP motifs do, and does nearly as well on ChIP data. |
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 |
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 |
YDR259C |
YAP6 |
599 |
High |
|
PBM and ChIP-chip can derive basically the same motif, which is a classical YAP motif. They score similarly on all criteria. The ChIP-chip motif (599) has fewer low-information flanking bases. |
V |
YIR018W |
YAP5 |
777 |
High |
|
ChIP-chip yields a classic 7-mer Yap motif that scores well on ChIP and significantly on expression. |
V |
YHL009C |
YAP3 |
1411 |
High |
|
Mitomi yields a nearly palindromic 8-mer motif with strong similarity to that of Yap6. PBM motif is similar but appears to be partial. |
V |
YHL009C |
YAP3 |
672 |
High |
|
ChIP-chip yields a classic 7-mer Yap motif that scores well on ChIP and significantly on expression. Could be a heterodimer. Chose 672 over 1463 because it has a higher score on expression data, which is independent. |
V |
YML007W |
YAP1 |
2186 |
High |
|
PBM motif 2186 looks like a monomeric bZIP site but it has the highest scores on both ChIP and expression |
V |
YIL101C |
XBP1 |
2039 |
High |
|
PBM and in vitro selection-derived motifs have highest scores across the board. 842 is higher on GO, but only slightly in AUC, and it has a very large number of empty flanking bases. 2039 (in vitro selection) seems a reasonable compromise - it's highest on ChIP and almost the highest on 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 |
YDR520C |
URC2 |
553 |
High |
|
This is a monomeric GAL4-class motif. Two PBM studies essentially agree, and have some relationship to ChIP-chip data. No other informative data. |
V |
YDR213W |
UPC2 |
544 |
High |
|
The SRE is bound by UPC2 and the "canonical" sequence is TCGTATA. However, the more degenerate version obtained by PBM (motif 544) scores better in both expression analysis and OE experiments. Newer motif 2109 scores better on ChIP-chip, but lower on expression, and the SRE is well-characterized....I think this one deserves further experimental analysis. |
V |
YDR207C |
UME6 |
2239 |
High |
|
All motifs are similar to each other. BEEML-PBM motif 2239 scores highest across the board. |