S.ScerTFYeast transcription factor database Aaron Spivak
← All factors / TF RECORD

MSN4

YKL062W

View at SGD ↗

Transcriptional activator related to Msn2p; activated in stress conditions, which results in translocation from the cytoplasm to the nucleus; binds DNA at stress response elements of responsive genes, inducing gene expression

01 / RECOMMENDED MATRIX

Best-performing DNA-binding model.

RecommendedSource: Harbison et. al.
Fisher’s P-value4.75e-07
Information content11.03
Max PWM score9.15
Recommended cutoff8.57
View and copy the recommended matrices ↘
Position frequency matrix (PFM)
A | 0.488 0.965 0.012 0.012 0.012 0.012 0.250 
C | 0.488 0.012 0.012 0.012 0.012 0.012 0.250 
G | 0.012 0.012 0.964 0.964 0.964 0.964 0.250 
T | 0.012 0.012 0.012 0.012 0.012 0.012 0.250
Position count matrix (PCM)
A |  48  96   1   1   1   1  25 
C |  48   1   1   1   1   1  25 
G |   1   1  96  96  96  96  25 
T |   1   1   1   1   1   1  25
Position weight matrix (PWM)
A |  0.42  1.10 -3.28 -3.28 -3.28 -3.28 -0.25 
C |  1.00 -2.71 -2.71 -2.71 -2.71 -2.71  0.33 
G | -2.71 -2.71  1.68  1.68  1.68  1.68  0.33 
T | -3.28 -3.28 -3.28 -3.28 -3.28 -3.28 -0.25
02 / COMPARATIVE BENCHMARKS

Alternative candidate matrices 8

Historical matrix candidates from the original ScerTF database. Expand a source to inspect its original logo, scores, and matrix values.

MSN4Badis et. al.P = 0.01084View matrix ↘
Sequence logo for MSN4
Fisher’s P-value0.01084
Information content9.856
Max PWM score7.66
Recommended cutoff6.6
Position frequency matrix (PFM)
A | 0.82 0.01 0.01 0.01 0.01 
C | 0.01 0.01 0.01 0.01 0.01 
G | 0.16 0.97 0.97 0.97 0.97 
T | 0.01 0.01 0.01 0.01 0.01
Position count matrix (PCM)
A |  82   1   1   1   1 
C |   1   1   1   1   1 
G |  16  97  97  97  97 
T |   1   1   1   1   1
Position weight matrix (PWM)
A |  0.94 -3.47 -3.47 -3.47 -3.47 
C | -2.89 -2.89 -2.89 -2.89 -2.89 
G | -0.12  1.68  1.68  1.68  1.68 
T | -3.47 -3.47 -3.47 -3.47 -3.47
Badis et. al.
MSN4_AFoat et. al.P = 6.82e-06View matrix ↘
Sequence logo for MSN4_A
Fisher’s P-value6.82e-06
Information content16.89
Max PWM score14.89
Recommended cutoff10
Position frequency matrix (PFM)
A | 0.01 0.03 0.07 0.07 0.63 0.01 0.01 0.04 0.01 0.59 0.68 0.05 
C | 0.33 0.95 0.18 0.72 0.02 0.09 0.01 0.01 0.03 0.04 0.01 0.90 
G | 0.01 0.01 0.01 0.21 0.33 0.89 0.97 0.94 0.92 0.36 0.01 0.02 
T | 0.65 0.01 0.74 0.01 0.02 0.01 0.01 0.01 0.04 0.01 0.31 0.03
Position count matrix (PCM)
A |   1   3   7   7  63   1   1   4   1  59  68   5 
C |  33  95  18  72   2   9   1   1   3   4   1  90 
G |   1   1   1  21  33  89  97  94  92  36   1   2 
T |  65   1  74   1   2   1   1   1   4   1  31   3
Position weight matrix (PWM)
A | -3.47 -2.37 -1.52 -1.52  0.68 -3.47 -3.47 -2.08 -3.47  0.61  0.75 -1.86 
C |  0.61  1.66  0.00  1.39 -2.20 -0.69 -2.89 -2.89 -1.79 -1.50 -2.89  1.61 
G | -2.89 -2.89 -2.89  0.15  0.61  1.60  1.68  1.65  1.63  0.69 -2.89 -2.20 
T |  0.71 -3.47  0.84 -3.47 -2.77 -3.47 -3.47 -3.47 -2.08 -3.47 -0.03 -2.37
Foat et. al.
MSN4_BFoat et. al.P = 1.14e-05View matrix ↘
Sequence logo for MSN4_B
Fisher’s P-value1.14e-05
Information content11.82
Max PWM score12.76
Recommended cutoff9.57
Position frequency matrix (PFM)
A | 0.46 0.27 0.09 0.58 0.20 0.01 0.04 0.01 0.07 0.06 0.05 
C | 0.02 0.51 0.67 0.01 0.01 0.01 0.01 0.01 0.38 0.52 0.28 
G | 0.11 0.11 0.03 0.25 0.79 0.97 0.94 0.97 0.44 0.07 0.50 
T | 0.41 0.11 0.21 0.17 0.01 0.01 0.01 0.01 0.11 0.35 0.17
Position count matrix (PCM)
A |  46  27   9  57  20   1   4   1   7   6   5 
C |   2  51  67   1   1   1   1   1  38  52  28 
G |  11  11   3  25  79  97  94  97  44   7  50 
T |  41  11  21  17   1   1   1   1  11  35  17
Position weight matrix (PWM)
A |  0.36 -0.17 -1.27  0.59 -0.47 -3.47 -2.08 -3.47 -1.52 -1.67 -1.86 
C | -2.20  1.04  1.31 -2.89 -2.89 -2.89 -2.89 -2.89  0.75  1.06  0.44 
G | -0.49 -0.49 -1.79  0.33  1.48  1.68  1.65  1.68  0.89 -0.94  1.02 
T |  0.25 -1.07 -0.42 -0.63 -3.47 -3.47 -3.47 -3.47 -1.07  0.09 -0.63
Foat et. al.
MSN4_CFoat et. al.P = 0.2425View matrix ↘
Sequence logo for MSN4_C
Fisher’s P-value0.2425
Information content19.41
Max PWM score19.93
Recommended cutoff10.42
Position frequency matrix (PFM)
A | 0.06 0.58 0.01 0.01 0.01 0.01 0.43 0.92 0.19 0.63 0.37 0.13 0.24 0.02 0.01 0.04 0.01 0.76 0.49 0.39 
C | 0.08 0.01 0.01 0.01 0.14 0.01 0.11 0.01 0.15 0.10 0.61 0.26 0.53 0.12 0.01 0.01 0.01 0.19 0.01 0.09 
G | 0.21 0.38 0.94 0.96 0.61 0.19 0.25 0.01 0.02 0.04 0.01 0.19 0.10 0.80 0.97 0.92 0.01 0.04 0.01 0.05 
T | 0.65 0.03 0.04 0.02 0.25 0.79 0.21 0.06 0.65 0.23 0.01 0.41 0.13 0.07 0.01 0.04 0.97 0.01 0.49 0.47
Position count matrix (PCM)
A |   6  57   1   1   1   1  43  92  19  63  37  13  24   2   1   4   1  76  49  39 
C |   8   1   1   1  14   1  11   1  15  10  61  26  53  12   1   1   1  19   1   9 
G |  21  38  94  96  61  19  25   1   2   4   1  19  10  80  97  92   1   4   1   5 
T |  65   3   4   2  25  79  21   6  65  23   1  41  13   7   1   4  97   1  49  47
Position weight matrix (PWM)
A | -1.67  0.59 -3.47 -3.47 -3.47 -3.47  0.30  1.06 -0.52  0.68  0.15 -0.90 -0.29 -2.77 -3.47 -2.08 -3.47  0.86  0.43  0.20 
C | -0.81 -2.89 -2.89 -2.89 -0.25 -2.89 -0.49 -2.89 -0.18 -0.59  1.22  0.37  1.08 -0.41 -2.89 -2.89 -2.89  0.05 -2.89 -0.69 
G |  0.15  0.75  1.65  1.67  1.22  0.05  0.33 -2.89 -2.20 -1.50 -2.89  0.05 -0.59  1.49  1.68  1.63 -2.89 -1.50 -2.89 -1.28 
T |  0.71 -2.37 -2.08 -2.77 -0.25  0.90 -0.42 -1.67  0.71 -0.33 -3.47  0.25 -0.90 -1.52 -3.47 -2.08  1.11 -3.47  0.43  0.38
Foat et. al.
MSN4_DFoat et. al.P = 0.00135View matrix ↘
Sequence logo for MSN4_D
Fisher’s P-value0.00135
Information content13.6
Max PWM score12.66
Recommended cutoff10.06
Position frequency matrix (PFM)
A | 0.48 0.33 0.75 0.01 0.71 0.01 0.51 0.03 0.10 0.26 0.45 0.01 
C | 0.51 0.25 0.24 0.97 0.17 0.96 0.25 0.95 0.89 0.09 0.11 0.17 
G | 0.01 0.01 0.01 0.01 0.07 0.02 0.21 0.01 0.01 0.65 0.02 0.01 
T | 0.01 0.41 0.01 0.01 0.04 0.01 0.04 0.01 0.01 0.01 0.43 0.82
Position count matrix (PCM)
A |  48  33  75   1  71   1  51   3  10  26  45   1 
C |  51  25  24  97  17  96  25  95  89   9  11  17 
G |   1   1   1   1   7   2  21   1   1  65   2   1 
T |   1  41   1   1   4   1   4   1   1   1  43  82
Position weight matrix (PWM)
A |  0.41  0.03  0.85 -3.47  0.80 -3.47  0.47 -2.37 -1.16 -0.21  0.34 -3.47 
C |  1.04  0.33  0.29  1.68 -0.06  1.67  0.33  1.66  1.60 -0.69 -0.49 -0.06 
G | -2.89 -2.89 -2.89 -2.89 -0.94 -2.20  0.15 -2.89 -2.89  1.28 -2.20 -2.89 
T | -3.47  0.25 -3.47 -3.47 -2.08 -3.47 -2.08 -3.47 -3.47 -3.47  0.30  0.94
Foat et. al.
MSN4_EFoat et. al.P = 1.03e-07View matrix ↘
Sequence logo for MSN4_E
Fisher’s P-value1.03e-07
Information content17.75
Max PWM score17.89
Recommended cutoff10
Position frequency matrix (PFM)
A | 0.62 0.89 0.01 0.97 0.01 0.01 0.08 0.38 0.39 0.70 0.18 0.23 0.01 0.46 0.01 0.41 0.01 
C | 0.01 0.01 0.12 0.01 0.84 0.73 0.45 0.01 0.01 0.28 0.66 0.74 0.97 0.01 0.22 0.31 0.39 
G | 0.25 0.02 0.01 0.01 0.14 0.07 0.46 0.07 0.59 0.01 0.15 0.02 0.01 0.53 0.23 0.04 0.59 
T | 0.12 0.07 0.86 0.01 0.01 0.19 0.01 0.54 0.01 0.02 0.01 0.01 0.01 0.01 0.55 0.25 0.01
Position count matrix (PCM)
A |  62  89   1  97   1   1   8  38  39  70  18  23   1  46   1  41   1 
C |   1   1  12   1  84  73  45   1   1  28  66  74  97   1  22  31  39 
G |  25   2   1   1  14   7  46   7  59   1  15   2   1  53  23   4  59 
T |  12   7  86   1   1  19   1  54   1   2   1   1   1   1  55  25   1
Position weight matrix (PWM)
A |  0.66  1.02 -3.47  1.11 -3.47 -3.47 -1.39  0.17  0.20  0.78 -0.58 -0.33 -3.47  0.36 -3.47  0.25 -3.47 
C | -2.89 -2.89 -0.41 -2.89  1.54  1.40  0.92 -2.89 -2.89  0.44  1.30  1.41  1.68 -2.89  0.20  0.54  0.77 
G |  0.33 -2.20 -2.89 -2.89 -0.25 -0.94  0.94 -0.94  1.19 -2.89 -0.18 -2.20 -2.89  1.08  0.25 -1.50  1.19 
T | -0.98 -1.52  0.99 -3.47 -3.47 -0.52 -3.47  0.52 -3.47 -2.77 -3.47 -3.47 -3.47 -3.47  0.54 -0.25 -3.47
Foat et. al.
MSN4Macisaac et. alP = 0.0004128View matrix ↘
Sequence logo for MSN4
Fisher’s P-value0.0004128
Information content10.25
Max PWM score8.92
Recommended cutoff8.67
Position frequency matrix (PFM)
A | 0.689 0.958 0.230 0.001 0.014 0.014 0.311 
C | 0.162 0.014 0.001 0.001 0.001 0.001 0.243 
G | 0.108 0.014 0.755 0.984 0.984 0.958 0.311 
T | 0.041 0.014 0.014 0.014 0.001 0.027 0.135
Position count matrix (PCM)
A |  68  95  23   0   1   1  31 
C |  16   1   0   0   0   0  24 
G |  10   1  75  98  98  95  31 
T |   4   1   1   1   0   2  13
Position weight matrix (PWM)
A |  0.77  1.10 -0.33 -5.77 -3.13 -3.13 -0.03 
C | -0.11 -2.55 -5.19 -5.19 -5.19 -5.19  0.30 
G | -0.51 -2.55  1.43  1.70  1.70  1.67  0.55 
T | -2.05 -3.13 -3.13 -3.13 -5.77 -2.47 -0.86
Macisaac et. al
MSN4Pachkov et alP = 0.001666View matrix ↘
Sequence logo for MSN4
Fisher’s P-value0.001666
Information content11.6
Max PWM score9.08
Recommended cutoff5.66
Position frequency matrix (PFM)
A | 0.341 0.802 0.764 0.004 0.017 0.001 0.003 
C | 0.110 0.148 0.001 0.025 0.001 0.001 0.001 
G | 0.028 0.002 0.236 0.970 0.983 1.000 0.997 
T | 0.521 0.048 0.001 0.001 0.001 0.001 0.001
Position count matrix (PCM)
A |  34  80  76   0   1   0   0 
C |  11  14   0   2   0   0   0 
G |   2   0  23  97  98 100  99 
T |  52   4   0   0   0   0   0
Position weight matrix (PWM)
A |  0.06  0.92  0.87 -4.38 -2.94 -5.77 -4.67 
C | -0.49 -0.20 -5.19 -1.97 -5.19 -5.19 -5.19 
G | -1.86 -4.50  0.27  1.68  1.70  1.71  1.71 
T |  0.49 -1.90 -5.77 -5.77 -5.77 -5.77 -5.77
Pachkov et al
03 / EXPERIMENTAL CONTEXT

Gene-level annotations and interactions.

Genes bound in ChIP-chip experiments 145 genes

YAL003W, YAL005C, YBL027W, YBL028C, YBL069W, YBL071C, YBL087C, YBL108W, YBR057C, YBR072W, YBR073W, YBR074W, YBR086C, YBR087W, YBR089W, YDR010C, YDR011W, YDR072C, YDR073W, YDR075W, YDR085C, YDR117C, YDR118W, YDR169C, YDR227W, YDR228C, YDR229W, YDR372C, YDR373W, YDR543C, YDR544C, YDR545W, YEL020W-A, YEL021W, YEL051W, YEL073C, YEL076W-C, YEL077C, YER007C-A, YER022W, YER103W, YER164W, YER166W, YER189W, YER190W, YFL063W, YFL064C, YFL065C, YFR001W, YFR031C-A, YGL108C, YGR027C, YGR032W, YGR142W, YGR210C, YGR211W, YGR251W, YGR254W, YGR296W, YHL048W, YHR033W, YHR034C, YHR035W, YHR079C, YHR087W, YHR091C, YIL050W, YIL051C, YIL120W, YIL122W, YIL128W, YIL129C, YIL173W, YIL174W, YIL175W, YIL176C, YIL177C, YJL188C, YJL225C, YJR123W, YKL004W, YKL005C, YKL006C-A, YKL006W, YKL061W, YLL026W, YLL063C, YLR194C, YLR199C, YLR200W, YLR254C, YLR255C, YLR256W, YLR256W-A, YLR390W-A, YLR439W, YLR462W, YLR463C, YLR464W, YLR465C, YLR466W, YLR467W, YML057W, YML063W, YML064C, YML111W, YML125C, YML131W, YML132W, YMR026C, YMR027W, YMR119W, YMR119W-A, YMR144W, YMR165C, YMR251W-A, YMR252C, YMR254C, YMR255W, YNL025C, YNL077W, YNL335W, YNL336W, YNL337W, YNL338W, YNL339C, YOR134W, YOR236W, YOR275C, YOR276W, YPL150W, YPL151C, YPL152W, YPL153C, YPL198W, YPL283C, YPR102C, YPR103W, YPR104C, YPR107C, YPR108W, YPR154W, YPR184W, YPR202W, YPR203W

Genes affected by TF deletion 41 genes

YPL240C, YJR114W, YLL030C, YOR289W, YBR093C, YDR281C, YCR050C, YIL156W, YML004C, YPR124W, YJR148W, YFL051C, YOR298W, YHR039C, YMR110C, YOR298C-A, YBR296C, YNR032W, YIL160C, YGR109W-B, YKL062W, YKR086W, YOR080W, YCR095C, YML098W, YER164W, YKR035W-A, YER017C, YML015C, YMR186W, YOR027W, YPL041C, YGL255W, YDR492W, YHR105W, YIR020W-B, YJL045W, YDR306C, YGL095C, YNL007C, YPR173C

Genes supported by both experiments 1 genes

YER164W

Predicted TF–TF partners 13 genes

ACA1, GSM1, MIG1, MIG3, PHD1, RPH1, RSC3, RSF2, SKN7, STP1, SUT1, UGA3, YER184C

Explore 13 original interaction plots →