|
|
|
|
|
|
|
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 |
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 |
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 |
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 |
YOR363C |
PIP2 |
0 |
|
|
See Oaf1-Pip2-dimer |
V |
YPR022C |
|
588 |
High |
|
Only one motif available, from PBMs; classical yeast C2H2 motif, and has some relationship to ChIP-chip data. |
V |
YDR026C |
|
696 |
High |
|
Three ChIP-chip motifs are virtually identical in appearance; resemble Reb1 motifs; high correspondence to 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 |
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 |
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 |
YLR278C |
|
2112 |
High |
|
Only 2112 (from PBMs) stands out; dimeric GAL4 motif with high score on ChIP-chip. |
V |
YGR067C |
|
2191 |
High |
|
PBM motif is a classical C2H2 motif that has good correspondence to ChIP-chip data. 2191 corresponds best and has fewer empty columns in the PWM. |
V |
YKL222C |
|
2192 |
High |
|
Two motifs from PBMs resemble monomeric GAL4-like motif. 2192 agrees best with ChIP-chip data and expression data. |
V |
YML081W |
|
2194 |
High |
|
PBM motifs are a classical C2H2 motif that match each other and have some correspondence to ChIP-chip data. 2194 has highest correspondence to ChIP chip. |
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 |
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 |
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 |
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 |
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 |
YML099C |
ARG81 |
1506 |
High |
|
ChIP motif 1506 correlates well with ChIP and also with expression data. Resembles dimeric GAL4 class motif. |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
YMR168C |
CEP3 |
524 |
High |
|
Two PBM motifs agree. Went with 524 because it appears neater. No other supporting data for any of them. |
V |
YLR098C |
CHA4 |
2120 |
High |
|
Two PBM motifs agree, and PBM motif 2120 has highest correspondence to ChIP-chip data, even highter than the best ChIP-chip motif. Has a GAL4-like appearance, albeit a variant. Monomeric. (Highest scoring motif - 1607 - is actually a Rap1 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 |
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 |
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 |
YNL027W |
CRZ1 |
516 |
High |
|
PBM motif 516 scores highest on ChIP and expression; resembles classic literature motifs |
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 |
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 |
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 |
YER088C |
DOT6 |
2221 |
High |
|
PBM motif 812 most closely resembles that of homolog TOD6, which is well-supported; has highest correlation to both ChIP and expression data. |
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 |
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 |
YPL021W |
ECM23 |
578 |
High |
|
PBM motif 578 strongly resembles that from other yeast GATA-class TFs |
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 |
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 |
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 |
YNL068C |
FKH2 |
830 |
High |
|
Most motifs are classic Forkhead. PBM motif 830 is one of the highest scoring and is not circular. |
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 |
YFL021W |
GAT1 |
962 |
High |
|
ChIP-chip motif 962 scores higher on both ChIP-chip and expression data |
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 |
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 |
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 |
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 |
YDR096W |
GIS1 |
562 |
High |
|
All motifs similar; PBM motif 562 has highest correspondence to deletion expression data and overexpression data |
V |
YER040W |
GLN3 |
539 |
High |
|
Most motifs are classic GATA or GATAAG. PBM motif 539 scores highest on ChIP. |
V |
YJL110C |
GZF3 |
2133 |
High |
|
Classic GATA motif 2133 from PBM scores highest on ChIP-chip and expression data |
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 |
YOL089C |
HAL9 |
799 |
High |
|
PBM motifs 799 and 2134 score highest on ChIP-chip data; classic dimeric and monomeric GAL4 sites, respectively. |
V |
YOL089C |
HAL9 |
2134 |
High |
|
PBM motifs 799 and 2134 score highest on ChIP-chip data; classic dimeric and monomeric GAL4 sites, respectively. |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
YGL209W |
MIG2 |
2143 |
High |
|
PBM motif 2143 has highest correspondence to ChIP-chip data |
V |
YER028C |
MIG3 |
2144 |
High |
|
PBM motif 2144 has highest correspondence to ChIP-chip 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 |
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 |
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 |
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 |
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 |
YML065W |
ORC1 |
1549 |
High |
|
Looks like ORC1 motif. Which is not really a TF, but it is a sequence-specific DNA-binding protein. |
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 |
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 |
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 |
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 |
YNL216W |
RAP1 |
254 |
High |
|
Most motifs look similar. ChIP-chip motif 254 has highest correspondence to expression data. |
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 |
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 |
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. |