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

MSN2

YMR037C

View at SGD ↗

Transcriptional activator related to Msn4p; 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-value5.66e-19
Information content13.59
Max PWM score12.24
Recommended cutoff8.47
View and copy the recommended matrices ↘
Position frequency matrix (PFM)
A | 0.684 0.921 0.001 0.001 0.026 0.001 0.001 0.001 0.211 
C | 0.184 0.001 0.001 0.001 0.001 0.001 0.526 0.132 0.001 
G | 0.001 0.079 0.974 1.000 0.789 1.000 0.237 0.763 0.684 
T | 0.132 0.001 0.026 0.001 0.184 0.001 0.237 0.105 0.105
Position count matrix (PCM)
A |  68  92   0   0   2   0   0   0  21 
C |  18   0   0   0   0   0  52  13   0 
G |   0   7  97 100  78 100  23  76  68 
T |  13   0   2   0  18   0  23  10  10
Position weight matrix (PWM)
A |  0.76  1.06 -5.77 -5.77 -2.51 -5.77 -5.77 -5.77 -0.42 
C |  0.02 -5.19 -5.19 -5.19 -5.19 -5.19  1.07 -0.31 -5.19 
G | -5.19 -0.82  1.69  1.71  1.48  1.71  0.28  1.44  1.34 
T | -0.89 -5.77 -2.51 -5.77 -0.55 -5.77 -0.30 -1.11 -1.11
02 / COMPARATIVE BENCHMARKS

Alternative candidate matrices 11

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

MSN2Badis et. al.P = 6.20e-06View matrix ↘
Sequence logo for MSN2
Fisher’s P-value6.20e-06
Information content9.526
Max PWM score7.35
Recommended cutoff7.35
Position frequency matrix (PFM)
A | 0.60 0.01 0.01 0.01 0.01 
C | 0.07 0.01 0.01 0.01 0.01 
G | 0.32 0.97 0.97 0.97 0.97 
T | 0.01 0.01 0.01 0.01 0.01
Position count matrix (PCM)
A |  60   1   1   1   1 
C |   7   1   1   1   1 
G |  32  97  97  97  97 
T |   1   1   1   1   1
Position weight matrix (PWM)
A |  0.63 -3.47 -3.47 -3.47 -3.47 
C | -0.94 -2.89 -2.89 -2.89 -2.89 
G |  0.58  1.68  1.68  1.68  1.68 
T | -3.47 -3.47 -3.47 -3.47 -3.47
Badis et. al.
MSN2_AFoat et. al.P = 0.00171View matrix ↘
Sequence logo for MSN2_A
Fisher’s P-value0.00171
Information content9.659
Max PWM score10.71
Recommended cutoff8.09
Position frequency matrix (PFM)
A | 0.19 0.09 0.16 0.88 0.79 0.43 0.61 0.33 0.42 0.81 
C | 0.58 0.01 0.01 0.01 0.01 0.56 0.17 0.01 0.01 0.18 
G | 0.22 0.89 0.64 0.10 0.20 0.01 0.21 0.66 0.38 0.01 
T | 0.01 0.01 0.19 0.01 0.01 0.01 0.01 0.01 0.20 0.01
Position count matrix (PCM)
A |  19   9  16  88  79  43  61  33  42  81 
C |  57   1   1   1   1  56  17   1   1  18 
G |  22  89  64  10  20   1  21  66  38   1 
T |   1   1  19   1   1   1   1   1  20   1
Position weight matrix (PWM)
A | -0.52 -1.27 -0.69  1.01  0.90  0.30  0.65  0.03  0.27  0.93 
C |  1.17 -2.89 -2.89 -2.89 -2.89  1.13 -0.06 -2.89 -2.89  0.00 
G |  0.20  1.60  1.27 -0.59  0.11 -2.89  0.15  1.30  0.75 -2.89 
T | -3.47 -3.47 -0.52 -3.47 -3.47 -3.47 -3.47 -3.47 -0.47 -3.47
Foat et. al.
MSN2_BFoat et. al.P = 1.22e-08View matrix ↘
Sequence logo for MSN2_B
Fisher’s P-value1.22e-08
Information content10.5
Max PWM score10.2
Recommended cutoff7.78
Position frequency matrix (PFM)
A | 0.27 0.35 0.40 0.01 0.01 0.01 0.11 0.01 
C | 0.35 0.45 0.02 0.01 0.01 0.01 0.10 0.47 
G | 0.02 0.16 0.57 0.97 0.97 0.97 0.78 0.05 
T | 0.36 0.04 0.01 0.01 0.01 0.01 0.01 0.48
Position count matrix (PCM)
A |  27  35  40   1   1   1  11   1 
C |  35  45   2   1   1   1  10  47 
G |   2  16  56  97  97  97  78   5 
T |  36   4   1   1   1   1   1  48
Position weight matrix (PWM)
A | -0.17  0.09  0.22 -3.47 -3.47 -3.47 -1.07 -3.47 
C |  0.66  0.92 -2.20 -2.89 -2.89 -2.89 -0.59  0.96 
G | -2.20 -0.12  1.15  1.68  1.68  1.68  1.47 -1.28 
T |  0.12 -2.08 -3.47 -3.47 -3.47 -3.47 -3.47  0.41
Foat et. al.
MSN2_CFoat et. al.P = 1.56e-09View matrix ↘
Sequence logo for MSN2_C
Fisher’s P-value1.56e-09
Information content12.2
Max PWM score13.08
Recommended cutoff7.96
Position frequency matrix (PFM)
A | 0.47 0.12 0.28 0.28 0.04 0.01 0.01 0.09 0.01 0.02 
C | 0.42 0.47 0.43 0.01 0.01 0.02 0.01 0.03 0.67 0.18 
G | 0.10 0.05 0.17 0.70 0.94 0.96 0.97 0.71 0.04 0.70 
T | 0.01 0.36 0.12 0.02 0.01 0.01 0.01 0.17 0.28 0.09
Position count matrix (PCM)
A |  47  12  28  28   4   1   1   9   1   2 
C |  42  47  43   1   1   2   1   3  67  18 
G |  10   5  17  70  94  96  97  71   4  70 
T |   1  36  12   2   1   1   1  17  28   9
Position weight matrix (PWM)
A |  0.38 -0.98 -0.13 -0.13 -2.08 -3.47 -3.47 -1.27 -3.47 -2.77 
C |  0.85  0.96  0.87 -2.89 -2.89 -2.20 -2.89 -1.79  1.31  0.00 
G | -0.59 -1.28 -0.06  1.36  1.65  1.67  1.68  1.37 -1.50  1.36 
T | -3.47  0.12 -0.98 -2.77 -3.47 -3.47 -3.47 -0.63 -0.13 -1.27
Foat et. al.
MSN2_DFoat et. al.P = 0.08914View matrix ↘
Sequence logo for MSN2_D
Fisher’s P-value0.08914
Information content19.15
Max PWM score20.64
Recommended cutoff10.34
Position frequency matrix (PFM)
A | 0.42 0.01 0.17 0.01 0.09 0.01 0.09 0.01 0.41 0.04 0.06 0.11 0.01 0.34 0.42 0.01 0.01 0.01 0.71 0.04 0.29 
C | 0.22 0.01 0.11 0.03 0.01 0.01 0.01 0.10 0.21 0.01 0.21 0.01 0.41 0.58 0.20 0.01 0.05 0.23 0.19 0.20 0.01 
G | 0.01 0.57 0.53 0.95 0.01 0.01 0.39 0.60 0.01 0.01 0.30 0.78 0.01 0.02 0.34 0.97 0.01 0.01 0.01 0.64 0.39 
T | 0.35 0.42 0.19 0.01 0.89 0.97 0.52 0.30 0.36 0.94 0.43 0.11 0.58 0.05 0.05 0.01 0.93 0.75 0.09 0.12 0.32
Position count matrix (PCM)
A |  42   1  17   1   9   1   9   1  41   4   6  11   1  34  42   1   1   1  71   4  28 
C |  22   1  11   3   1   1   1  10  21   1  21   1  41  57  20   1   5  23  19  20   1 
G |   1  56  53  95   1   1  39  60   1   1  30  78   1   2  34  97   1   1   1  64  39 
T |  35  42  19   1  89  97  52  30  36  94  43  11  57   5   5   1  93  75   9  12  32
Position weight matrix (PWM)
A |  0.27 -3.47 -0.63 -3.47 -1.27 -3.47 -1.27 -3.47  0.25 -2.08 -1.67 -1.07 -3.47  0.06  0.27 -3.47 -3.47 -3.47  0.80 -2.08 -0.10 
C |  0.20 -2.89 -0.49 -1.79 -2.89 -2.89 -2.89 -0.59  0.15 -2.89  0.15 -2.89  0.82  1.17  0.11 -2.89 -1.28  0.25  0.05  0.11 -2.89 
G | -2.89  1.15  1.08  1.66 -2.89 -2.89  0.77  1.20 -2.89 -2.89  0.51  1.47 -2.89 -2.20  0.64  1.68 -2.89 -2.89 -2.89  1.27  0.77 
T |  0.09  0.27 -0.52 -3.47  1.02  1.11  0.49 -0.06  0.12  1.08  0.30 -1.07  0.59 -1.86 -1.86 -3.47  1.07  0.85 -1.27 -0.98  0.00
Foat et. al.
MSN2_EFoat et. al.P = 1View matrix ↘
Sequence logo for MSN2_E
Fisher’s P-value1
Information content16.28
Max PWM score21.08
Recommended cutoff15.81
Position frequency matrix (PFM)
A | 0.03 0.44 0.36 0.01 0.01 0.09 0.26 0.26 0.16 0.18 0.30 0.31 0.15 0.31 0.29 0.30 0.22 0.18 0.01 0.86 0.02 0.16 0.27 0.24 
C | 0.07 0.42 0.36 0.97 0.02 0.01 0.50 0.33 0.15 0.25 0.14 0.04 0.10 0.01 0.25 0.19 0.39 0.02 0.97 0.12 0.01 0.04 0.17 0.04 
G | 0.05 0.04 0.26 0.02 0.21 0.89 0.18 0.07 0.47 0.31 0.54 0.19 0.13 0.17 0.16 0.07 0.11 0.23 0.01 0.01 0.96 0.53 0.34 0.10 
T | 0.86 0.10 0.02 0.01 0.76 0.01 0.06 0.33 0.23 0.26 0.01 0.46 0.62 0.51 0.31 0.43 0.28 0.57 0.01 0.01 0.01 0.26 0.22 0.61
Position count matrix (PCM)
A |   3  44  36   1   1   9  26  26  16  18  30  31  15  31  28  30  22  18   1  86   2  16  27  24 
C |   7  42  36  97   2   1  50  33  15  25  14   4  10   1  25  19  39   2  97  12   1   4  17   4 
G |   5   4  26   2  21  89  18   7  47  31  54  19  13  17  16   7  11  23   1   1  96  53  34  10 
T |  86  10   2   1  76   1   6  33  23  26   1  46  62  51  31  43  28  56   1   1   1  26  22  61
Position weight matrix (PWM)
A | -2.37  0.32  0.12 -3.47 -3.47 -1.27 -0.21 -0.21 -0.69 -0.58 -0.06 -0.03 -0.76 -0.03 -0.10 -0.06 -0.37 -0.58 -3.47  0.99 -2.77 -0.69 -0.17 -0.29 
C | -0.94  0.85  0.69  1.68 -2.20 -2.89  1.02  0.61 -0.18  0.33 -0.25 -1.50 -0.59 -2.89  0.33  0.05  0.77 -2.20  1.68 -0.41 -2.89 -1.50 -0.06 -1.50 
G | -1.28 -1.50  0.37 -2.20  0.15  1.60  0.00 -0.94  0.96  0.54  1.10  0.05 -0.33 -0.06 -0.12 -0.94 -0.49  0.25 -2.89 -2.89  1.67  1.08  0.64 -0.59 
T |  0.99 -1.16 -2.77 -3.47  0.86 -3.47 -1.67  0.03 -0.33 -0.21 -3.47  0.36  0.66  0.47 -0.03  0.30 -0.13  0.58 -3.47 -3.47 -3.47 -0.21 -0.37  0.65
Foat et. al.
MSN2_AFordyce et. al.P = 8.59e-11View matrix ↘
Fisher’s P-value8.59e-11
Information content5.376
Max PWM score6.84
Recommended cutoff5.74
Position frequency matrix (PFM)
A | 0.24 0.35 0.16 0.01 0.02 0.03 0.15 
C | 0.28 0.29 0.47 0.70 0.96 0.61 0.01 
G | 0.16 0.26 0.01 0.03 0.01 0.10 0.19 
T | 0.32 0.09 0.36 0.27 0.01 0.25 0.65
Position count matrix (PCM)
A |  24  35  16   1   2   3  15 
C |  28  28  47  70  96  61   1 
G |  16  26   1   3   1  10  19 
T |  32   9  36  27   1  25  65
Position weight matrix (PWM)
A | -0.29  0.09 -0.69 -3.47 -2.77 -2.37 -0.76 
C |  0.44  0.48  0.96  1.36  1.67  1.22 -2.89 
G | -0.12  0.37 -2.89 -1.79 -2.89 -0.59  0.05 
T |  0.00 -1.27  0.12 -0.17 -3.47 -0.25  0.71
Fordyce et. al.
MSN2_BFordyce et. al.P = 2.55e-13View matrix ↘
Fisher’s P-value2.55e-13
Information content5.881
Max PWM score6.85
Recommended cutoff6.51
Position frequency matrix (PFM)
A | 0.33 0.22 0.01 0.03 0.01 0.15 0.20 
C | 0.26 0.48 0.61 0.95 0.86 0.01 0.17 
G | 0.26 0.03 0.01 0.01 0.01 0.23 0.27 
T | 0.15 0.27 0.37 0.01 0.13 0.61 0.36
Position count matrix (PCM)
A |  33  22   1   3   1  15  20 
C |  26  48  61  95  86   1  17 
G |  26   3   1   1   1  23  27 
T |  15  27  37   1  13  61  36
Position weight matrix (PWM)
A |  0.03 -0.37 -3.47 -2.37 -3.47 -0.76 -0.47 
C |  0.37  0.98  1.22  1.66  1.56 -2.89 -0.06 
G |  0.37 -1.79 -2.89 -2.89 -2.89  0.25  0.41 
T | -0.76 -0.17  0.15 -3.47 -0.90  0.65  0.12
Fordyce et. al.
MSN2_CFordyce et. al.P = 7.43e-11View matrix ↘
Fisher’s P-value7.43e-11
Information content5.249
Max PWM score6.38
Recommended cutoff5.88
Position frequency matrix (PFM)
A | 0.37 0.13 0.01 0.04 0.03 0.17 
C | 0.33 0.46 0.74 0.94 0.55 0.01 
G | 0.22 0.01 0.03 0.01 0.11 0.21 
T | 0.09 0.41 0.23 0.01 0.32 0.61
Position count matrix (PCM)
A |  37  13   1   4   3  17 
C |  33  46  74  94  55   1 
G |  22   1   3   1  11  21 
T |   9  41  23   1  32  61
Position weight matrix (PWM)
A |  0.15 -0.90 -3.47 -2.08 -2.37 -0.63 
C |  0.61  0.94  1.41  1.65  1.12 -2.89 
G |  0.20 -2.89 -1.79 -2.89 -0.49  0.15 
T | -1.27  0.25 -0.33 -3.47  0.00  0.65
Fordyce et. al.
MSN2Macisaac et. alP = 7.33e-13View matrix ↘
Sequence logo for MSN2
Fisher’s P-value7.33e-13
Information content10.84
Max PWM score9.22
Recommended cutoff7.75
Position frequency matrix (PFM)
A | 0.514 0.973 0.066 0.013 0.013 0.026 0.132 
C | 0.263 0.013 0.001 0.001 0.001 0.001 0.461 
G | 0.105 0.013 0.920 0.985 0.985 0.960 0.197 
T | 0.118 0.001 0.013 0.001 0.001 0.013 0.211
Position count matrix (PCM)
A |  51  97   6   1   1   2  13 
C |  26   1   0   0   0   0  46 
G |  10   1  92  98  98  96  19 
T |  11   0   1   0   0   1  21
Position weight matrix (PWM)
A |  0.47  1.11 -1.58 -3.20 -3.20 -2.51 -0.89 
C |  0.38 -2.63 -5.19 -5.19 -5.19 -5.19  0.94 
G | -0.54 -2.63  1.63  1.70  1.70  1.67  0.09 
T | -1.00 -5.77 -3.20 -5.77 -5.77 -3.20 -0.42
Macisaac et. al
MSN2Pachkov et alP = 5.03e-08View matrix ↘
Sequence logo for MSN2
Fisher’s P-value5.03e-08
Information content11.6
Max PWM score9.08
Recommended cutoff6.98
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 43 genes

YBL037W, YBR058C-A, YBR059C, YDL008W, YDL009C, YDL011C, YDR071C, YDR080W, YDR177W, YEL076W-C, YEL077C, YER087C-A, YFR001W, YFR023W, YGL100W, YGL204C, YGL248W, YGR027C, YGR066C, YHR034C, YHR035W, YIL050W, YIL051C, YIL173W, YIL176C, YLR345W, YML022W, YML023C, YML024W, YML025C, YNL025C, YNL335W, YNL336W, YOL089C, YOR148C, YOR236W, YOR238W, YOR241W, YOR242C, YPL195W, YPL198W, YPL200W, YPL201C

Genes affected by TF deletion 98 genes

YJR054W, YKR039W, YOL047C, YER013W, YMR016C, YHR146W, YOR004W, YOR377W, YDR207C, YPL016W, YCR076C, YDL001W, YDR500C, YGL262W, YIR028W, YOL077C, YPL266W, YAR068W, YJL145W, YMR314W, YMR290C, YNL337W, YBR093C, YBR129C, YDR099W, YMR131C, YMR072W, YOL139C, YNL295W, YDR281C, YLR155C, YLR157C, YMR251W-A, YIL122W, YML119W, YLR323C, YAR015W, YDR200C, YHR156C, YJL059W, YLR102C, YLR412W, YMR173W, YJL122W, YLR099C, YNL248C, YBL001C, YGL111W, YHR214W, YKL178C, YLR158C, YLR160C, YLR192C, YLR164W, YNL315C, YPL122C, YPL156C, YNL152W, YOR294W, YAR071W, YCL025C, YGR251W, YLR159W, YLR232W, YNR077C, YOR209C, YLR449W, YOR051C, YOR021C, YPL066W, YMR173W-A, YOR052C, YFL024C, YJR128W, YMR147W, YNL165W, YOL094C, YOR367W, YDR323C, YDR481C, YOL155C, YGR195W, YLR197W, YNR015W, YPL163C, YFL003C, YHL009W-A, YLR236C, YMR037C, YIL169C, YBR244W, YDL085W, YHR135C, YJL076W, YLR049C, YNL234W, YBL047C, YIL011W

Predicted TF–TF partners 10 genes

ACA1, GSM1, MIG1, MIG3, PHD1, RPH1, RSF2, SKN7, SUT1, YDR026C

Explore 10 original interaction plots →