|
|
|
|
|
|
|
| V |
YOR363C |
PIP2 |
0 |
|
|
See Oaf1-Pip2-dimer |
| 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 |
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 |
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 |
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 |
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 |
MBP1-SWI6-dimer |
MBP1-SWI6-dimer |
0 |
|
|
Redundant with MBP1 |
| V |
MATA1 |
|
0 |
|
|
Need to study literature more carefully and consult experts.but at first glance none of these motifs seems right |
| 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 |
YNL216W |
RAP1 |
254 |
High |
|
Most motifs look similar. ChIP-chip motif 254 has highest correspondence to expression data. |
| 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 |
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 |
YPL202C |
AFT2 |
389 |
High |
|
All motifs look similar. ChIP-chip motif 389 scores high on ChIP-chip data and also best on expression data. |
| 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 |
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 |
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 |
YKR099W |
BAS1 |
402 |
High |
|
Virtually all motifs are similar, with GAGTCA core. ChIP motif 402 has highest correspondence to both ChIP-chip and expression data. |
| 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 |
YOR028C |
CIN5 |
409 |
High |
|
Most motifs match the classic YAP motif. This is the best in vivo motif (highest match to ChIP-chip). |
| V |
YDR310C |
SUM1 |
478 |
High |
|
This is the motif for the SUM1 AT_hook; scores highest in deletion 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 |
YBR267W |
REI1 |
489 |
High |
|
PBM motif looks like a yeast C2H2 motif (row of C's); highly significant relationship to ChIP-chip data |
| 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 |
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 |
YOR113W |
AZF1 |
499 |
High |
|
PBM motif 499 scores as well as the ChIP-chip motifs, but without the circularity. No significant data except ChIP-chip, however. |
| 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 |
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 |
YNL027W |
CRZ1 |
516 |
High |
|
PBM motif 516 scores highest on ChIP and expression; resembles classic literature motifs |
| 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 |
YMR168C |
CEP3 |
524 |
High |
|
Two PBM motifs agree. Went with 524 because it appears neater. No other supporting data for any of them. |
| 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 |
YER130C |
COM2 |
534 |
High |
|
PBM motif 534 has the highest correspondence to expression data. Not much else supporting any of the motifs, although the two PBM motifs look about the same. Also look like typical yeast C2H2 motifs. |
| V |
YER040W |
GLN3 |
539 |
High |
|
Most motifs are classic GATA or GATAAG. PBM motif 539 scores highest on ChIP. |
| 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 |
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 |
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 |
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 |
YDR096W |
GIS1 |
562 |
High |
|
All motifs similar; PBM motif 562 has highest correspondence to deletion expression data and overexpression data |
| V |
YIR013C |
GAT4 |
565 |
High |
|
Two PBM motifs look similar, also similar to a subset of other GATAs. 565 scores higher on expression and OE data. |
| 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 |
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 |
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 |
YDR216W |
ADR1 |
576 |
High |
|
PBM motif 576 has significant correspondence to both ChIP-chip and highest to expression data. And has a classic yeast C2H2 look. |
| V |
YPL021W |
ECM23 |
578 |
High |
|
PBM motif 578 strongly resembles that from other yeast GATA-class TFs |
| 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 |
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 |
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 |
YIL036W |
CST6 |
585 |
High |
|
PBM motif 585 correlates with expression data (deletion and overexpression). ChIP motif 1466 has higher ChIP score but is lower on expression. |
| V |
YPR022C |
|
588 |
High |
|
Only one motif available, from PBMs; classical yeast C2H2 motif, and has some relationship to ChIP-chip data. |
| 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 |
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 |
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 |
YGL071W |
AFT1 |
658 |
High |
|
Most motifs are similar. Also very similar to AFT2 motifs. ChIP-chip motif 658 scores highest on both ChIP-chip and expression data. |
| 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 |
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 |
YNL314W |
DAL82 |
690 |
High |
|
PBM and ChIP-chip motifs agree; select ChIP-chip as it scores higher on ChIP-chip although the extra A's on the side could be either due to the FL protein or some other in vivo factor. |
| 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 |
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 |
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 |
YDR026C |
|
696 |
High |
|
Three ChIP-chip motifs are virtually identical in appearance; resemble Reb1 motifs; high correspondence to ChIP-chip 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 |
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 |
YDR421W |
ARO80 |
725 |
High |
|
PBM motif 2115 appears monomeric and has highest correspondence to ChIP-chip data. ChIP motif 1509 appears dimeric and correlates with ChIP data. Literature motif 725 appears trimeric and has experimental support. Retain all three. |
| V |
YIR018W |
YAP5 |
777 |
High |
|
ChIP-chip yields a classic 7-mer Yap motif that scores well on ChIP and significantly on expression. |
| 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 |
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 |
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 |
YOL089C |
HAL9 |
799 |
High |
|
PBM motifs 799 and 2134 score highest on ChIP-chip data; classic dimeric and monomeric GAL4 sites, respectively. |
| V |
YNR063W |
|
804 |
High |
|
Motifs from PBMs are virtually identical. This is a monomeric GAL4-like motif. 804 agrees more with ChIP-chip 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 |
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 |
YNL068C |
FKH2 |
830 |
High |
|
Most motifs are classic Forkhead. PBM motif 830 is one of the highest scoring and is not circular. |
| 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 |
YLR228C |
ECM22 |
849 |
High |
|
PBM motif 2122 is a monomeric GAL4 class motif, and scores highest on both ChIP and expression ata. 849 is a classic dimeric GAL4 motif with lower but still reasonable scores and is moderately predictive across the board. |
| 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 |
YPR013C |
CMR3 |
859 |
High |
|
PBM motifs are very similar. No other supporting data, but it's a clean motif. Chose 859 because it most closely resembles motif from paralog YPR015c. |
| V |
YPR196W |
|
861 |
High |
|
Motifs from PBMs are very similar and are a variant monomeric GAL4-like motif. Chose 861 as it passes the significance threshold against ChIP-chip data. |
| 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 |
YPR015C |
|
871 |
High |
|
Only one motif available, from PBMs; resembles motof from CMR3 which is a paralogous gene (and nearly adjacent on the chromosome). And, scores significantly against expression 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 |
YFL021W |
GAT1 |
962 |
High |
|
ChIP-chip motif 962 scores higher on both ChIP-chip and expression data |
| V |
YLR131C |
ACE2 |
1332 |
High |
|
Highest-scoring ChIP-chip motif is Rap1 site. MITOMI motif 1332 is next, and resembles the classic Swi5/Ace2 motif. |
| V |
YJR060W |
CBF1 |
1346 |
High |
|
Classic E-box. MITOMI motif 1346 nearly has highest correspondence to ChIP-chip data and is non-circular; no other supporting data |
| V |
YEL009C |
GCN4 |
1363 |
High |
|
Virtually all motifs look the same. MITOMI motif 1363 is as good as any of the ChIP-chip motifs but not circular; scores high across the board. |
| 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 |
YPL038W |
MET31 |
1370 |
High |
|
Most motifs look similar. MITOMI motif 1370 has highest overall correlation to ChIP-chip, OE, and deletion data. |
| 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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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. |
