|
|
|
|
|
|
|
| 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 |
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 |
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 |
MATA1 |
|
0 |
|
|
Need to study literature more carefully and consult experts.but at first glance none of these motifs seems right |
| 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 |
YOR363C |
PIP2 |
0 |
|
|
See Oaf1-Pip2-dimer |
| 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 |
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. |
| 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 |
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 |
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 |
YDR207C |
UME6 |
2239 |
High |
|
All motifs are similar to each other. BEEML-PBM motif 2239 scores highest across the board. |
| 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 |
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 |
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 |
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 |
YDR096W |
GIS1 |
562 |
High |
|
All motifs similar; PBM motif 562 has highest correspondence to deletion expression data and overexpression data |
| 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 |
YLR013W |
GAT3 |
2128 |
High |
|
All PBM motifs look similar, also similar to a subset of other GATAs. 2128 scores quite highly on ChIP-chip (albeit with negative correlation!), and also higher on expression and OE 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 |
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 |
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 |
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 |
YML099C |
ARG81 |
1506 |
High |
|
ChIP motif 1506 correlates well with ChIP and also with expression data. Resembles dimeric GAL4 class motif. |
| V |
YPL248C |
GAL4 |
1510 |
High |
|
ChIP-chip motif 1510 resembles literature motif, and PBM motif 875, but scores highly on ChIP and expression data, across the board. Note, however, that the high ChIP-chip scores stem from an experiment with high negative correlation. PBM motif 2206 appears to be a monomeric version, socres even higher on ChIP-chip and expression. |
| V |
YPL248C |
GAL4 |
2206 |
High |
|
ChIP-chip motif 1510 resembles literature motif, and PBM motif 875, but scores highly on ChIP and expression data, across the board. Note, however, that the high ChIP-chip scores stem from an experiment with high negative correlation. PBM motif 2206 appears to be a monomeric version, socres even higher on ChIP-chip and expression. |
| 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 |
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 |
YFL021W |
GAT1 |
962 |
High |
|
ChIP-chip motif 962 scores higher on both ChIP-chip and expression data |
| V |
YPR104C |
FHL1 |
2203 |
High |
|
ChIP-chip motifs are all Rap1. PBMs identify a different motif which also corresponds to ChIP-chip data. Selected 2203 as it scores highest on ChIP-chip and expression data. |
| 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 |
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 |
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 |
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 |
YIL131C |
FKH1 |
2002 |
High |
|
Classic Forkhead motif for most of them. 2002 strongly resembles PBM motif but scores higher on both ChIP (which is circular) and expression (which is not). |
| V |
YJL110C |
GZF3 |
2133 |
High |
|
Classic GATA motif 2133 from PBM scores highest on ChIP-chip and expression data |
| 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 |
YDR423C |
CAD1 |
2098 |
High |
|
Classic YAP motif in most cases. Include examples of both overlapping and adjacent monomeric sites - there are examples of both in PBM data and they both score highly on ChIP data. This one is adjacent. |
| V |
YDR423C |
CAD1 |
2073 |
High |
|
Classic YAP motif in most cases. Include examples of both overlapping and adjacent monomeric sites - there are examples of both in PBM data and they both score highly on ChIP data. This one is overlapping. |
| V |
YPL075W |
GCR1 |
2071 |
High |
|
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 |
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 |
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 |
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 |
YPR009W |
SUT2 |
2236 |
High |
|
Highest-scoring motif (PBM) is a classical GAL4-type monomeric motif and is very significant in ChIP-chip |
| 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 |
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 |
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 |
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 |
YML065W |
ORC1 |
1549 |
High |
|
Looks like ORC1 motif. Which is not really a TF, but it is a sequence-specific DNA-binding protein. |
| V |
YPL177C |
CUP9 |
2121 |
High |
|
MITOMI and PBM motifs are similar. PBM motif 2121 has slightly lower correspondence to ChIP data, but more significant correspondence to expression 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 |
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 |
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 |
YNL068C |
FKH2 |
830 |
High |
|
Most motifs are classic Forkhead. PBM motif 830 is one of the highest scoring and is not circular. |
| V |
YER040W |
GLN3 |
539 |
High |
|
Most motifs are classic GATA or GATAAG. PBM motif 539 scores highest on ChIP. |
| 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 |
YKL112W |
ABF1 |
1993 |
High |
|
Most motifs are similar, and five have pegged the ChIP P-value. Choose 791- it's the highest scoring overall, and is from PBMs |
| 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 |
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 |
YNL216W |
RAP1 |
254 |
High |
|
Most motifs look similar. ChIP-chip motif 254 has highest correspondence to expression data. |
| V |
YPL038W |
MET31 |
1370 |
High |
|
Most motifs look similar. MITOMI motif 1370 has highest overall correlation to ChIP-chip, OE, and deletion data. |
| V |
YDR253C |
MET32 |
2140 |
High |
|
Most motifs look similar. PBM motif 2140 has highest correspondence to both ChIP and expression. |
| 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 |
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 |
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 |
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 |
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 |
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 |
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 |
YNR063W |
|
804 |
High |
|
Motifs from PBMs are virtually identical. This is a monomeric GAL4-like motif. 804 agrees more with 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 |
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 |
YLR278C |
|
2112 |
High |
|
Only 2112 (from PBMs) stands out; dimeric GAL4 motif with high score on ChIP-chip. |
| V |
YPR022C |
|
588 |
High |
|
Only one motif available, from PBMs; classical yeast C2H2 motif, and has some relationship to ChIP-chip data. |
| 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 |
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 |
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 |
YBR033W |
EDS1 |
2093 |
High |
|
PBM and ChIP-chip motifs are very similar. PBM motif 2093 scores most significantly on ChIP data. Classic GAL4 class motif. |
| 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 |
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 |
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 |
YDR421W |
ARO80 |
1509 |
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 |
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 |
YDR421W |
ARO80 |
2115 |
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 |
YLR228C |
ECM22 |
2122 |
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 |
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 |
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. |
