|
|
|
|
|
|
|
| V |
YOR363C |
PIP2 |
0 |
|
|
See Oaf1-Pip2-dimer |
| 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 |
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 |
MBP1-SWI6-dimer |
MBP1-SWI6-dimer |
0 |
|
|
Redundant with MBP1 |
| 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 |
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 |
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 |
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 |
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. |
| V |
YDL170W |
UGA3 |
651 |
High |
|
Appears to be a dimeric GAL4-class motif. Scores highest in ChIP-chip data, but is derived from the same data. GO seems to match known function! |
| 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 |
YGL096W |
TOS8 |
494 |
High |
|
No corroborating data on this TF, and only one PBM motif known and one ChIP motif. But, it resembles TGTCA, which was also obtained for paralog Cup9 by multiple approaches (GTGNCA), as well as PBM results for the Meis/Mrg/Pknox/Tgif family, which are the closest mammalian homologs. The ChIP motif (1902) does not resemble a homeodomain binding sequence, and scores lower on expression data. |
| V |
YBL054W |
TOD6 |
852 |
High |
|
Two PBM motifs largely agree; 852 has higher correspondence to expression data while 495 has higher correspondence to ChIP-chip. Use 852; score is way higher. Also for GO. |
| V |
YBR240C |
THI2 |
1449 |
High |
|
This is a GAL4-class protein. All motifs are ChIP-chip derived, none resembles each other. 1449 is the only one with respectable scores on ChIP and expression,and it also has the appearance of a GAL4 class motif..although, the structural prior presumably forces it to have this property. |
| V |
YBR083W |
TEC1 |
815 |
High |
|
All motifs agree, and are significant by several criteria. PBM motif 815 has the second-highest scores overall, and it is non-circular for in vivo binding. Also has highest GO score. |
| V |
YBR150C |
TBS1 |
552 |
High |
|
Two motifs from PBMs are nearly identical GAL4-class motifs with defined spacing and orientation. Motif 552 has slightly higher scores. Two motifs from BEEML analysis of PBM data give monomeric motif - also give this high confidence. |
| V |
YBR150C |
TBS1 |
2179 |
High |
|
Two motifs from PBMs are nearly identical GAL4-class motifs with defined spacing and orientation. Motif 552 has slightly higher scores. Two motifs from BEEML analysis of PBM data give monomeric motif - also give this high 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 |
YDR146C |
SWI5 |
569 |
High |
|
PBM, Chip-chip, and conservation all yield similar motifs. ChIP-chip scores highest in ChIP-chip but that is circular. Choose PBM motif 569 which is nearly identical. |
| V |
YER111C |
SWI4 |
584 |
High |
|
Motif is well-characterized and most published motifs match the expected one. PBM motif (584) scores highly (although not highest) in Chip-chip data. It is, however, non-circular, and specifically captures "DNA metabolic process" in GO analysis. |
| V |
YPR009W |
SUT2 |
2236 |
High |
|
Highest-scoring motif (PBM) is a classical GAL4-type monomeric motif and is very significant in ChIP-chip |
| V |
YDR310C |
SUM1 |
478 |
High |
|
This is the motif for the SUM1 AT_hook; scores highest in deletion expression data |
| V |
YDR310C |
SUM1 |
383 |
High |
|
This is the motif for the FL SUM1; scores highest on ChIP-chip and resembles the canonical literature motif; also has some relationship to deletion expression data |
| V |
YHR006W |
STP2 |
2174 |
High |
|
STP1 and 2 have very similar DNA-binding domains. However, they are not similar to those of STP3 and 4. PBM motif for STP2 (2174) correlates highest with ChIP-chip and expression data. ChIP-chip motif for STP1 (660) most strongly resembles motif 800, and scores highly on ChIP-chip data. In addition, these motifs resemble halfmers of literature-derived binding sites. |
| V |
YDR463W |
STP1 |
660 |
High |
|
STP1 and 2 have very similar DNA-binding domains. However, they are not similar to those of STP3 and 4. PBM motif for STP2 (800) correlates with ChIP-chip and expression data. ChIP-chip motif for STP1 (660) most strongly resembles motif 800, and scores highly on ChIP-chip data. In addition, these motifs resemble halfmers of literature-derived binding sites. |
| V |
YHR084W |
STE12 |
400 |
High |
|
All motifs but one resemble the canonical literature site. Motif 400 is derived from ChIP-chip data (on which it scores highest) but also scores highest on expression data. |
| V |
YHR178W |
STB5 |
1405 |
High |
|
All motifs have CGG core and most have CGGnG. Most ChIP-derived motifs have no relationship to expression data. Mitomi motif 1405 and PBM motif 514 score decently on both ChIP-chip and expression data, and seem to nail the GO category (oxidative stress response), and look like classic Gal4 halfmers. MITOMI motif scores slighly higher overall. This is presumably the monomeric motif |
| V |
YMR019W |
STB4 |
2107 |
High |
|
PBM motif 2107 is clearly a dimeric GAL4-class motif, and it blows all the other motifs out of the water. |
| 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 |
YER148W |
SPT15 |
798 |
High |
|
This is TATA-binding protein. PBM motif 798 chosen because 1326 was derived from the 96-sequence TIRF-PBM array instead of a full 40K PBM |
| V |
YMR016C |
SOK2 |
404 |
High |
|
ChIP-chip motif 404 has highest correspondence to both ChIP-chip and expression data - and strongly resembles PBM motif |
| 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 |
YHR206W |
SKN7 |
583 |
High |
|
Motifs are remarkably discordant considering that they all resemble each other in being G+C rich and containing a GGCC core. Possibly reflecting different modes of multimerization? Include the two that score highest on independent data: PBM motif 583, which represents a monomer, and ChIP-chip motif 380, which appears to represent a dimer. |
| V |
YHR206W |
SKN7 |
380 |
High |
|
Motifs are remarkably discordant considering that they all resemble each other in being G+C rich and containing a GGCC core. Possibly reflecting different modes of multimerization? Include the two that score highest on independent data: PBM motif 583, which represents a monomer, and ChIP-chip motif 380, which appears to represent a dimer. |
| V |
YLR403W |
SFP1 |
797 |
High |
|
Most ChIP-seq studies identified the Rap1 motif. PBM motif 797 is less significant by ChIP-seq (although still highly significant) but is the winner across the board for all types of expression data. |
| V |
YJR127C |
RSF2 |
575 |
High |
|
No supporting data, but the PBM motif 575 looks like a typical yeast C2H2 motif (Adr1, which has similar zinc fingers, Mig1, etc). |
| V |
YDR303C |
RSC3 |
580 |
High |
|
PBM motif 580 has best correspondence to expression data - the only significant independent criterion - considering that the correlations are all in the same orientation (they are not for 2165). All motifs look similar. Propose that longer motifs could be due to multiple binding sites in the same sequence. |
| V |
YDL020C |
RPN4 |
1700 |
High |
|
In vitro motifs do not contain the TTT sequence on the end. But they were derived from the DBD only. The rest of the protein may contribute to binding the TTT segment. Motif 1700 has the highest correspondence to ChIP-chip and expression and GO. |
| 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. |
| V |
YHL027W |
RIM101 |
600 |
High |
|
ChIP-chip motif 600 is almost identical to PBM motif 513, but scores slightly higher on expression data. Three of six motifs are very similar. |
| 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. |
| 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 |
YBR267W |
REI1 |
489 |
High |
|
PBM motif looks like a yeast C2H2 motif (row of C's); highly significant relationship to ChIP-chip data |
| V |
YBR049C |
REB1 |
907 |
High |
|
All motifs are similar. ChIP-chip motif 907 has highest correspondence to both ChIP-chip and expression data, and strongly resembles MITOMI and PBM motifs. |
| V |
YCR106W |
RDS1 |
506 |
High |
|
All motifs look similar. PBM motif 506 has a higher score on ChIP-chip than any of the ChIP-chip derived motifs. |
| 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 |
YNL216W |
RAP1 |
254 |
High |
|
Most motifs look similar. ChIP-chip motif 254 has highest correspondence to expression data. |
| V |
YFR034C |
PHO4 |
2222 |
High |
|
Almost all motifs match classic HLH E-box. PBM motif 2222 has highest match to both ChIP-chip and expression data, without being circular. |
| V |
YDL106C |
PHO2 |
2154 |
High |
|
Motifs are largely all different from each other. PBM motif 2154 scores highly on ChIP data and resembles classic TAAT homeobox core. Note that PBM motif 794 even more strongly resembles homeobox (TAATTA) but scores slightly less highly. |
| V |
YKL043W |
PHD1 |
2153 |
High |
|
High-scoring motifs are all similar, with characteristic APSES GC core and palindromic. PBM motifs score highest on ChIP-seq data, while ChIP-chip motif 393 (which contains flanking G/C residues) scores highest on expression data. Retain both - possibly, the rest of the protein contributes to binding flanking residues. This is the higher-scoring PBM motif (2153). |
| V |
YKL043W |
PHD1 |
393 |
High |
|
High-scoring motifs are all similar, with characteristic APSES GC core and palindromic. PBM motifs score highest on ChIP-seq data, while ChIP-chip motif 393 (which contains flanking G/C residues) scores highest on expression data. Retain both - possibly, the rest of the protein contributes to binding flanking residues. This is the ChIP motif that scores highest on expression data. |
| V |
YGL013C |
PDR1 |
485 |
High |
|
PBM motif 485 looks like a traditional literature motif and has highest correspondence to ChIP and expression data. Dimeric GAL4 motif. |
| V |
YML065W |
ORC1 |
1549 |
High |
|
Looks like ORC1 motif. Which is not really a TF, but it is a sequence-specific DNA-binding protein. |
| V |
YBR066C |
NRG2 |
1383 |
High |
|
MITOMI motif 1383 looks like a classic yeast C2H2 binding site (row of G's). Also resembles motifs obtained by both ChIP and PBMs for related protein Nrg1. |
| V |
YDR043C |
NRG1 |
2148 |
High |
|
PBM, ChIP-chip, and literature motifs all appear very similar, and resemble motif for the related protein NRG2. Choose top PBM motif (2148). There is also a recurring ChIP-chip motif (TGTGCCT) which I believe is actually the MOT3 binding site. |
| V |
YHR124W |
NDT80 |
1464 |
High |
|
Motif 1464 matches literature motifs and PBM motif, and nails sporulation on GO. It also has the highest correspondence to ChIP-chip data. |
| V |
YKL062W |
MSN4 |
518 |
High |
|
PBM motif 518 resembles both the classical MSN motif and the PBM motif, and scores highest on both expression and ChIP-chip. |
| V |
YMR037C |
MSN2 |
1380 |
High |
|
MITOMI motif 1380 has the highest overall correspondence to ChIP-chip, overexpression, and deletion data. Resembles classic Msn2/4 motif. |
| 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 |
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 |
YER028C |
MIG3 |
2144 |
High |
|
PBM motif 2144 has highest correspondence to ChIP-chip data |
| V |
YGL209W |
MIG2 |
2143 |
High |
|
PBM motif 2143 has highest correspondence to ChIP-chip data |
| V |
YGL035C |
MIG1 |
2142 |
High |
|
PBM motif 2142 has highest correspondence to ChIP-chip AND AUC for GO category "generation of precursor metabolites and energy". The adjacent A/T stretch, which is also noted in the literature, is found in ChIP-chip motif 654 and others; however, that motif does not sort as well for GO category "generation of precursor metabolites and energy" and also scores lower for both ChIP and expression, so it seems unlikely to represent a key intrinsic activity of the protein itself. |
| V |
YDR253C |
MET32 |
2140 |
High |
|
Most motifs look similar. PBM motif 2140 has highest correspondence to both ChIP and expression. |
| V |
YPL038W |
MET31 |
1370 |
High |
|
Most motifs look similar. MITOMI motif 1370 has highest overall correlation to ChIP-chip, OE, and deletion data. |
| 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. |
| V |
YDL056W |
MBP1 |
2138 |
High |
|
Almost all motifs look similar to literature binding site. PBM motif 2138 scores at the top on ChIP-chip and expression. And is non-circular. |
| V |
YCR039C |
MATALPHA2 |
1364 |
High |
|
According to PMID: 9858582, "A comparison of the 2 binding sites in both asg and hsg operators yields the same consensus sequence, 5'-CATGTA-3"; results in Figure 2 of the same paper support a consensus of CATGTAA. MITOMI yields ACATG, which is the reverse complement of most of the literature consensus. Motif 1364 has highest information content; use this. |
| V |
YMR021C |
MAC1 |
1540 |
High |
|
Literature motif 1540 most closely most closely corresponds to ChIP-chip data (albeit barely significant). Nothing else to gauge by, but no reason to doubt literature motif. |
| V |
YDR034C |
LYS14 |
133 |
High |
|
PBM motifs are virtually identical and appear monomeric; literature motif is dimeric. Include both. Choose PBM motif 865 as it appears to have more robust CGG. |
| V |
YDR034C |
LYS14 |
865 |
High |
|
PBM motifs are virtually identical and appear monomeric; literature motif is dimeric. Include both. Choose PBM motif 865 as it appears to have more robust CGG. |
| V |
YLR451W |
LEU3 |
2135 |
High |
|
Most motifs look similar - dimeric GAL4 motif. Literature motif (781) has high correspondence to ChIP-chip and expression data and is not circular. But, PBM motif 2135, which is a monomeric GAL4 motif, scores highest on both ChIP-chip and expression data. |
| V |
YLR451W |
LEU3 |
781 |
High |
|
Most motifs look similar - dimeric GAL4 motif. Literature motif (781) has high correspondence to ChIP-chip and expression data and is not circular. But, PBM motif 2135, which is a monomeric GAL4 motif, scores highest on both ChIP-chip and expression data. |
| 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 |
YDR123C |
INO2 |
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 |
YCR065W |
HCM1 |
570 |
High |
|
PBM and SAAB/EMSA motifs both look similar to standard FH motif. PBM motif 570 has stronger correspondence to expression data. |
| 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 |
YKL109W |
HAP4 |
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 |
YBL021C |
HAP3 |
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 |
YGL237C |
HAP2 |
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 |
YLR256W |
HAP1 |
2078 |
High |
|
Literature binding site is direct CGG repeats with a 6bp spacer (PMID: 7958882). PBM motif 2078 gets this; it scores highest overall, including significant scores on both ChIP-chip and expression. |
| V |
YOL089C |
HAL9 |
799 |
High |
|
PBM motifs 799 and 2134 score highest on ChIP-chip data; classic dimeric and monomeric GAL4 sites, respectively. |
